diff --git a/.gitignore b/.gitignore index d67f5419..7e5b48fe 100644 --- a/.gitignore +++ b/.gitignore @@ -2,4 +2,7 @@ .DS_Store node_modules __MACOSX -dist \ No newline at end of file +dist +idmapping.csv +sample.csv +summary.csv \ No newline at end of file diff --git a/Makefile b/Makefile index 8d0c6f5c..6ef03d31 100644 --- a/Makefile +++ b/Makefile @@ -8,6 +8,9 @@ help: @echo " phase3 - Start Phase 3 deployment" @echo " stage-dev - Start Stage development environment" @echo "" + @echo "Data Management:" + @echo " data-setup - Upload dictionaries, register entities, and load data" + @echo "" @echo "Conductor System Management:" @echo " down - Gracefully shutdown all containers" @echo " reset - DANGER: Remove all containers and volumes (DATA LOSS)" @@ -45,6 +48,12 @@ stage-dev: @echo "Starting Stage development environment..." PROFILE=stageDev docker compose -f ./docker-compose.yml --profile stageDev up --attach conductor +# Run data setup: upload dictionaries, register entities, and load data +data-setup: + @echo "Starting data setup deployment..." + @echo "This will upload dictionaries to Lectern, register entities with Lyric, and load tabular data." + PROFILE=dataSetup docker compose -f ./docker-compose.yml --profile dataSetup up --attach data-setup + # Gracefully shutdown all containers while preserving volumes down: @echo "Shutting down all running containers..." @@ -53,7 +62,7 @@ down: # Restart containers and run deployment scripts for a specific profile restart: @echo "Restarting containers with fresh deployment..." - @read -p "Enter profile to restart (phase1, phase2, phase3, stageDev): " profile; \ + @read -p "Enter profile to restart (phase1, phase2, phase3, stageDev, dataSetup): " profile; \ echo "Shutting down containers..."; \ PROFILE=$$profile docker compose -f ./docker-compose.yml --profile $$profile down; \ echo "Starting containers with profile $$profile..."; \ @@ -67,5 +76,4 @@ reset: PROFILE=default docker compose -f ./docker-compose.yml --profile default down -v ; \ else \ echo "Operation cancelled"; \ - fi - + fi \ No newline at end of file diff --git a/README.md b/README.md index 3571b40a..b7b0e0f6 100644 --- a/README.md +++ b/README.md @@ -29,6 +29,54 @@ make phase0 The CLI will provide you with instructions on next steps. +### Phase 2 Command Setup + +Install the CLI utilities: + +For Conductor: + +```bash +cd apps/conductor +npm ci +npm install -g . +``` + +If using configuration automation services install Composer + +```bash +cd apps/composer +npm ci +npm install -g . +``` + +Run: + +```bash +make phase2 +``` + +Then run the following commands to populate the portal with data: + +```bash +# Upload consolidated dictionary +conductor lecternUpload -s ./configs/lecternDictionaries/lbr-dictionary.json + +# Register entities with schema +conductor lyricRegister -c idmapping --dict-name lbr-dictionary -v 1.0 -e idmapping +conductor lyricRegister -c sample --dict-name lbr-dictionary -v 1.0 -e sample +conductor lyricRegister -c summary --dict-name lbr-dictionary -v 1.0 -e summary + +# Upload tabular data +conductor lyricUpload -d ./data/idmapping -c 1 --max-retries 100 --lyric-url http://pantrack.genomeinformatics.org/lyric +conductor lyricUpload -d ./data/sample -c 2 --max-retries 100 +conductor lyricUpload -d ./data/summary -c 3 --max-retries 100 + +# Index data +conductor maestroIndex --repository-code idmapping +conductor maestroIndex --repository-code sample +conductor maestroIndex --repository-code summary +``` + ## Development Phases Prelude is structured into four incremental phases: diff --git a/apps/conductor/configs/arrangerConfigs/datatable1/base.json b/apps/conductor/configs/arrangerConfigs/datatable1/base.json deleted file mode 100644 index 31af159c..00000000 --- a/apps/conductor/configs/arrangerConfigs/datatable1/base.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "documentType": "file", - "index": "datatable1_centric" -} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/datatable1/extended.json b/apps/conductor/configs/arrangerConfigs/datatable1/extended.json deleted file mode 100644 index b7fed5b0..00000000 --- a/apps/conductor/configs/arrangerConfigs/datatable1/extended.json +++ /dev/null @@ -1,99 +0,0 @@ -{ - "extended": [ - { - "displayName": "Gender", - "fieldName": "data.gender" - }, - { - "displayName": "Donor Id", - "fieldName": "data.donor_id" - }, - { - "displayName": "Vital Status", - "fieldName": "data.vital_status" - }, - { - "displayName": "Diagnosis", - "fieldName": "data.diagnosis", - "isArray": true - }, - { - "displayName": "Diagnosis Stage", - "fieldName": "data.diagnosis.stage" - }, - { - "displayName": "Diagnosis Donor Id", - "fieldName": "data.diagnosis.donor_id" - }, - { - "displayName": "Diagnosis Cancer Type", - "fieldName": "data.diagnosis.cancer_type" - }, - { - "displayName": "Diagnosis Diagnosis Id", - "fieldName": "data.diagnosis.diagnosis_id" - }, - { - "displayName": "Diagnosis Primary Site", - "fieldName": "data.diagnosis.primary_site" - }, - { - "displayName": "Diagnosis Staging System", - "fieldName": "data.diagnosis.staging_system" - }, - { - "displayName": "Diagnosis Age At Diagnosis", - "fieldName": "data.diagnosis.age_at_diagnosis" - }, - { - "displayName": "Treatment", - "fieldName": "data.treatment", - "isArray": true - }, - { - "displayName": "Treatment Donor Id", - "fieldName": "data.treatment.donor_id" - }, - { - "displayName": "Treatment Treatment Id", - "fieldName": "data.treatment.treatment_id" - }, - { - "displayName": "Treatment Treatment Type", - "fieldName": "data.treatment.treatment_type" - }, - { - "displayName": "Treatment Treatment Start", - "fieldName": "data.treatment.treatment_start" - }, - { - "displayName": "Treatment Treatment Duration", - "fieldName": "data.treatment.treatment_duration" - }, - { - "displayName": "Treatment Treatment Response", - "fieldName": "data.treatment.treatment_response" - }, - { - "displayName": "Treatment Followup", - "fieldName": "data.treatment.followup", - "isArray": true - }, - { - "displayName": "Treatment Followup Followup Id", - "fieldName": "data.treatment.followup.followup_id" - }, - { - "displayName": "Treatment Followup Treatment Id", - "fieldName": "data.treatment.followup.treatment_id" - }, - { - "displayName": "Treatment Followup Disease Status", - "fieldName": "data.treatment.followup.disease_status" - }, - { - "displayName": "Treatment Followup Followup Interval", - "fieldName": "data.treatment.followup.followup_interval" - } - ] -} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/datatable1/facets.json b/apps/conductor/configs/arrangerConfigs/datatable1/facets.json deleted file mode 100644 index 3e08337f..00000000 --- a/apps/conductor/configs/arrangerConfigs/datatable1/facets.json +++ /dev/null @@ -1,106 +0,0 @@ -{ - "facets": { - "aggregations": [ - { - "active": true, - "fieldName": "data__gender", - "show": true - }, - { - "active": true, - "fieldName": "data__donor_id", - "show": true - }, - { - "active": true, - "fieldName": "data__vital_status", - "show": true - }, - { - "active": true, - "fieldName": "data__diagnosis__stage", - "show": true - }, - { - "active": true, - "fieldName": "data__diagnosis__donor_id", - "show": true - }, - { - "active": true, - "fieldName": "data__diagnosis__cancer_type", - "show": true - }, - { - "active": true, - "fieldName": "data__diagnosis__diagnosis_id", - "show": true - }, - { - "active": true, - "fieldName": "data__diagnosis__primary_site", - "show": true - }, - { - "active": true, - "fieldName": "data__diagnosis__staging_system", - "show": true - }, - { - "active": true, - "fieldName": "data__diagnosis__age_at_diagnosis", - "show": true - }, - { - "active": true, - "fieldName": "data__treatment__donor_id", - "show": true - }, - { - "active": true, - "fieldName": "data__treatment__treatment_id", - "show": true - }, - { - "active": true, - "fieldName": "data__treatment__treatment_type", - "show": true - }, - { - "active": true, - "fieldName": "data__treatment__treatment_start", - "show": true - }, - { - "active": true, - "fieldName": "data__treatment__treatment_duration", - "show": true - }, - { - "active": true, - "fieldName": "data__treatment__treatment_response", - "show": true - }, - { - "active": true, - "fieldName": "data__treatment__followup__followup_id", - "show": true - }, - { - "active": true, - "fieldName": "data__treatment__followup__treatment_id", - "show": true - }, - { - "active": true, - "fieldName": "data__treatment__followup__disease_status", - "show": true - }, - { - "active": true, - "fieldName": "data__treatment__followup__followup_interval", - "show": true - } - ] - } -} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/datatable1/table.json b/apps/conductor/configs/arrangerConfigs/datatable1/table.json deleted file mode 100644 index 221293b4..00000000 --- a/apps/conductor/configs/arrangerConfigs/datatable1/table.json +++ /dev/null @@ -1,166 +0,0 @@ -{ - "table": { - "columns": [ - { - "canChangeShow": true, - "fieldName": "data.gender", - "show": true, - "sortable": true, - "jsonPath": "$.data.gender", - "query": "data { gender }" - }, - { - "canChangeShow": true, - "fieldName": "data.donor_id", - "show": true, - "sortable": true, - "jsonPath": "$.data.donor_id", - "query": "data { donor_id }" - }, - { - "canChangeShow": true, - "fieldName": "data.vital_status", - "show": true, - "sortable": true, - "jsonPath": "$.data.vital_status", - "query": "data { vital_status }" - }, - { - "canChangeShow": true, - "fieldName": "data.diagnosis.stage", - "show": true, - "sortable": true, - "jsonPath": "$.data.diagnosis.hits.edges[*].node.stage", - "query": "data { diagnosis { hits { edges { node { stage } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.diagnosis.donor_id", - "show": true, - "sortable": true, - "jsonPath": "$.data.diagnosis.hits.edges[*].node.donor_id", - "query": "data { diagnosis { hits { edges { node { donor_id } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.diagnosis.cancer_type", - "show": true, - "sortable": true, - "jsonPath": "$.data.diagnosis.hits.edges[*].node.cancer_type", - "query": "data { diagnosis { hits { edges { node { cancer_type } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.diagnosis.diagnosis_id", - "show": true, - "sortable": true, - "jsonPath": "$.data.diagnosis.hits.edges[*].node.diagnosis_id", - "query": "data { diagnosis { hits { edges { node { diagnosis_id } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.diagnosis.primary_site", - "show": true, - "sortable": true, - "jsonPath": "$.data.diagnosis.hits.edges[*].node.primary_site", - "query": "data { diagnosis { hits { edges { node { primary_site } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.diagnosis.staging_system", - "show": true, - "sortable": true, - "jsonPath": "$.data.diagnosis.hits.edges[*].node.staging_system", - "query": "data { diagnosis { hits { edges { node { staging_system } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.diagnosis.age_at_diagnosis", - "show": true, - "sortable": true, - "jsonPath": "$.data.diagnosis.hits.edges[*].node.age_at_diagnosis", - "query": "data { diagnosis { hits { edges { node { age_at_diagnosis } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.treatment.donor_id", - "show": true, - "sortable": true, - "jsonPath": "$.data.treatment.hits.edges[*].node.donor_id", - "query": "data { treatment { hits { edges { node { donor_id } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.treatment.treatment_id", - "show": true, - "sortable": true, - "jsonPath": "$.data.treatment.hits.edges[*].node.treatment_id", - "query": "data { treatment { hits { edges { node { treatment_id } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.treatment.treatment_type", - "show": true, - "sortable": true, - "jsonPath": "$.data.treatment.hits.edges[*].node.treatment_type", - "query": "data { treatment { hits { edges { node { treatment_type } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.treatment.treatment_start", - "show": true, - "sortable": true, - "jsonPath": "$.data.treatment.hits.edges[*].node.treatment_start", - "query": "data { treatment { hits { edges { node { treatment_start } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.treatment.treatment_duration", - "show": true, - "sortable": true, - "jsonPath": "$.data.treatment.hits.edges[*].node.treatment_duration", - "query": "data { treatment { hits { edges { node { treatment_duration } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.treatment.treatment_response", - "show": true, - "sortable": true, - "jsonPath": "$.data.treatment.hits.edges[*].node.treatment_response", - "query": "data { treatment { hits { edges { node { treatment_response } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.treatment.followup.followup_id", - "show": false, - "sortable": true, - "jsonPath": "$.data.treatment.hits.edges[*].node.followup.hits.edges[*].node.followup_id", - "query": "data { treatment { hits { edges { node { followup { hits { edges { node { followup_id } } } } } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.treatment.followup.treatment_id", - "show": false, - "sortable": true, - "jsonPath": "$.data.treatment.hits.edges[*].node.followup.hits.edges[*].node.treatment_id", - "query": "data { treatment { hits { edges { node { followup { hits { edges { node { treatment_id } } } } } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.treatment.followup.disease_status", - "show": false, - "sortable": true, - "jsonPath": "$.data.treatment.hits.edges[*].node.followup.hits.edges[*].node.disease_status", - "query": "data { treatment { hits { edges { node { followup { hits { edges { node { disease_status } } } } } } } } }" - }, - { - "canChangeShow": true, - "fieldName": "data.treatment.followup.followup_interval", - "show": false, - "sortable": true, - "jsonPath": "$.data.treatment.hits.edges[*].node.followup.hits.edges[*].node.followup_interval", - "query": "data { treatment { hits { edges { node { followup { hits { edges { node { followup_interval } } } } } } } } }" - } - ] - } -} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/idmapping/base.json b/apps/conductor/configs/arrangerConfigs/idmapping/base.json new file mode 100644 index 00000000..e93a9e56 --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/idmapping/base.json @@ -0,0 +1,4 @@ +{ + "documentType": "file", + "index": "idmapping_centric" +} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/idmapping/extended.json b/apps/conductor/configs/arrangerConfigs/idmapping/extended.json new file mode 100644 index 00000000..55217be4 --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/idmapping/extended.json @@ -0,0 +1,216 @@ +{ + "extended": [ + { + "displayName": "Index Id", + "fieldName": "id" + }, + { + "displayName": "External Id", + "fieldName": "data.external_id" + }, + { + "displayName": "Donor", + "fieldName": "data.donor" + }, + { + "displayName": "Age At Diagnosis", + "fieldName": "data.Age_at_diagnosis" + }, + { + "displayName": "Sex", + "fieldName": "data.Sex" + }, + { + "displayName": "Date Of Tissue", + "fieldName": "data.Date_of_Tissue" + }, + { + "displayName": "Sample", + "fieldName": "data.Sample" + }, + { + "displayName": "PPID", + "fieldName": "data.PPID" + }, + { + "displayName": "PDO Available", + "fieldName": "data.PDO_available" + }, + { + "displayName": "PDO ID Notta", + "fieldName": "data.PDO_ID_Notta" + }, + { + "displayName": "PDO ID PMLB", + "fieldName": "data.PDO_ID_PMLB" + }, + { + "displayName": "PDO WT RNAseq", + "fieldName": "data.PDO_WT_RNAseq" + }, + { + "displayName": "PDO WGS", + "fieldName": "data.PDO_WGS" + }, + { + "displayName": "PDO Exome", + "fieldName": "data.PDO_Exome" + }, + { + "displayName": "PDO Drugscreen", + "fieldName": "data.PDO_drugscreen" + }, + { + "displayName": "Tumour ScRNAseq", + "fieldName": "data.Tumour_scRNAseq" + }, + { + "displayName": "Tumour ScCNV", + "fieldName": "data.Tumour_scCNV" + }, + { + "displayName": "Tumour Multiome", + "fieldName": "data.Tumour_multiome" + }, + { + "displayName": "Tumour Spatial", + "fieldName": "data.Tumour_spatial" + }, + { + "displayName": "Plasma WGS", + "fieldName": "data.Plasma_WGS" + }, + { + "displayName": "Plasma CfRNA", + "fieldName": "data.Plasma_cfRNA" + }, + { + "displayName": "Histology", + "fieldName": "data.Histology" + }, + { + "displayName": "Staging At Diagnosis T", + "fieldName": "data.Staging_at_Diagnosis_T" + }, + { + "displayName": "Staging At Diagnosis N", + "fieldName": "data.Staging_at_Diagnosis_N" + }, + { + "displayName": "Staging At Diagnosis M", + "fieldName": "data.Staging_at_Diagnosis_M" + }, + { + "displayName": "Biopsy At Diagnosis", + "fieldName": "data.Biopsy_at_Diagnosis" + }, + { + "displayName": "Date Of Rx", + "fieldName": "data.Date_of_Rx" + }, + { + "displayName": "Systemic Tx", + "fieldName": "data.Systemic_Tx" + }, + { + "displayName": "Tx Type", + "fieldName": "data.Tx_Type" + }, + { + "displayName": "Biopsy At Progression", + "fieldName": "data.Biopsy_at_Progression" + }, + { + "displayName": "CRUK", + "fieldName": "data.CRUK" + }, + { + "displayName": "PIMO", + "fieldName": "data.PIMO" + }, + { + "displayName": "COMPASS", + "fieldName": "data.COMPASS" + }, + { + "displayName": "NeoPancONE", + "fieldName": "data.NeoPancONE" + }, + { + "displayName": "PASS", + "fieldName": "data.PASS" + }, + { + "displayName": "ARCAP", + "fieldName": "data.ARCAP" + }, + { + "displayName": "PA7", + "fieldName": "data.PA7" + }, + { + "displayName": "PA6", + "fieldName": "data.PA6" + }, + { + "displayName": "Prosper Panc", + "fieldName": "data.Prosper_Panc" + }, + { + "displayName": "HPB Banking", + "fieldName": "data.HPB_Banking" + }, + { + "displayName": "OPCS", + "fieldName": "data.OPCS" + }, + { + "displayName": "Surgical DB", + "fieldName": "data.Surgical_DB" + }, + { + "displayName": "TMA 1", + "fieldName": "data.TMA_1" + }, + { + "displayName": "TMA 2", + "fieldName": "data.TMA_2" + }, + { + "displayName": "Rapid Autopsy", + "fieldName": "data.Rapid_Autopsy" + }, + { + "displayName": "Jackson Lab ID", + "fieldName": "data.Jackson_Lab_ID" + }, + { + "displayName": "McGaha Lab ID", + "fieldName": "data.McGaha_Lab_ID" + }, + { + "displayName": "Sheba SPC", + "fieldName": "data.Sheba_SPC" + }, + { + "displayName": "QPCS ID", + "fieldName": "data.QPCS_ID" + }, + { + "displayName": "OCIP ID", + "fieldName": "data.OCIP_ID" + }, + { + "displayName": "PCD ID", + "fieldName": "data.PCD_ID" + }, + { + "displayName": "RB Xxxx", + "fieldName": "data.RB_xxxx" + }, + { + "displayName": "GPxx", + "fieldName": "data.GPxx" + } + ] +} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/idmapping/facets.json b/apps/conductor/configs/arrangerConfigs/idmapping/facets.json new file mode 100644 index 00000000..a83624a4 --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/idmapping/facets.json @@ -0,0 +1,266 @@ +{ + "facets": { + "aggregations": [ + { + "active": true, + "fieldName": "data__external_id", + "show": true + }, + { + "active": true, + "fieldName": "data__donor", + "show": true + }, + { + "active": true, + "fieldName": "data__Age_at_diagnosis", + "show": true + }, + { + "active": true, + "fieldName": "data__Sex", + "show": true + }, + { + "active": true, + "fieldName": "data__Date_of_Tissue", + "show": true + }, + { + "active": true, + "fieldName": "data__Sample", + "show": true + }, + { + "active": true, + "fieldName": "data__PPID", + "show": true + }, + { + "active": true, + "fieldName": "data__PDO_available", + "show": true + }, + { + "active": true, + "fieldName": "data__PDO_ID_Notta", + "show": true + }, + { + "active": true, + "fieldName": "data__PDO_ID_PMLB", + "show": true + }, + { + "active": true, + "fieldName": "data__PDO_WT_RNAseq", + "show": true + }, + { + "active": true, + "fieldName": "data__PDO_WGS", + "show": true + }, + { + "active": true, + "fieldName": "data__PDO_Exome", + "show": true + }, + { + "active": true, + "fieldName": "data__PDO_drugscreen", + "show": true + }, + { + "active": true, + "fieldName": "data__Tumour_scRNAseq", + "show": true + }, + { + "active": true, + "fieldName": "data__Tumour_scCNV", + "show": true + }, + { + "active": true, + "fieldName": "data__Tumour_multiome", + "show": true + }, + { + "active": true, + "fieldName": "data__Tumour_spatial", + "show": true + }, + { + "active": true, + "fieldName": "data__Plasma_WGS", + "show": true + }, + { + "active": true, + "fieldName": "data__Plasma_cfRNA", + "show": true + }, + { + "active": true, + "fieldName": "data__Histology", + "show": true + }, + { + "active": true, + "fieldName": "data__Staging_at_Diagnosis_T", + "show": true + }, + { + "active": true, + "fieldName": "data__Staging_at_Diagnosis_N", + "show": true + }, + { + "active": true, + "fieldName": "data__Staging_at_Diagnosis_M", + "show": true + }, + { + "active": true, + "fieldName": "data__Biopsy_at_Diagnosis", + "show": true + }, + { + "active": true, + "fieldName": "data__Date_of_Rx", + "show": true + }, + { + "active": true, + "fieldName": "data__Systemic_Tx", + "show": true + }, + { + "active": true, + "fieldName": "data__Tx_Type", + "show": true + }, + { + "active": true, + "fieldName": "data__Biopsy_at_Progression", + "show": true + }, + { + "active": true, + "fieldName": "data__CRUK", + "show": true + }, + { + "active": true, + "fieldName": "data__PIMO", + "show": true + }, + { + "active": true, + "fieldName": "data__COMPASS", + "show": true + }, + { + "active": true, + "fieldName": "data__NeoPancONE", + "show": true + }, + { + "active": true, + "fieldName": "data__PASS", + "show": true + }, + { + "active": true, + "fieldName": "data__ARCAP", + "show": true + }, + { + "active": true, + "fieldName": "data__PA7", + "show": true + }, + { + "active": true, + "fieldName": "data__PA6", + "show": true + }, + { + "active": true, + "fieldName": "data__Prosper_Panc", + "show": true + }, + { + "active": true, + "fieldName": "data__HPB_Banking", + "show": true + }, + { + "active": true, + "fieldName": "data__OPCS", + "show": true + }, + { + "active": true, + "fieldName": "data__Surgical_DB", + "show": true + }, + { + "active": true, + "fieldName": "data__TMA_1", + "show": true + }, + { + "active": true, + "fieldName": "data__TMA_2", + "show": true + }, + { + "active": true, + "fieldName": "data__Rapid_Autopsy", + "show": true + }, + { + "active": true, + "fieldName": "data__Jackson_Lab_ID", + "show": true + }, + { + "active": true, + "fieldName": "data__McGaha_Lab_ID", + "show": true + }, + { + "active": true, + "fieldName": "data__Sheba_SPC", + "show": true + }, + { + "active": true, + "fieldName": "data__QPCS_ID", + "show": true + }, + { + "active": true, + "fieldName": "data__OCIP_ID", + "show": true + }, + { + "active": true, + "fieldName": "data__PCD_ID", + "show": true + }, + { + "active": true, + "fieldName": "data__RB_xxxx", + "show": true + }, + { + "active": true, + "fieldName": "data__GPxx", + "show": true + } + ] + } +} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/idmapping/table.json b/apps/conductor/configs/arrangerConfigs/idmapping/table.json new file mode 100644 index 00000000..137225b5 --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/idmapping/table.json @@ -0,0 +1,428 @@ +{ + "table": { + "columns": [ + { + "canChangeShow": true, + "fieldName": "id", + "show": true, + "sortable": true + }, + { + "canChangeShow": true, + "fieldName": "data.external_id", + "show": true, + "sortable": true, + "jsonPath": "$.data.external_id", + "query": "data { external_id }" + }, + { + "canChangeShow": true, + "fieldName": "data.donor", + "show": true, + "sortable": true, + "jsonPath": "$.data.donor", + "query": "data { donor }" + }, + { + "canChangeShow": true, + "fieldName": "data.Age_at_diagnosis", + "show": true, + "sortable": true, + "jsonPath": "$.data.Age_at_diagnosis", + "query": "data { Age_at_diagnosis }" + }, + { + "canChangeShow": true, + "fieldName": "data.Sex", + "show": true, + "sortable": true, + "jsonPath": "$.data.Sex", + "query": "data { Sex }" + }, + { + "canChangeShow": true, + "fieldName": "data.Date_of_Tissue", + "show": true, + "sortable": true, + "jsonPath": "$.data.Date_of_Tissue", + "query": "data { Date_of_Tissue }" + }, + { + "canChangeShow": true, + "fieldName": "data.Sample", + "show": true, + "sortable": true, + "jsonPath": "$.data.Sample", + "query": "data { Sample }" + }, + { + "canChangeShow": true, + "fieldName": "data.PPID", + "show": true, + "sortable": true, + "jsonPath": "$.data.PPID", + "query": "data { PPID }" + }, + { + "canChangeShow": true, + "fieldName": "data.PDO_available", + "show": true, + "sortable": true, + "jsonPath": "$.data.PDO_available", + "query": "data { PDO_available }" + }, + { + "canChangeShow": true, + "fieldName": "data.PDO_ID_Notta", + "show": true, + "sortable": true, + "jsonPath": "$.data.PDO_ID_Notta", + "query": "data { PDO_ID_Notta }" + }, + { + "canChangeShow": true, + "fieldName": "data.PDO_ID_PMLB", + "show": true, + "sortable": true, + "jsonPath": "$.data.PDO_ID_PMLB", + "query": "data { PDO_ID_PMLB }" + }, + { + "canChangeShow": true, + "fieldName": "data.PDO_WT_RNAseq", + "show": true, + "sortable": true, + "jsonPath": "$.data.PDO_WT_RNAseq", + "query": "data { PDO_WT_RNAseq }" + }, + { + "canChangeShow": true, + "fieldName": "data.PDO_WGS", + "show": true, + "sortable": true, + "jsonPath": "$.data.PDO_WGS", + "query": "data { PDO_WGS }" + }, + { + "canChangeShow": true, + "fieldName": "data.PDO_Exome", + "show": true, + "sortable": true, + "jsonPath": "$.data.PDO_Exome", + "query": "data { PDO_Exome }" + }, + { + "canChangeShow": true, + "fieldName": "data.PDO_drugscreen", + "show": true, + "sortable": true, + "jsonPath": "$.data.PDO_drugscreen", + "query": "data { PDO_drugscreen }" + }, + { + "canChangeShow": true, + "fieldName": "data.Tumour_scRNAseq", + "show": true, + "sortable": true, + "jsonPath": "$.data.Tumour_scRNAseq", + "query": "data { Tumour_scRNAseq }" + }, + { + "canChangeShow": true, + "fieldName": "data.Tumour_scCNV", + "show": true, + "sortable": true, + "jsonPath": "$.data.Tumour_scCNV", + "query": "data { Tumour_scCNV }" + }, + { + "canChangeShow": true, + "fieldName": "data.Tumour_multiome", + "show": true, + "sortable": true, + "jsonPath": "$.data.Tumour_multiome", + "query": "data { Tumour_multiome }" + }, + { + "canChangeShow": true, + "fieldName": "data.Tumour_spatial", + "show": true, + "sortable": true, + "jsonPath": "$.data.Tumour_spatial", + "query": "data { Tumour_spatial }" + }, + { + "canChangeShow": true, + "fieldName": "data.Plasma_WGS", + "show": true, + "sortable": true, + "jsonPath": "$.data.Plasma_WGS", + "query": "data { Plasma_WGS }" + }, + { + "canChangeShow": true, + "fieldName": "data.Plasma_cfRNA", + "show": true, + "sortable": true, + "jsonPath": "$.data.Plasma_cfRNA", + "query": "data { Plasma_cfRNA }" + }, + { + "canChangeShow": true, + "fieldName": "data.Histology", + "show": true, + "sortable": true, + "jsonPath": "$.data.Histology", + "query": "data { Histology }" + }, + { + "canChangeShow": true, + "fieldName": "data.Staging_at_Diagnosis_T", + "show": true, + "sortable": true, + "jsonPath": "$.data.Staging_at_Diagnosis_T", + "query": "data { Staging_at_Diagnosis_T }" + }, + { + "canChangeShow": true, + "fieldName": "data.Staging_at_Diagnosis_N", + "show": true, + "sortable": true, + "jsonPath": "$.data.Staging_at_Diagnosis_N", + "query": "data { Staging_at_Diagnosis_N }" + }, + { + "canChangeShow": true, + "fieldName": "data.Staging_at_Diagnosis_M", + "show": true, + "sortable": true, + "jsonPath": "$.data.Staging_at_Diagnosis_M", + "query": "data { Staging_at_Diagnosis_M }" + }, + { + "canChangeShow": true, + "fieldName": "data.Biopsy_at_Diagnosis", + "show": true, + "sortable": true, + "jsonPath": "$.data.Biopsy_at_Diagnosis", + "query": "data { Biopsy_at_Diagnosis }" + }, + { + "canChangeShow": true, + "fieldName": "data.Date_of_Rx", + "show": true, + "sortable": true, + "jsonPath": "$.data.Date_of_Rx", + "query": "data { Date_of_Rx }" + }, + { + "canChangeShow": true, + "fieldName": "data.Systemic_Tx", + "show": true, + "sortable": true, + "jsonPath": "$.data.Systemic_Tx", + "query": "data { Systemic_Tx }" + }, + { + "canChangeShow": true, + "fieldName": "data.Tx_Type", + "show": true, + "sortable": true, + "jsonPath": "$.data.Tx_Type", + "query": "data { Tx_Type }" + }, + { + "canChangeShow": true, + "fieldName": "data.Biopsy_at_Progression", + "show": true, + "sortable": true, + "jsonPath": "$.data.Biopsy_at_Progression", + "query": "data { Biopsy_at_Progression }" + }, + { + "canChangeShow": true, + "fieldName": "data.CRUK", + "show": true, + "sortable": true, + "jsonPath": "$.data.CRUK", + "query": "data { CRUK }" + }, + { + "canChangeShow": true, + "fieldName": "data.PIMO", + "show": true, + "sortable": true, + "jsonPath": "$.data.PIMO", + "query": "data { PIMO }" + }, + { + "canChangeShow": true, + "fieldName": "data.COMPASS", + "show": true, + "sortable": true, + "jsonPath": "$.data.COMPASS", + "query": "data { COMPASS }" + }, + { + "canChangeShow": true, + "fieldName": "data.NeoPancONE", + "show": true, + "sortable": true, + "jsonPath": "$.data.NeoPancONE", + "query": "data { NeoPancONE }" + }, + { + "canChangeShow": true, + "fieldName": "data.PASS", + "show": true, + "sortable": true, + "jsonPath": "$.data.PASS", + "query": "data { PASS }" + }, + { + "canChangeShow": true, + "fieldName": "data.ARCAP", + "show": true, + "sortable": true, + "jsonPath": "$.data.ARCAP", + "query": "data { ARCAP }" + }, + { + "canChangeShow": true, + "fieldName": "data.PA7", + "show": true, + "sortable": true, + "jsonPath": "$.data.PA7", + "query": "data { PA7 }" + }, + { + "canChangeShow": true, + "fieldName": "data.PA6", + "show": true, + "sortable": true, + "jsonPath": "$.data.PA6", + "query": "data { PA6 }" + }, + { + "canChangeShow": true, + "fieldName": "data.Prosper_Panc", + "show": true, + "sortable": true, + "jsonPath": "$.data.Prosper_Panc", + "query": "data { Prosper_Panc }" + }, + { + "canChangeShow": true, + "fieldName": "data.HPB_Banking", + "show": true, + "sortable": true, + "jsonPath": "$.data.HPB_Banking", + "query": "data { HPB_Banking }" + }, + { + "canChangeShow": true, + "fieldName": "data.OPCS", + "show": true, + "sortable": true, + "jsonPath": "$.data.OPCS", + "query": "data { OPCS }" + }, + { + "canChangeShow": true, + "fieldName": "data.Surgical_DB", + "show": true, + "sortable": true, + "jsonPath": "$.data.Surgical_DB", + "query": "data { Surgical_DB }" + }, + { + "canChangeShow": true, + "fieldName": "data.TMA_1", + "show": true, + "sortable": true, + "jsonPath": "$.data.TMA_1", + "query": "data { TMA_1 }" + }, + { + "canChangeShow": true, + "fieldName": "data.TMA_2", + "show": true, + "sortable": true, + "jsonPath": "$.data.TMA_2", + "query": "data { TMA_2 }" + }, + { + "canChangeShow": true, + "fieldName": "data.Rapid_Autopsy", + "show": true, + "sortable": true, + "jsonPath": "$.data.Rapid_Autopsy", + "query": "data { Rapid_Autopsy }" + }, + { + "canChangeShow": true, + "fieldName": "data.Jackson_Lab_ID", + "show": true, + "sortable": true, + "jsonPath": "$.data.Jackson_Lab_ID", + "query": "data { Jackson_Lab_ID }" + }, + { + "canChangeShow": true, + "fieldName": "data.McGaha_Lab_ID", + "show": true, + "sortable": true, + "jsonPath": "$.data.McGaha_Lab_ID", + "query": "data { McGaha_Lab_ID }" + }, + { + "canChangeShow": true, + "fieldName": "data.Sheba_SPC", + "show": true, + "sortable": true, + "jsonPath": "$.data.Sheba_SPC", + "query": "data { Sheba_SPC }" + }, + { + "canChangeShow": true, + "fieldName": "data.QPCS_ID", + "show": true, + "sortable": true, + "jsonPath": "$.data.QPCS_ID", + "query": "data { QPCS_ID }" + }, + { + "canChangeShow": true, + "fieldName": "data.OCIP_ID", + "show": true, + "sortable": true, + "jsonPath": "$.data.OCIP_ID", + "query": "data { OCIP_ID }" + }, + { + "canChangeShow": true, + "fieldName": "data.PCD_ID", + "show": true, + "sortable": true, + "jsonPath": "$.data.PCD_ID", + "query": "data { PCD_ID }" + }, + { + "canChangeShow": true, + "fieldName": "data.RB_xxxx", + "show": true, + "sortable": true, + "jsonPath": "$.data.RB_xxxx", + "query": "data { RB_xxxx }" + }, + { + "canChangeShow": true, + "fieldName": "data.GPxx", + "show": true, + "sortable": true, + "jsonPath": "$.data.GPxx", + "query": "data { GPxx }" + } + ] + } +} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/sample/base.json b/apps/conductor/configs/arrangerConfigs/sample/base.json new file mode 100644 index 00000000..57314445 --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/sample/base.json @@ -0,0 +1,4 @@ +{ + "documentType": "file", + "index": "sample_centric" +} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/sample/extended.json b/apps/conductor/configs/arrangerConfigs/sample/extended.json new file mode 100644 index 00000000..b53cc3ae --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/sample/extended.json @@ -0,0 +1,140 @@ +{ + "extended": [ + { + "displayName": "Index Id", + "fieldName": "id" + }, + { + "displayName": "Donor Name", + "fieldName": "data.donor_name" + }, + { + "displayName": "Sample Name", + "fieldName": "data.sample_name" + }, + { + "displayName": "Seq Type", + "fieldName": "data.seq_type" + }, + { + "displayName": "Case Id", + "fieldName": "data.case_id" + }, + { + "displayName": "Test Id", + "fieldName": "data.test_id" + }, + { + "displayName": "Req Id", + "fieldName": "data.req_id" + }, + { + "displayName": "Project", + "fieldName": "data.project" + }, + { + "displayName": "External Id", + "fieldName": "data.external_id" + }, + { + "displayName": "Tissue Origin", + "fieldName": "data.tissue_origin" + }, + { + "displayName": "Tissue Type", + "fieldName": "data.tissue_type" + }, + { + "displayName": "Group Id", + "fieldName": "data.group_id" + }, + { + "displayName": "Library Design", + "fieldName": "data.library_design" + }, + { + "displayName": "Library Name", + "fieldName": "data.library_name" + }, + { + "displayName": "Sequencer Run", + "fieldName": "data.sequencer_run" + }, + { + "displayName": "Sequencing Id", + "fieldName": "data.sequencing_id" + }, + { + "displayName": "Instrument Model", + "fieldName": "data.instrument_model" + }, + { + "displayName": "Gsi Workflow Run Id", + "fieldName": "data.gsi_workflow_run_id" + }, + { + "displayName": "Gsi Workflow", + "fieldName": "data.gsi_workflow" + }, + { + "displayName": "Gsi Workflow Version", + "fieldName": "data.gsi_workflow_version" + }, + { + "displayName": "Gsi Md5sum", + "fieldName": "data.gsi_md5sum" + }, + { + "displayName": "Gsi Time", + "fieldName": "data.gsi_time" + }, + { + "displayName": "Fastq Path", + "fieldName": "data.fastq_path" + }, + { + "displayName": "Modification Date", + "fieldName": "data.modification_date" + }, + { + "displayName": "Linked File", + "fieldName": "data.linked_file" + }, + { + "displayName": "Linked File Time", + "fieldName": "data.linked_file_time" + }, + { + "displayName": "Submission Metadata", + "fieldName": "submission.metadata" + }, + { + "displayName": "Submission Metadata Submitter Id", + "fieldName": "submission.metadata.submitter_id" + }, + { + "displayName": "Submission Metadata Processing Started", + "fieldName": "submission.metadata.processing_started" + }, + { + "displayName": "Submission Metadata Processed At", + "fieldName": "submission.metadata.processed_at" + }, + { + "displayName": "Submission Metadata Source File", + "fieldName": "submission.metadata.source_file" + }, + { + "displayName": "Submission Metadata Record Number", + "fieldName": "submission.metadata.record_number" + }, + { + "displayName": "Submission Metadata Hostname", + "fieldName": "submission.metadata.hostname" + }, + { + "displayName": "Submission Metadata Username", + "fieldName": "submission.metadata.username" + } + ] +} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/sample/facets.json b/apps/conductor/configs/arrangerConfigs/sample/facets.json new file mode 100644 index 00000000..7624de7d --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/sample/facets.json @@ -0,0 +1,166 @@ +{ + "facets": { + "aggregations": [ + { + "active": true, + "fieldName": "data__donor_name", + "show": true + }, + { + "active": true, + "fieldName": "data__sample_name", + "show": true + }, + { + "active": true, + "fieldName": "data__seq_type", + "show": true + }, + { + "active": true, + "fieldName": "data__case_id", + "show": true + }, + { + "active": true, + "fieldName": "data__test_id", + "show": true + }, + { + "active": true, + "fieldName": "data__req_id", + "show": true + }, + { + "active": true, + "fieldName": "data__project", + "show": true + }, + { + "active": true, + "fieldName": "data__external_id", + "show": true + }, + { + "active": true, + "fieldName": "data__tissue_origin", + "show": true + }, + { + "active": true, + "fieldName": "data__tissue_type", + "show": true + }, + { + "active": true, + "fieldName": "data__group_id", + "show": true + }, + { + "active": true, + "fieldName": "data__library_design", + "show": true + }, + { + "active": true, + "fieldName": "data__library_name", + "show": true + }, + { + "active": true, + "fieldName": "data__sequencer_run", + "show": true + }, + { + "active": true, + "fieldName": "data__sequencing_id", + "show": true + }, + { + "active": true, + "fieldName": "data__instrument_model", + "show": true + }, + { + "active": true, + "fieldName": "data__gsi_workflow_run_id", + "show": true + }, + { + "active": true, + "fieldName": "data__gsi_workflow", + "show": true + }, + { + "active": true, + "fieldName": "data__gsi_workflow_version", + "show": true + }, + { + "active": true, + "fieldName": "data__gsi_md5sum", + "show": true + }, + { + "active": true, + "fieldName": "data__gsi_time", + "show": true + }, + { + "active": true, + "fieldName": "data__fastq_path", + "show": true + }, + { + "active": true, + "fieldName": "data__modification_date", + "show": true + }, + { + "active": true, + "fieldName": "data__linked_file", + "show": true + }, + { + "active": true, + "fieldName": "data__linked_file_time", + "show": true + }, + { + "active": false, + "fieldName": "submission_metadata__submitter_id", + "show": false + }, + { + "active": false, + "fieldName": "submission_metadata__processing_started", + "show": false + }, + { + "active": false, + "fieldName": "submission_metadata__processed_at", + "show": false + }, + { + "active": false, + "fieldName": "submission_metadata__source_file", + "show": false + }, + { + "active": false, + "fieldName": "submission_metadata__record_number", + "show": false + }, + { + "active": false, + "fieldName": "submission_metadata__hostname", + "show": false + }, + { + "active": false, + "fieldName": "submission_metadata__username", + "show": false + } + ] + } +} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/sample/table.json b/apps/conductor/configs/arrangerConfigs/sample/table.json new file mode 100644 index 00000000..48d45f96 --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/sample/table.json @@ -0,0 +1,269 @@ +{ + "table": { + "rowIdFieldName": "id" , + "columns": [ + { + "canChangeShow": true, + "fieldName": "id", + "show": true, + "sortable": true + }, + { + "canChangeShow": true, + "fieldName": "data.donor_name", + "show": true, + "sortable": true, + "jsonPath": "$.data.donor_name", + "query": "data { donor_name }" + }, + { + "canChangeShow": true, + "fieldName": "data.sample_name", + "show": true, + "sortable": true, + "jsonPath": "$.data.sample_name", + "query": "data { sample_name }" + }, + { + "canChangeShow": true, + "fieldName": "data.seq_type", + "show": true, + "sortable": true, + "jsonPath": "$.data.seq_type", + "query": "data { seq_type }" + }, + { + "canChangeShow": true, + "fieldName": "data.case_id", + "show": true, + "sortable": true, + "jsonPath": "$.data.case_id", + "query": "data { case_id }" + }, + { + "canChangeShow": true, + "fieldName": "data.test_id", + "show": true, + "sortable": true, + "jsonPath": "$.data.test_id", + "query": "data { test_id }" + }, + { + "canChangeShow": true, + "fieldName": "data.req_id", + "show": true, + "sortable": true, + "jsonPath": "$.data.req_id", + "query": "data { req_id }" + }, + { + "canChangeShow": true, + "fieldName": "data.project", + "show": true, + "sortable": true, + "jsonPath": "$.data.project", + "query": "data { project }" + }, + { + "canChangeShow": true, + "fieldName": "data.external_id", + "show": true, + "sortable": true, + "jsonPath": "$.data.external_id", + "query": "data { external_id }" + }, + { + "canChangeShow": true, + "fieldName": "data.tissue_origin", + "show": true, + "sortable": true, + "jsonPath": "$.data.tissue_origin", + "query": "data { tissue_origin }" + }, + { + "canChangeShow": true, + "fieldName": "data.tissue_type", + "show": true, + "sortable": true, + "jsonPath": "$.data.tissue_type", + "query": "data { tissue_type }" + }, + { + "canChangeShow": true, + "fieldName": "data.group_id", + "show": true, + "sortable": true, + "jsonPath": "$.data.group_id", + "query": "data { group_id }" + }, + { + "canChangeShow": true, + "fieldName": "data.library_design", + "show": true, + "sortable": true, + "jsonPath": "$.data.library_design", + "query": "data { library_design }" + }, + { + "canChangeShow": true, + "fieldName": "data.library_name", + "show": true, + "sortable": true, + "jsonPath": "$.data.library_name", + "query": "data { library_name }" + }, + { + "canChangeShow": true, + "fieldName": "data.sequencer_run", + "show": true, + "sortable": true, + "jsonPath": "$.data.sequencer_run", + "query": "data { sequencer_run }" + }, + { + "canChangeShow": true, + "fieldName": "data.sequencing_id", + "show": true, + "sortable": true, + "jsonPath": "$.data.sequencing_id", + "query": "data { sequencing_id }" + }, + { + "canChangeShow": true, + "fieldName": "data.instrument_model", + "show": true, + "sortable": true, + "jsonPath": "$.data.instrument_model", + "query": "data { instrument_model }" + }, + { + "canChangeShow": true, + "fieldName": "data.gsi_workflow_run_id", + "show": true, + "sortable": true, + "jsonPath": "$.data.gsi_workflow_run_id", + "query": "data { gsi_workflow_run_id }" + }, + { + "canChangeShow": true, + "fieldName": "data.gsi_workflow", + "show": true, + "sortable": true, + "jsonPath": "$.data.gsi_workflow", + "query": "data { gsi_workflow }" + }, + { + "canChangeShow": true, + "fieldName": "data.gsi_workflow_version", + "show": true, + "sortable": true, + "jsonPath": "$.data.gsi_workflow_version", + "query": "data { gsi_workflow_version }" + }, + { + "canChangeShow": true, + "fieldName": "data.gsi_md5sum", + "show": true, + "sortable": true, + "jsonPath": "$.data.gsi_md5sum", + "query": "data { gsi_md5sum }" + }, + { + "canChangeShow": true, + "fieldName": "data.gsi_time", + "show": true, + "sortable": true, + "jsonPath": "$.data.gsi_time", + "query": "data { gsi_time }" + }, + { + "canChangeShow": true, + "fieldName": "data.fastq_path", + "show": true, + "sortable": true, + "jsonPath": "$.data.fastq_path", + "query": "data { fastq_path }" + }, + { + "canChangeShow": true, + "fieldName": "data.modification_date", + "show": true, + "sortable": true, + "jsonPath": "$.data.modification_date", + "query": "data { modification_date }" + }, + { + "canChangeShow": true, + "fieldName": "data.linked_file", + "show": true, + "sortable": true, + "jsonPath": "$.data.linked_file", + "query": "data { linked_file }" + }, + { + "canChangeShow": true, + "fieldName": "data.linked_file_time", + "show": true, + "sortable": true, + "jsonPath": "$.data.linked_file_time", + "query": "data { linked_file_time }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.submitter_id", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.submitter_id", + "query": "submission_metadata { submitter_id }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.processing_started", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.processing_started", + "query": "submission_metadata { processing_started }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.processed_at", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.processed_at", + "query": "submission_metadata { processed_at }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.source_file", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.source_file", + "query": "submission_metadata { source_file }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.record_number", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.record_number", + "query": "submission_metadata { record_number }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.hostname", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.hostname", + "query": "submission_metadata { hostname }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.username", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.username", + "query": "submission_metadata { username }" + } + ] + } +} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/summary/base.json b/apps/conductor/configs/arrangerConfigs/summary/base.json new file mode 100644 index 00000000..50d003b3 --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/summary/base.json @@ -0,0 +1,4 @@ +{ + "documentType": "file", + "index": "summary_centric" +} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/summary/extended.json b/apps/conductor/configs/arrangerConfigs/summary/extended.json new file mode 100644 index 00000000..46bf0fdb --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/summary/extended.json @@ -0,0 +1,1052 @@ +{ + "extended": [ + { + "displayName": "Index Id", + "fieldName": "id" + }, + { + "displayName": "Donor", + "fieldName": "data.donor" + }, + { + "displayName": "Tumour", + "fieldName": "data.tumour" + }, + { + "displayName": "Normal", + "fieldName": "data.normal" + }, + { + "displayName": "External Id", + "fieldName": "data.external_id" + }, + { + "displayName": "Seq Type", + "fieldName": "data.seq_type" + }, + { + "displayName": "Tumour Coverage", + "fieldName": "data.tumour_coverage" + }, + { + "displayName": "Normal Coverage", + "fieldName": "data.normal_coverage" + }, + { + "displayName": "Mouse Content", + "fieldName": "data.mouse_content" + }, + { + "displayName": "Tumour Reads Per Sp", + "fieldName": "data.tumour_reads_per_sp" + }, + { + "displayName": "Normal Reads Per Sp", + "fieldName": "data.normal_reads_per_sp" + }, + { + "displayName": "Tumour Error Rate", + "fieldName": "data.tumour_error_rate" + }, + { + "displayName": "Normal Error Rate", + "fieldName": "data.normal_error_rate" + }, + { + "displayName": "Tumour Soft Clip", + "fieldName": "data.tumour_soft_clip" + }, + { + "displayName": "Normal Soft Clip", + "fieldName": "data.normal_soft_clip" + }, + { + "displayName": "Inferred Sex", + "fieldName": "data.inferred_sex" + }, + { + "displayName": "Genotype Concordance", + "fieldName": "data.genotype_concordance" + }, + { + "displayName": "Snv Count", + "fieldName": "data.snv_count" + }, + { + "displayName": "Del Count", + "fieldName": "data.del_count" + }, + { + "displayName": "Ins Count", + "fieldName": "data.ins_count" + }, + { + "displayName": "Indel Count", + "fieldName": "data.indel_count" + }, + { + "displayName": "Deleterious Count", + "fieldName": "data.deleterious_count" + }, + { + "displayName": "Nonsyn Count", + "fieldName": "data.nonsyn_count" + }, + { + "displayName": "Stopgain Count", + "fieldName": "data.stopgain_count" + }, + { + "displayName": "Stoploss Count", + "fieldName": "data.stoploss_count" + }, + { + "displayName": "Splice Count", + "fieldName": "data.splice_count" + }, + { + "displayName": "Noncoding Count", + "fieldName": "data.noncoding_count" + }, + { + "displayName": "Frameshift Count", + "fieldName": "data.frameshift_count" + }, + { + "displayName": "Nonframeshift Count", + "fieldName": "data.nonframeshift_count" + }, + { + "displayName": "Del Frameshift Count", + "fieldName": "data.del_frameshift_count" + }, + { + "displayName": "Del Nonframeshift Count", + "fieldName": "data.del_nonframeshift_count" + }, + { + "displayName": "Ins Frameshift Count", + "fieldName": "data.ins_frameshift_count" + }, + { + "displayName": "Ins Nonframeshift Count", + "fieldName": "data.ins_nonframeshift_count" + }, + { + "displayName": "Sv Count", + "fieldName": "data.sv_count" + }, + { + "displayName": "Sv Del Count", + "fieldName": "data.sv_del_count" + }, + { + "displayName": "Sv Dup Count", + "fieldName": "data.sv_dup_count" + }, + { + "displayName": "Sv Inv Count", + "fieldName": "data.sv_inv_count" + }, + { + "displayName": "Sv Tra Count", + "fieldName": "data.sv_tra_count" + }, + { + "displayName": "Sv Del Bp Gene Count", + "fieldName": "data.sv_del_bp_gene_count" + }, + { + "displayName": "Sv Dup Bp Gene Count", + "fieldName": "data.sv_dup_bp_gene_count" + }, + { + "displayName": "Sv Inv Bp Gene Count", + "fieldName": "data.sv_inv_bp_gene_count" + }, + { + "displayName": "Sv Tra Bp Gene Count", + "fieldName": "data.sv_tra_bp_gene_count" + }, + { + "displayName": "Waddell", + "fieldName": "data.waddell" + }, + { + "displayName": "Neo Antigens", + "fieldName": "data.neo_antigens" + }, + { + "displayName": "Neo Antigens Weak", + "fieldName": "data.neo_antigens_weak" + }, + { + "displayName": "Neo Antigens Strong", + "fieldName": "data.neo_antigens_strong" + }, + { + "displayName": "Hla Types", + "fieldName": "data.hla_types" + }, + { + "displayName": "Cellularity", + "fieldName": "data.cellularity" + }, + { + "displayName": "Ploidy", + "fieldName": "data.ploidy" + }, + { + "displayName": "Alexandrov Class", + "fieldName": "data.alexandrov_class" + }, + { + "displayName": "Alexandrov Etiology", + "fieldName": "data.alexandrov_etiology" + }, + { + "displayName": "Moffitt", + "fieldName": "data.moffitt" + }, + { + "displayName": "Collisson", + "fieldName": "data.collisson" + }, + { + "displayName": "Bailey", + "fieldName": "data.bailey" + }, + { + "displayName": "Dsbr Deficient", + "fieldName": "data.dsbr_deficient" + }, + { + "displayName": "Dsbr First Hit", + "fieldName": "data.dsbr_first_hit" + }, + { + "displayName": "Dsbr Second Hit", + "fieldName": "data.dsbr_second_hit" + }, + { + "displayName": "Mmr Deficient", + "fieldName": "data.mmr_deficient" + }, + { + "displayName": "Mmr First Hit", + "fieldName": "data.mmr_first_hit" + }, + { + "displayName": "Mmr Second Hit", + "fieldName": "data.mmr_second_hit" + }, + { + "displayName": "Csnnls Sig1", + "fieldName": "data.csnnls_sig1" + }, + { + "displayName": "Csnnls Sig2", + "fieldName": "data.csnnls_sig2" + }, + { + "displayName": "Csnnls Sig3", + "fieldName": "data.csnnls_sig3" + }, + { + "displayName": "Csnnls Sig5", + "fieldName": "data.csnnls_sig5" + }, + { + "displayName": "Csnnls Sig6", + "fieldName": "data.csnnls_sig6" + }, + { + "displayName": "Csnnls Sig8", + "fieldName": "data.csnnls_sig8" + }, + { + "displayName": "Csnnls Sig13", + "fieldName": "data.csnnls_sig13" + }, + { + "displayName": "Csnnls Sig17", + "fieldName": "data.csnnls_sig17" + }, + { + "displayName": "Csnnls Sig18", + "fieldName": "data.csnnls_sig18" + }, + { + "displayName": "Csnnls Sig20", + "fieldName": "data.csnnls_sig20" + }, + { + "displayName": "Csnnls Sig26", + "fieldName": "data.csnnls_sig26" + }, + { + "displayName": "Csnnls Residuals", + "fieldName": "data.csnnls_residuals" + }, + { + "displayName": "Csnnls N Mutations", + "fieldName": "data.csnnls_n_mutations" + }, + { + "displayName": "Germline Snv Count", + "fieldName": "data.germline_snv_count" + }, + { + "displayName": "Germline Indel Count", + "fieldName": "data.germline_indel_count" + }, + { + "displayName": "Germline Titv Ratio", + "fieldName": "data.germline_titv_ratio" + }, + { + "displayName": "Germline Missense Count", + "fieldName": "data.germline_missense_count" + }, + { + "displayName": "Germline Nonsense Count", + "fieldName": "data.germline_nonsense_count" + }, + { + "displayName": "Snv Ca", + "fieldName": "data.snv_ca" + }, + { + "displayName": "Snv Cg", + "fieldName": "data.snv_cg" + }, + { + "displayName": "Snv Ct", + "fieldName": "data.snv_ct" + }, + { + "displayName": "Snv Ta", + "fieldName": "data.snv_ta" + }, + { + "displayName": "Snv Tc", + "fieldName": "data.snv_tc" + }, + { + "displayName": "Snv Tg", + "fieldName": "data.snv_tg" + }, + { + "displayName": "Del 1 Count", + "fieldName": "data.del_1_count" + }, + { + "displayName": "Del 4 Count", + "fieldName": "data.del_4_count" + }, + { + "displayName": "Ins 1 Count", + "fieldName": "data.ins_1_count" + }, + { + "displayName": "Ins 4 Count", + "fieldName": "data.ins_4_count" + }, + { + "displayName": "DEL 100", + "fieldName": "data.DEL_100" + }, + { + "displayName": "DEL 1k", + "fieldName": "data.DEL_1k" + }, + { + "displayName": "DEL 10k", + "fieldName": "data.DEL_10k" + }, + { + "displayName": "DEL 100k", + "fieldName": "data.DEL_100k" + }, + { + "displayName": "DEL 1m", + "fieldName": "data.DEL_1m" + }, + { + "displayName": "DEL 10m", + "fieldName": "data.DEL_10m" + }, + { + "displayName": "DEL GREATER THAN 10m", + "fieldName": "data.DEL_GREATER_THAN_10m" + }, + { + "displayName": "DUP 100", + "fieldName": "data.DUP_100" + }, + { + "displayName": "DUP 1k", + "fieldName": "data.DUP_1k" + }, + { + "displayName": "DUP 10k", + "fieldName": "data.DUP_10k" + }, + { + "displayName": "DUP 100k", + "fieldName": "data.DUP_100k" + }, + { + "displayName": "DUP 1m", + "fieldName": "data.DUP_1m" + }, + { + "displayName": "DUP 10m", + "fieldName": "data.DUP_10m" + }, + { + "displayName": "DUP GREATER THAN 10m", + "fieldName": "data.DUP_GREATER_THAN_10m" + }, + { + "displayName": "INV 100", + "fieldName": "data.INV_100" + }, + { + "displayName": "INV 1k", + "fieldName": "data.INV_1k" + }, + { + "displayName": "INV 10k", + "fieldName": "data.INV_10k" + }, + { + "displayName": "INV 100k", + "fieldName": "data.INV_100k" + }, + { + "displayName": "INV 1m", + "fieldName": "data.INV_1m" + }, + { + "displayName": "INV 10m", + "fieldName": "data.INV_10m" + }, + { + "displayName": "INV GREATER THAN 10m", + "fieldName": "data.INV_GREATER_THAN_10m" + }, + { + "displayName": "Snv Ca Aa", + "fieldName": "data.snv_ca_aa" + }, + { + "displayName": "Snv Ca Ac", + "fieldName": "data.snv_ca_ac" + }, + { + "displayName": "Snv Ca Ag", + "fieldName": "data.snv_ca_ag" + }, + { + "displayName": "Snv Ca At", + "fieldName": "data.snv_ca_at" + }, + { + "displayName": "Snv Ca Ca", + "fieldName": "data.snv_ca_ca" + }, + { + "displayName": "Snv Ca Cc", + "fieldName": "data.snv_ca_cc" + }, + { + "displayName": "Snv Ca Cg", + "fieldName": "data.snv_ca_cg" + }, + { + "displayName": "Snv Ca Ct", + "fieldName": "data.snv_ca_ct" + }, + { + "displayName": "Snv Ca Ga", + "fieldName": "data.snv_ca_ga" + }, + { + "displayName": "Snv Ca Gc", + "fieldName": "data.snv_ca_gc" + }, + { + "displayName": "Snv Ca Gg", + "fieldName": "data.snv_ca_gg" + }, + { + "displayName": "Snv Ca Gt", + "fieldName": "data.snv_ca_gt" + }, + { + "displayName": "Snv Ca Ta", + "fieldName": "data.snv_ca_ta" + }, + { + "displayName": "Snv Ca Tc", + "fieldName": "data.snv_ca_tc" + }, + { + "displayName": "Snv Ca Tg", + "fieldName": "data.snv_ca_tg" + }, + { + "displayName": "Snv Ca Tt", + "fieldName": "data.snv_ca_tt" + }, + { + "displayName": "Snv Cg Aa", + "fieldName": "data.snv_cg_aa" + }, + { + "displayName": "Snv Cg Ac", + "fieldName": "data.snv_cg_ac" + }, + { + "displayName": "Snv Cg Ag", + "fieldName": "data.snv_cg_ag" + }, + { + "displayName": "Snv Cg At", + "fieldName": "data.snv_cg_at" + }, + { + "displayName": "Snv Cg Ca", + "fieldName": "data.snv_cg_ca" + }, + { + "displayName": "Snv Cg Cc", + "fieldName": "data.snv_cg_cc" + }, + { + "displayName": "Snv Cg Cg", + "fieldName": "data.snv_cg_cg" + }, + { + "displayName": "Snv Cg Ct", + "fieldName": "data.snv_cg_ct" + }, + { + "displayName": "Snv Cg Ga", + "fieldName": "data.snv_cg_ga" + }, + { + "displayName": "Snv Cg Gc", + "fieldName": "data.snv_cg_gc" + }, + { + "displayName": "Snv Cg Gg", + "fieldName": "data.snv_cg_gg" + }, + { + "displayName": "Snv Cg Gt", + "fieldName": "data.snv_cg_gt" + }, + { + "displayName": "Snv Cg Ta", + "fieldName": "data.snv_cg_ta" + }, + { + "displayName": "Snv Cg Tc", + "fieldName": "data.snv_cg_tc" + }, + { + "displayName": "Snv Cg Tg", + "fieldName": "data.snv_cg_tg" + }, + { + "displayName": "Snv Cg Tt", + "fieldName": "data.snv_cg_tt" + }, + { + "displayName": "Snv Ct Aa", + "fieldName": "data.snv_ct_aa" + }, + { + "displayName": "Snv Ct Ac", + "fieldName": "data.snv_ct_ac" + }, + { + "displayName": "Snv Ct Ag", + "fieldName": "data.snv_ct_ag" + }, + { + "displayName": "Snv Ct At", + "fieldName": "data.snv_ct_at" + }, + { + "displayName": "Snv Ct Ca", + "fieldName": "data.snv_ct_ca" + }, + { + "displayName": "Snv Ct Cc", + "fieldName": "data.snv_ct_cc" + }, + { + "displayName": "Snv Ct Cg", + "fieldName": "data.snv_ct_cg" + }, + { + "displayName": "Snv Ct Ct", + "fieldName": "data.snv_ct_ct" + }, + { + "displayName": "Snv Ct Ga", + "fieldName": "data.snv_ct_ga" + }, + { + "displayName": "Snv Ct Gc", + "fieldName": "data.snv_ct_gc" + }, + { + "displayName": "Snv Ct Gg", + "fieldName": "data.snv_ct_gg" + }, + { + "displayName": "Snv Ct Gt", + "fieldName": "data.snv_ct_gt" + }, + { + "displayName": "Snv Ct Ta", + "fieldName": "data.snv_ct_ta" + }, + { + "displayName": "Snv Ct Tc", + "fieldName": "data.snv_ct_tc" + }, + { + "displayName": "Snv Ct Tg", + "fieldName": "data.snv_ct_tg" + }, + { + "displayName": "Snv Ct Tt", + "fieldName": "data.snv_ct_tt" + }, + { + "displayName": "Snv Ta Aa", + "fieldName": "data.snv_ta_aa" + }, + { + "displayName": "Snv Ta Ac", + "fieldName": "data.snv_ta_ac" + }, + { + "displayName": "Snv Ta Ag", + "fieldName": "data.snv_ta_ag" + }, + { + "displayName": "Snv Ta At", + "fieldName": "data.snv_ta_at" + }, + { + "displayName": "Snv Ta Ca", + "fieldName": "data.snv_ta_ca" + }, + { + "displayName": "Snv Ta Cc", + "fieldName": "data.snv_ta_cc" + }, + { + "displayName": "Snv Ta Cg", + "fieldName": "data.snv_ta_cg" + }, + { + "displayName": "Snv Ta Ct", + "fieldName": "data.snv_ta_ct" + }, + { + "displayName": "Snv Ta Ga", + "fieldName": "data.snv_ta_ga" + }, + { + "displayName": "Snv Ta Gc", + "fieldName": "data.snv_ta_gc" + }, + { + "displayName": "Snv Ta Gg", + "fieldName": "data.snv_ta_gg" + }, + { + "displayName": "Snv Ta Gt", + "fieldName": "data.snv_ta_gt" + }, + { + "displayName": "Snv Ta Ta", + "fieldName": "data.snv_ta_ta" + }, + { + "displayName": "Snv Ta Tc", + "fieldName": "data.snv_ta_tc" + }, + { + "displayName": "Snv Ta Tg", + "fieldName": "data.snv_ta_tg" + }, + { + "displayName": "Snv Ta Tt", + "fieldName": "data.snv_ta_tt" + }, + { + "displayName": "Snv Tc Aa", + "fieldName": "data.snv_tc_aa" + }, + { + "displayName": "Snv Tc Ac", + "fieldName": "data.snv_tc_ac" + }, + { + "displayName": "Snv Tc Ag", + "fieldName": "data.snv_tc_ag" + }, + { + "displayName": "Snv Tc At", + "fieldName": "data.snv_tc_at" + }, + { + "displayName": "Snv Tc Ca", + "fieldName": "data.snv_tc_ca" + }, + { + "displayName": "Snv Tc Cc", + "fieldName": "data.snv_tc_cc" + }, + { + "displayName": "Snv Tc Cg", + "fieldName": "data.snv_tc_cg" + }, + { + "displayName": "Snv Tc Ct", + "fieldName": "data.snv_tc_ct" + }, + { + "displayName": "Snv Tc Ga", + "fieldName": "data.snv_tc_ga" + }, + { + "displayName": "Snv Tc Gc", + "fieldName": "data.snv_tc_gc" + }, + { + "displayName": "Snv Tc Gg", + "fieldName": "data.snv_tc_gg" + }, + { + "displayName": "Snv Tc Gt", + "fieldName": "data.snv_tc_gt" + }, + { + "displayName": "Snv Tc Ta", + "fieldName": "data.snv_tc_ta" + }, + { + "displayName": "Snv Tc Tc", + "fieldName": "data.snv_tc_tc" + }, + { + "displayName": "Snv Tc Tg", + "fieldName": "data.snv_tc_tg" + }, + { + "displayName": "Snv Tc Tt", + "fieldName": "data.snv_tc_tt" + }, + { + "displayName": "Snv Tg Aa", + "fieldName": "data.snv_tg_aa" + }, + { + "displayName": "Snv Tg Ac", + "fieldName": "data.snv_tg_ac" + }, + { + "displayName": "Snv Tg Ag", + "fieldName": "data.snv_tg_ag" + }, + { + "displayName": "Snv Tg At", + "fieldName": "data.snv_tg_at" + }, + { + "displayName": "Snv Tg Ca", + "fieldName": "data.snv_tg_ca" + }, + { + "displayName": "Snv Tg Cc", + "fieldName": "data.snv_tg_cc" + }, + { + "displayName": "Snv Tg Cg", + "fieldName": "data.snv_tg_cg" + }, + { + "displayName": "Snv Tg Ct", + "fieldName": "data.snv_tg_ct" + }, + { + "displayName": "Snv Tg Ga", + "fieldName": "data.snv_tg_ga" + }, + { + "displayName": "Snv Tg Gc", + "fieldName": "data.snv_tg_gc" + }, + { + "displayName": "Snv Tg Gg", + "fieldName": "data.snv_tg_gg" + }, + { + "displayName": "Snv Tg Gt", + "fieldName": "data.snv_tg_gt" + }, + { + "displayName": "Snv Tg Ta", + "fieldName": "data.snv_tg_ta" + }, + { + "displayName": "Snv Tg Tc", + "fieldName": "data.snv_tg_tc" + }, + { + "displayName": "Snv Tg Tg", + "fieldName": "data.snv_tg_tg" + }, + { + "displayName": "Snv Tg Tt", + "fieldName": "data.snv_tg_tt" + }, + { + "displayName": "Dsbr Snv Load", + "fieldName": "data.dsbr_snv_load" + }, + { + "displayName": "Dsbr Ct Ratio", + "fieldName": "data.dsbr_ct_ratio" + }, + { + "displayName": "Dsbr Del4 Load", + "fieldName": "data.dsbr_del4_load" + }, + { + "displayName": "Dsbr Del4 Ratio", + "fieldName": "data.dsbr_del4_ratio" + }, + { + "displayName": "Dsbr Delsv Load", + "fieldName": "data.dsbr_delsv_load" + }, + { + "displayName": "Dsbr Delsv Ratio", + "fieldName": "data.dsbr_delsv_ratio" + }, + { + "displayName": "Dsbr Dup Load", + "fieldName": "data.dsbr_dup_load" + }, + { + "displayName": "Dsbr Sv Load", + "fieldName": "data.dsbr_sv_load" + }, + { + "displayName": "Dsbr First Genes", + "fieldName": "data.dsbr_first_genes" + }, + { + "displayName": "Dsbr Second Genes", + "fieldName": "data.dsbr_second_genes" + }, + { + "displayName": "Dsbr Score", + "fieldName": "data.dsbr_score" + }, + { + "displayName": "Dsbr Snv Load Cut", + "fieldName": "data.dsbr_snv_load_cut" + }, + { + "displayName": "Dsbr Ct Ratio Cut", + "fieldName": "data.dsbr_ct_ratio_cut" + }, + { + "displayName": "Dsbr Del4 Load Cut", + "fieldName": "data.dsbr_del4_load_cut" + }, + { + "displayName": "Dsbr Del4 Ratio Cut", + "fieldName": "data.dsbr_del4_ratio_cut" + }, + { + "displayName": "Dsbr Delsv Load Cut", + "fieldName": "data.dsbr_delsv_load_cut" + }, + { + "displayName": "Dsbr Delsv Ratio Cut", + "fieldName": "data.dsbr_delsv_ratio_cut" + }, + { + "displayName": "Dsbr Dup Load Cut", + "fieldName": "data.dsbr_dup_load_cut" + }, + { + "displayName": "Dsbr Sv Load Cut", + "fieldName": "data.dsbr_sv_load_cut" + }, + { + "displayName": "Mmr Snv Load", + "fieldName": "data.mmr_snv_load" + }, + { + "displayName": "Mmr Indel Load", + "fieldName": "data.mmr_indel_load" + }, + { + "displayName": "Mmr First Genes", + "fieldName": "data.mmr_first_genes" + }, + { + "displayName": "Mmr Second Genes", + "fieldName": "data.mmr_second_genes" + }, + { + "displayName": "Mmr Score", + "fieldName": "data.mmr_score" + }, + { + "displayName": "Mmr Snv Load Cut", + "fieldName": "data.mmr_snv_load_cut" + }, + { + "displayName": "Mmr Indel Load Cut", + "fieldName": "data.mmr_indel_load_cut" + }, + { + "displayName": "Tdp Score", + "fieldName": "data.tdp_score" + }, + { + "displayName": "Hrdetect Score", + "fieldName": "data.hrdetect_score" + }, + { + "displayName": "Hrdetect Myriad Score", + "fieldName": "data.hrdetect_myriad_score" + }, + { + "displayName": "Hrdetect Deletion Microhomology Proportion", + "fieldName": "data.hrdetect_deletion_microhomology_proportion" + }, + { + "displayName": "Hrdetect Snv Signature 3", + "fieldName": "data.hrdetect_snv_signature_3" + }, + { + "displayName": "Hrdetect Snv Signature 8", + "fieldName": "data.hrdetect_snv_signature_8" + }, + { + "displayName": "Hrdetect Rearrangement Signature 3", + "fieldName": "data.hrdetect_rearrangement_signature_3" + }, + { + "displayName": "Hrdetect Rearrangement Signature 5", + "fieldName": "data.hrdetect_rearrangement_signature_5" + }, + { + "displayName": "Hrdetect Loh", + "fieldName": "data.hrdetect_loh" + }, + { + "displayName": "Hrdetect Tai", + "fieldName": "data.hrdetect_tai" + }, + { + "displayName": "Hrdetect Lst", + "fieldName": "data.hrdetect_lst" + }, + { + "displayName": "Snv File", + "fieldName": "data.snv_file" + }, + { + "displayName": "Indel File", + "fieldName": "data.indel_file" + }, + { + "displayName": "Sgv File", + "fieldName": "data.sgv_file" + }, + { + "displayName": "Sv File", + "fieldName": "data.sv_file" + }, + { + "displayName": "Param File", + "fieldName": "data.param_file" + }, + { + "displayName": "Seg File", + "fieldName": "data.seg_file" + }, + { + "displayName": "Neo Files", + "fieldName": "data.neo_files" + }, + { + "displayName": "Xenome Logs", + "fieldName": "data.xenome_logs" + }, + { + "displayName": "Rna Sig File", + "fieldName": "data.rna_sig_file" + }, + { + "displayName": "Alexandrov File", + "fieldName": "data.alexandrov_file" + }, + { + "displayName": "Json Files", + "fieldName": "data.json_files" + }, + { + "displayName": "Genotype Files", + "fieldName": "data.genotype_files" + }, + { + "displayName": "Submission Metadata", + "fieldName": "submission.metadata" + }, + { + "displayName": "Submission Metadata Submitter Id", + "fieldName": "submission.metadata.submitter_id" + }, + { + "displayName": "Submission Metadata Processing Started", + "fieldName": "submission.metadata.processing_started" + }, + { + "displayName": "Submission Metadata Processed At", + "fieldName": "submission.metadata.processed_at" + }, + { + "displayName": "Submission Metadata Source File", + "fieldName": "submission.metadata.source_file" + }, + { + "displayName": "Submission Metadata Record Number", + "fieldName": "submission.metadata.record_number" + }, + { + "displayName": "Submission Metadata Hostname", + "fieldName": "submission.metadata.hostname" + }, + { + "displayName": "Submission Metadata Username", + "fieldName": "submission.metadata.username" + } + ] +} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/summary/facets.json b/apps/conductor/configs/arrangerConfigs/summary/facets.json new file mode 100644 index 00000000..ca8747e6 --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/summary/facets.json @@ -0,0 +1,1306 @@ +{ + "facets": { + "aggregations": [ + { + "active": true, + "fieldName": "data__donor", + "show": true + }, + { + "active": true, + "fieldName": "data__tumour", + "show": true + }, + { + "active": true, + "fieldName": "data__normal", + "show": true + }, + { + "active": true, + "fieldName": "data__external_id", + "show": true + }, + { + "active": true, + "fieldName": "data__seq_type", + "show": true + }, + { + "active": true, + "fieldName": "data__tumour_coverage", + "show": true + }, + { + "active": true, + "fieldName": "data__normal_coverage", + "show": true + }, + { + "active": true, + "fieldName": "data__mouse_content", + "show": true + }, + { + "active": true, + "fieldName": "data__tumour_reads_per_sp", + "show": true + }, + { + "active": true, + "fieldName": "data__normal_reads_per_sp", + "show": true + }, + { + "active": true, + "fieldName": "data__tumour_error_rate", + "show": true + }, + { + "active": true, + "fieldName": "data__normal_error_rate", + "show": true + }, + { + "active": true, + "fieldName": "data__tumour_soft_clip", + "show": true + }, + { + "active": true, + "fieldName": "data__normal_soft_clip", + "show": true + }, + { + "active": true, + "fieldName": "data__inferred_sex", + "show": true + }, + { + "active": true, + "fieldName": "data__genotype_concordance", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_count", + "show": true + }, + { + "active": true, + "fieldName": "data__del_count", + "show": true + }, + { + "active": true, + "fieldName": "data__ins_count", + "show": true + }, + { + "active": true, + "fieldName": "data__indel_count", + "show": true + }, + { + "active": true, + "fieldName": "data__deleterious_count", + "show": true + }, + { + "active": true, + "fieldName": "data__nonsyn_count", + "show": true + }, + { + "active": true, + "fieldName": "data__stopgain_count", + "show": true + }, + { + "active": true, + "fieldName": "data__stoploss_count", + "show": true + }, + { + "active": true, + "fieldName": "data__splice_count", + "show": true + }, + { + "active": true, + "fieldName": "data__noncoding_count", + "show": true + }, + { + "active": true, + "fieldName": "data__frameshift_count", + "show": true + }, + { + "active": true, + "fieldName": "data__nonframeshift_count", + "show": true + }, + { + "active": true, + "fieldName": "data__del_frameshift_count", + "show": true + }, + { + "active": true, + "fieldName": "data__del_nonframeshift_count", + "show": true + }, + { + "active": true, + "fieldName": "data__ins_frameshift_count", + "show": true + }, + { + "active": true, + "fieldName": "data__ins_nonframeshift_count", + "show": true + }, + { + "active": true, + "fieldName": "data__sv_count", + "show": true + }, + { + "active": true, + "fieldName": "data__sv_del_count", + "show": true + }, + { + "active": true, + "fieldName": "data__sv_dup_count", + "show": true + }, + { + "active": true, + "fieldName": "data__sv_inv_count", + "show": true + }, + { + "active": true, + "fieldName": "data__sv_tra_count", + "show": true + }, + { + "active": true, + "fieldName": "data__sv_del_bp_gene_count", + "show": true + }, + { + "active": true, + "fieldName": "data__sv_dup_bp_gene_count", + "show": true + }, + { + "active": true, + "fieldName": "data__sv_inv_bp_gene_count", + "show": true + }, + { + "active": true, + "fieldName": "data__sv_tra_bp_gene_count", + "show": true + }, + { + "active": true, + "fieldName": "data__waddell", + "show": true + }, + { + "active": true, + "fieldName": "data__neo_antigens", + "show": true + }, + { + "active": true, + "fieldName": "data__neo_antigens_weak", + "show": true + }, + { + "active": true, + "fieldName": "data__neo_antigens_strong", + "show": true + }, + { + "active": true, + "fieldName": "data__hla_types", + "show": true + }, + { + "active": true, + "fieldName": "data__cellularity", + "show": true + }, + { + "active": true, + "fieldName": "data__ploidy", + "show": true + }, + { + "active": true, + "fieldName": "data__alexandrov_class", + "show": true + }, + { + "active": true, + "fieldName": "data__alexandrov_etiology", + "show": true + }, + { + "active": true, + "fieldName": "data__moffitt", + "show": true + }, + { + "active": true, + "fieldName": "data__collisson", + "show": true + }, + { + "active": true, + "fieldName": "data__bailey", + "show": true + }, + { + "active": true, + "fieldName": "data__dsbr_deficient", + "show": true + }, + { + "active": true, + "fieldName": "data__dsbr_first_hit", + "show": true + }, + { + "active": true, + "fieldName": "data__dsbr_second_hit", + "show": true + }, + { + "active": true, + "fieldName": "data__mmr_deficient", + "show": true + }, + { + "active": true, + "fieldName": "data__mmr_first_hit", + "show": true + }, + { + "active": true, + "fieldName": "data__mmr_second_hit", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_sig1", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_sig2", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_sig3", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_sig5", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_sig6", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_sig8", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_sig13", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_sig17", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_sig18", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_sig20", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_sig26", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_residuals", + "show": true + }, + { + "active": true, + "fieldName": "data__csnnls_n_mutations", + "show": true + }, + { + "active": true, + "fieldName": "data__germline_snv_count", + "show": true + }, + { + "active": true, + "fieldName": "data__germline_indel_count", + "show": true + }, + { + "active": true, + "fieldName": "data__germline_titv_ratio", + "show": true + }, + { + "active": true, + "fieldName": "data__germline_missense_count", + "show": true + }, + { + "active": true, + "fieldName": "data__germline_nonsense_count", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_tc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_tg", + "show": true + }, + { + "active": true, + "fieldName": "data__del_1_count", + "show": true + }, + { + "active": true, + "fieldName": "data__del_4_count", + "show": true + }, + { + "active": true, + "fieldName": "data__ins_1_count", + "show": true + }, + { + "active": true, + "fieldName": "data__ins_4_count", + "show": true + }, + { + "active": true, + "fieldName": "data__DEL_100", + "show": true + }, + { + "active": true, + "fieldName": "data__DEL_1k", + "show": true + }, + { + "active": true, + "fieldName": "data__DEL_10k", + "show": true + }, + { + "active": true, + "fieldName": "data__DEL_100k", + "show": true + }, + { + "active": true, + "fieldName": "data__DEL_1m", + "show": true + }, + { + "active": true, + "fieldName": "data__DEL_10m", + "show": true + }, + { + "active": true, + "fieldName": "data__DEL_GREATER_THAN_10m", + "show": true + }, + { + "active": true, + "fieldName": "data__DUP_100", + "show": true + }, + { + "active": true, + "fieldName": "data__DUP_1k", + "show": true + }, + { + "active": true, + "fieldName": "data__DUP_10k", + "show": true + }, + { + "active": true, + "fieldName": "data__DUP_100k", + "show": true + }, + { + "active": true, + "fieldName": "data__DUP_1m", + "show": true + }, + { + "active": true, + "fieldName": "data__DUP_10m", + "show": true + }, + { + "active": true, + "fieldName": "data__DUP_GREATER_THAN_10m", + "show": true + }, + { + "active": true, + "fieldName": "data__INV_100", + "show": true + }, + { + "active": true, + "fieldName": "data__INV_1k", + "show": true + }, + { + "active": true, + "fieldName": "data__INV_10k", + "show": true + }, + { + "active": true, + "fieldName": "data__INV_100k", + "show": true + }, + { + "active": true, + "fieldName": "data__INV_1m", + "show": true + }, + { + "active": true, + "fieldName": "data__INV_10m", + "show": true + }, + { + "active": true, + "fieldName": "data__INV_GREATER_THAN_10m", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_aa", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_ac", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_ag", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_at", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_ca", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_cc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_cg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_ct", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_ga", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_gc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_gg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_gt", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_ta", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_tc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_tg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ca_tt", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_aa", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_ac", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_ag", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_at", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_ca", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_cc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_cg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_ct", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_ga", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_gc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_gg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_gt", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_ta", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_tc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_tg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_cg_tt", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_aa", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_ac", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_ag", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_at", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_ca", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_cc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_cg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_ct", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_ga", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_gc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_gg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_gt", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_ta", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_tc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_tg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ct_tt", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_aa", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_ac", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_ag", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_at", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_ca", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_cc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_cg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_ct", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_ga", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_gc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_gg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_gt", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_ta", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_tc", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_tg", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_ta_tt", + "show": true + }, + { + "active": true, + "fieldName": "data__snv_tc_aa", + "show": true + }, + { + "active": true, + "fieldName": 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"show": false + }, + { + "active": false, + "fieldName": "submission_metadata__username", + "show": false + } + ] + } +} \ No newline at end of file diff --git a/apps/conductor/configs/arrangerConfigs/summary/table.json b/apps/conductor/configs/arrangerConfigs/summary/table.json new file mode 100644 index 00000000..bee1b485 --- /dev/null +++ b/apps/conductor/configs/arrangerConfigs/summary/table.json @@ -0,0 +1,2093 @@ +{ + "table": { + "rowIdFieldName": "id" , + "columns": [ + { + "canChangeShow": true, + "fieldName": "id", + "show": true, + "sortable": true + }, + { + "canChangeShow": true, + "fieldName": "data.donor", + "show": true, + "sortable": true, + "jsonPath": "$.data.donor", + "query": "data { donor }" + }, + { + "canChangeShow": true, + "fieldName": "data.tumour", + "show": true, + "sortable": true, + "jsonPath": "$.data.tumour", + "query": "data { tumour }" + }, + { + "canChangeShow": true, + "fieldName": "data.normal", + "show": true, + "sortable": true, + "jsonPath": 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"submission_metadata { processing_started }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.processed_at", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.processed_at", + "query": "submission_metadata { processed_at }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.source_file", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.source_file", + "query": "submission_metadata { source_file }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.record_number", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.record_number", + "query": "submission_metadata { record_number }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.hostname", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.hostname", + "query": "submission_metadata { hostname }" + }, + { + "canChangeShow": true, + "fieldName": "submission.metadata.username", + "show": false, + "sortable": true, + "jsonPath": "$.submission.metadata.username", + "query": "submission_metadata { username }" + } + ] + } +} \ No newline at end of file diff --git a/apps/conductor/configs/elasticsearchConfigs/datatable1-mapping.json b/apps/conductor/configs/elasticsearchConfigs/datatable1-mapping.json deleted file mode 100644 index 75046cff..00000000 --- a/apps/conductor/configs/elasticsearchConfigs/datatable1-mapping.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "index_patterns": [ - "datatable1-*" - ], - "aliases": { - "datatable1_centric": {} - }, - "mappings": { - "properties": { - "data": { - "type": "object", - "properties": { - "gender": { - "type": "keyword" - }, - "donor_id": { - "type": "keyword" - }, - "vital_status": { - "type": "keyword" - }, - "diagnosis": { - "type": "nested", - "properties": { - "stage": { - "type": "keyword" - }, - "donor_id": { - "type": "keyword" - }, - "cancer_type": { - "type": "keyword" - }, - "diagnosis_id": { - "type": "keyword" - }, - "primary_site": { - "type": "keyword" - }, - "staging_system": { - "type": "keyword" - }, - "age_at_diagnosis": { - "type": "integer" - } - } - }, - "treatment": { - "type": "nested", - "properties": { - "donor_id": { - "type": "keyword" - }, - "treatment_id": { - "type": "keyword" - }, - "treatment_type": { - "type": "keyword" - }, - "treatment_start": { - "type": "integer" - }, - "treatment_duration": { - "type": "integer" - }, - "treatment_response": { - "type": "keyword" - }, - "followup": { - "type": "nested", - "properties": { - "followup_id": { - "type": "keyword" - }, - "treatment_id": { - "type": "keyword" - }, - "disease_status": { - "type": "keyword" - }, - "followup_interval": { - "type": "integer" - } - } - } - } - } - } - } - } - }, - "settings": { - "number_of_shards": 1, - "number_of_replicas": 0 - } -} \ No newline at end of file diff --git a/apps/conductor/configs/elasticsearchConfigs/idmapping-mapping.json b/apps/conductor/configs/elasticsearchConfigs/idmapping-mapping.json new file mode 100644 index 00000000..a021183c --- /dev/null +++ b/apps/conductor/configs/elasticsearchConfigs/idmapping-mapping.json @@ -0,0 +1,180 @@ +{ + "index_patterns": [ + "idmapping-*" + ], + "aliases": { + "idmapping_centric": {} + }, + "mappings": { + "properties": { + "data": { + "type": "object", + "properties": { + "external_id": { + "type": "keyword" + }, + "donor": { + "type": "keyword" + }, + "Age_at_diagnosis": { + "type": "integer" + }, + "Sex": { + "type": "keyword" + }, + "Date_of_Tissue": { + "type": "keyword" + }, + "Sample": { + "type": "keyword" + }, + "PPID": { + "type": "keyword" + }, + "PDO_available": { + "type": "keyword" + }, + "PDO_ID_Notta": { + "type": "keyword", + "null_value": "No Data" + }, + "PDO_ID_PMLB": { + "type": "integer" + }, + "PDO_WT_RNAseq": { + "type": "keyword" + }, + "PDO_WGS": { + "type": "keyword" + }, + "PDO_Exome": { + "type": "keyword" + }, + "PDO_drugscreen": { + "type": "keyword" + }, + "Tumour_scRNAseq": { + "type": "keyword" + }, + "Tumour_scCNV": { + "type": "keyword" + }, + "Tumour_multiome": { + "type": "keyword" + }, + "Tumour_spatial": { + "type": "keyword" + }, + "Plasma_WGS": { + "type": "keyword" + }, + "Plasma_cfRNA": { + "type": "keyword" + }, + "Histology": { + "type": "keyword", + "null_value": "No Data" + }, + "Staging_at_Diagnosis_T": { + "type": "integer" + }, + "Staging_at_Diagnosis_N": { + "type": "integer" + }, + "Staging_at_Diagnosis_M": { + "type": "integer" + }, + "Biopsy_at_Diagnosis": { + "type": "keyword" + }, + "Date_of_Rx": { + "type": "keyword" + }, + "Systemic_Tx": { + "type": "keyword" + }, + "Tx_Type": { + "type": "keyword" + }, + "Biopsy_at_Progression": { + "type": "keyword" + }, + "CRUK": { + "type": "keyword" + }, + "PIMO": { + "type": "keyword" + }, + "COMPASS": { + "type": "keyword" + }, + "NeoPancONE": { + "type": "keyword" + }, + "PASS": { + "type": "keyword" + }, + "ARCAP": { + "type": "integer" + }, + "PA7": { + "type": "integer" + }, + "PA6": { + "type": "integer" + }, + "Prosper_Panc": { + "type": "keyword" + }, + "HPB_Banking": { + "type": "keyword" + }, + "OPCS": { + "type": "keyword" + }, + "Surgical_DB": { + "type": "keyword" + }, + "TMA_1": { + "type": "keyword" + }, + "TMA_2": { + "type": "keyword" + }, + "Rapid_Autopsy": { + "type": "keyword", + "null_value": "No Data" + }, + "Jackson_Lab_ID": { + "type": "keyword" + }, + "McGaha_Lab_ID": { + "type": "keyword" + }, + "Sheba_SPC": { + "type": "keyword" + }, + "QPCS_ID": { + "type": "keyword" + }, + "OCIP_ID": { + "type": "keyword" + }, + "PCD_ID": { + "type": "keyword" + }, + "RB_xxxx": { + "type": "keyword" + }, + "GPxx": { + "type": "keyword" + } + } + } + } + }, + "settings": { + "number_of_shards": 1, + "number_of_replicas": 0 + } +} \ No newline at end of file diff --git a/apps/conductor/configs/elasticsearchConfigs/mapping.json b/apps/conductor/configs/elasticsearchConfigs/mapping.json deleted file mode 100644 index 30a1e1be..00000000 --- a/apps/conductor/configs/elasticsearchConfigs/mapping.json +++ /dev/null @@ -1,120 +0,0 @@ -{ - "index_patterns": ["data-*"], - "aliases": { - "data_centric": {} - }, - "mappings": { - "properties": { - "data": { - "type": "object", - "properties": { - "gender": { - "type": "keyword" - }, - "donor_id": { - "type": "keyword" - }, - "vital_status": { - "type": "keyword" - }, - "diagnosis": { - "type": "nested", - "properties": { - "stage": { - "type": "keyword" - }, - "donor_id": { - "type": "keyword" - }, - "cancer_type": { - "type": "keyword" - }, - "diagnosis_id": { - "type": "keyword" - }, - "primary_site": { - "type": "keyword" - }, - "staging_system": { - "type": "keyword" - }, - "age_at_diagnosis": { - "type": "integer" - }, - "followup": { - "type": "nested", - "properties": { - "followup_id": { - "type": "keyword" - }, - "diagnosis_id": { - "type": "keyword" - }, - "disease_status": { - "type": "keyword" - }, - "followup_interval": { - "type": "integer" - } - } - }, - "specimen": { - "type": "nested", - "properties": { - "sample_id": { - "type": "keyword" - }, - "sample_type": { - "type": "keyword" - }, - "specimen_id": { - "type": "keyword" - }, - "diagnosis_id": { - "type": "keyword" - }, - "specimen_type": { - "type": "keyword" - }, - "tissue_source": { - "type": "keyword" - } - } - }, - "treatment": { - "type": "nested", - "properties": { - "drug_name": { - "type": "keyword" - }, - "diagnosis_id": { - "type": "keyword" - }, - "treatment_id": { - "type": "keyword" - }, - "treatment_type": { - "type": "keyword" - }, - "treatment_start": { - "type": "integer" - }, - "treatment_duration": { - "type": "integer" - }, - "treatment_response": { - "type": "keyword" - } - } - } - } - } - } - } - } - }, - "settings": { - "number_of_shards": 1, - "number_of_replicas": 0 - } -} diff --git a/apps/conductor/configs/elasticsearchConfigs/sample-mapping.json b/apps/conductor/configs/elasticsearchConfigs/sample-mapping.json new file mode 100644 index 00000000..5d9823b5 --- /dev/null +++ b/apps/conductor/configs/elasticsearchConfigs/sample-mapping.json @@ -0,0 +1,97 @@ +{ + "index_patterns": [ + "sample-*" + ], + "aliases": { + "sample_centric": {} + }, + "mappings": { + "properties": { + "data": { + "type": "object", + "properties": { + "donor_name": { + "type": "keyword" + }, + "sample_name": { + "type": "keyword" + }, + "seq_type": { + "type": "keyword" + }, + "case_id": { + "type": "keyword" + }, + "test_id": { + "type": "keyword" + }, + "req_id": { + "type": "keyword" + }, + "project": { + "type": "keyword" + }, + "external_id": { + "type": "keyword" + }, + "tissue_origin": { + "type": "keyword" + }, + "tissue_type": { + "type": "keyword" + }, + "group_id": { + "type": "integer" + }, + "library_design": { + "type": "keyword" + }, + "library_name": { + "type": "keyword" + }, + "sequencer_run": { + "type": "keyword" + }, + "sequencing_id": { + "type": "keyword", + "null_value": "No Data" + }, + "instrument_model": { + "type": "keyword" + }, + "gsi_workflow_run_id": { + "type": "keyword" + }, + "gsi_workflow": { + "type": "keyword" + }, + "gsi_workflow_version": { + "type": "keyword" + }, + "gsi_md5sum": { + "type": "keyword" + }, + "gsi_time": { + "type": "keyword" + }, + "fastq_path": { + "type": "keyword" + }, + "modification_date": { + "type": "keyword" + }, + "linked_file": { + "type": "keyword" + }, + "linked_file_time": { + "type": "keyword" + } + } + } + } + }, + "settings": { + "number_of_shards": 1, + "number_of_replicas": 0 + } +} diff --git a/apps/conductor/configs/elasticsearchConfigs/summary-mapping.json b/apps/conductor/configs/elasticsearchConfigs/summary-mapping.json new file mode 100644 index 00000000..9f5a7e58 --- /dev/null +++ b/apps/conductor/configs/elasticsearchConfigs/summary-mapping.json @@ -0,0 +1,819 @@ +{ + "index_patterns": [ + "summary-*" + ], + "aliases": { + "summary_centric": {} + }, + "mappings": { + "properties": { + "data": { + "type": "object", + "properties": { + "donor": { + "type": "keyword" + }, + "tumour": { + "type": "keyword" + }, + "normal": { + "type": "keyword" + }, + "external_id": { + "type": "keyword" + }, + "seq_type": { + "type": "keyword" + }, + "tumour_coverage": { + "type": "integer" + }, + "normal_coverage": { + "type": "integer" + }, + "mouse_content": { + "type": "keyword", + "null_value": "No Data" + }, + "tumour_reads_per_sp": { + "type": "keyword", + "null_value": "No Data" + }, + "normal_reads_per_sp": { + "type": "keyword", + "null_value": "No Data" + }, + "tumour_error_rate": { + "type": "keyword", + "null_value": "No Data" + }, + "normal_error_rate": { + "type": "keyword", + "null_value": "No Data" + }, + "tumour_soft_clip": { + "type": "keyword", + "null_value": "No Data" + }, + "normal_soft_clip": { + "type": "keyword", + "null_value": "No Data" + }, + "inferred_sex": { + "type": "keyword" + }, + "genotype_concordance": { + "type": "keyword", + "null_value": "No Data" + }, + "snv_count": { + "type": "integer" + }, + "del_count": { + "type": "integer" + }, + "ins_count": { + "type": "integer" + }, + "indel_count": { + "type": "integer" + }, + "deleterious_count": { + "type": "integer" + }, + "nonsyn_count": { + "type": "integer" + }, + "stopgain_count": { + "type": "integer" + }, + "stoploss_count": { + "type": "integer" + }, + "splice_count": { + "type": "integer" + }, + "noncoding_count": { + "type": "integer" + }, + "frameshift_count": { + "type": "integer" + }, + "nonframeshift_count": { + "type": "integer" + }, + "del_frameshift_count": { + "type": "integer" + }, + "del_nonframeshift_count": { + "type": "integer" + }, + "ins_frameshift_count": { + "type": "integer" + }, + "ins_nonframeshift_count": { + "type": "integer" + }, + "sv_count": { + "type": "integer" + }, + "sv_del_count": { + "type": "integer" + }, + "sv_dup_count": { + "type": "integer" + }, + "sv_inv_count": { + "type": "integer" + }, + "sv_tra_count": { + "type": "integer" + }, + "sv_del_bp_gene_count": { + "type": "integer" + }, + "sv_dup_bp_gene_count": { + "type": "integer" + }, + "sv_inv_bp_gene_count": { + "type": "integer" + }, + "sv_tra_bp_gene_count": { + "type": "integer" + }, + "waddell": { + "type": "keyword" + }, + "neo_antigens": { + "type": "keyword", + "null_value": "No Data" + }, + "neo_antigens_weak": { + "type": "keyword", + "null_value": "No Data" + }, + "neo_antigens_strong": { + "type": "keyword", + "null_value": "No Data" + }, + "hla_types": { + "type": "keyword", + "null_value": "No Data" + }, + "cellularity": { + "type": "float" + }, + "ploidy": { + "type": "float" + }, + "alexandrov_class": { + "type": "keyword", + "null_value": "No Data" + }, + "alexandrov_etiology": { + "type": "keyword", + "null_value": "No Data" + }, + "moffitt": { + "type": "keyword", + "null_value": "No Data" + }, + "collisson": { + "type": "keyword", + "null_value": "No Data" + }, + "bailey": { + "type": "keyword", + "null_value": "No Data" + }, + "dsbr_deficient": { + "type": "keyword", + "null_value": "No Data" + }, + "dsbr_first_hit": { + "type": "keyword", + "null_value": "No Data" + }, + "dsbr_second_hit": { + "type": "keyword", + "null_value": "No Data" + }, + "mmr_deficient": { + "type": "keyword", + "null_value": "No Data" + }, + "mmr_first_hit": { + "type": "keyword", + "null_value": "No Data" + }, + "mmr_second_hit": { + "type": "keyword", + "null_value": "No Data" + }, + "csnnls_sig1": { + "type": "float" + }, + "csnnls_sig2": { + "type": "float" + }, + "csnnls_sig3": { + "type": "integer" + }, + "csnnls_sig5": { + "type": "float" + }, + "csnnls_sig6": { + "type": "integer" + }, + "csnnls_sig8": { + "type": "float" + }, + "csnnls_sig13": { + "type": "integer" + }, + "csnnls_sig17": { + "type": "integer" + }, + "csnnls_sig18": { + "type": "integer" + }, + "csnnls_sig20": { + "type": "integer" + }, + "csnnls_sig26": { + "type": "integer" + }, + "csnnls_residuals": { + "type": "float" + }, + "csnnls_n_mutations": { + "type": "keyword", + "null_value": "No Data" + }, + "germline_snv_count": { + "type": "integer" + }, + "germline_indel_count": { + "type": "integer" + }, + "germline_titv_ratio": { + "type": "float" + }, + "germline_missense_count": { + "type": "integer" + }, + "germline_nonsense_count": { + "type": "integer" + }, + "snv_ca": { + "type": "integer" + }, + "snv_cg": { + "type": "integer" + }, + "snv_ct": { + "type": "integer" + }, + "snv_ta": { + "type": "integer" + }, + "snv_tc": { + "type": "integer" + }, + "snv_tg": { + "type": "integer" + }, + "del_1_count": { + "type": "integer" + }, + "del_4_count": { + "type": "integer" + }, + "ins_1_count": { + "type": "integer" + }, + "ins_4_count": { + "type": "integer" + }, + "DEL_100": { + "type": "integer" + }, + "DEL_1k": { + "type": "integer" + }, + "DEL_10k": { + "type": "integer" + }, + "DEL_100k": { + "type": "integer" + }, + "DEL_1m": { + "type": "integer" + }, + "DEL_10m": { + "type": "integer" + }, + "DEL_GREATER_THAN_10m": { + "type": "integer" + }, + "DUP_100": { + "type": "integer" + }, + "DUP_1k": { + "type": "integer" + }, + "DUP_10k": { + "type": "integer" + }, + "DUP_100k": { + "type": "integer" + }, + "DUP_1m": { + "type": "integer" + }, + "DUP_10m": { + "type": "integer" + }, + "DUP_GREATER_THAN_10m": { + "type": "integer" + }, + "INV_100": { + "type": "integer" + }, + "INV_1k": { + "type": "integer" + }, + "INV_10k": { + "type": "integer" + }, + "INV_100k": { + "type": "integer" + }, + "INV_1m": { + "type": "integer" + }, + "INV_10m": { + "type": "integer" + }, + "INV_GREATER_THAN_10m": { + "type": "integer" + }, + "snv_ca_aa": { + "type": "integer" + }, + "snv_ca_ac": { + "type": "integer" + }, + "snv_ca_ag": { + "type": "integer" + }, + "snv_ca_at": { + "type": "integer" + }, + "snv_ca_ca": { + "type": "integer" + }, + "snv_ca_cc": { + "type": "integer" + }, + "snv_ca_cg": { + "type": "integer" + }, + "snv_ca_ct": { + "type": "integer" + }, + "snv_ca_ga": { + "type": "integer" + }, + "snv_ca_gc": { + "type": "integer" + }, + "snv_ca_gg": { + "type": "integer" + }, + "snv_ca_gt": { + "type": "integer" + }, + "snv_ca_ta": { + "type": "integer" + }, + "snv_ca_tc": { + "type": "integer" + }, + "snv_ca_tg": { + "type": "integer" + }, + "snv_ca_tt": { + "type": "integer" + }, + "snv_cg_aa": { + "type": "integer" + }, + "snv_cg_ac": { + "type": "integer" + }, + "snv_cg_ag": { + "type": "integer" + }, + "snv_cg_at": { + "type": "integer" + }, + "snv_cg_ca": { + "type": "integer" + }, + "snv_cg_cc": { + "type": "integer" + }, + "snv_cg_cg": { + "type": "integer" + }, + "snv_cg_ct": { + "type": "integer" + }, + "snv_cg_ga": { + "type": "integer" + }, + "snv_cg_gc": { + "type": "integer" + }, + "snv_cg_gg": { + "type": "integer" + }, + "snv_cg_gt": { + "type": "integer" + }, + "snv_cg_ta": { + "type": "integer" + }, + "snv_cg_tc": { + "type": "integer" + }, + "snv_cg_tg": { + "type": "integer" + }, + "snv_cg_tt": { + "type": "integer" + }, + "snv_ct_aa": { + "type": "integer" + }, + "snv_ct_ac": { + "type": "integer" + }, + "snv_ct_ag": { + "type": "integer" + }, + "snv_ct_at": { + "type": "integer" + }, + "snv_ct_ca": { + "type": "integer" + }, + "snv_ct_cc": { + "type": "integer" + }, + "snv_ct_cg": { + "type": "integer" + }, + "snv_ct_ct": { + "type": "integer" + }, + "snv_ct_ga": { + "type": "integer" + }, + "snv_ct_gc": { + "type": "integer" + }, + "snv_ct_gg": { + "type": "integer" + }, + "snv_ct_gt": { + "type": "integer" + }, + "snv_ct_ta": { + "type": "integer" + }, + "snv_ct_tc": { + "type": "integer" + }, + "snv_ct_tg": { + "type": "integer" + }, + "snv_ct_tt": { + "type": "integer" + }, + "snv_ta_aa": { + "type": "integer" + }, + "snv_ta_ac": { + "type": "integer" + }, + "snv_ta_ag": { + "type": "integer" + }, + "snv_ta_at": { + "type": "integer" + }, + "snv_ta_ca": { + "type": "integer" + }, + "snv_ta_cc": { + "type": "integer" + }, + "snv_ta_cg": { + "type": "integer" + }, + "snv_ta_ct": { + "type": "integer" + }, + "snv_ta_ga": { + "type": "integer" + }, + "snv_ta_gc": { + "type": "integer" + }, + "snv_ta_gg": { + "type": "integer" + }, + "snv_ta_gt": { + "type": "integer" + }, + "snv_ta_ta": { + "type": "integer" + }, + "snv_ta_tc": { + "type": "integer" + }, + "snv_ta_tg": { + "type": "integer" + }, + "snv_ta_tt": { + "type": "integer" + }, + "snv_tc_aa": { + "type": "integer" + }, + "snv_tc_ac": { + "type": "integer" + }, + "snv_tc_ag": { + "type": "integer" + }, + "snv_tc_at": { + "type": "integer" + }, + "snv_tc_ca": { + "type": "integer" + }, + "snv_tc_cc": { + "type": "integer" + }, + "snv_tc_cg": { + "type": "integer" + }, + "snv_tc_ct": { + "type": "integer" + }, + "snv_tc_ga": { + "type": "integer" + }, + "snv_tc_gc": { + "type": "integer" + }, + "snv_tc_gg": { + "type": "integer" + }, + "snv_tc_gt": { + "type": "integer" + }, + "snv_tc_ta": { + "type": "integer" + }, + "snv_tc_tc": { + "type": "integer" + }, + "snv_tc_tg": { + "type": "integer" + }, + "snv_tc_tt": { + "type": "integer" + }, + "snv_tg_aa": { + "type": "integer" + }, + "snv_tg_ac": { + "type": "integer" + }, + "snv_tg_ag": { + "type": "integer" + }, + "snv_tg_at": { + "type": "integer" + }, + "snv_tg_ca": { + "type": "integer" + }, + "snv_tg_cc": { + "type": "integer" + }, + "snv_tg_cg": { + "type": "integer" + }, + "snv_tg_ct": { + "type": "integer" + }, + "snv_tg_ga": { + "type": "integer" + }, + "snv_tg_gc": { + "type": "integer" + }, + "snv_tg_gg": { + "type": "integer" + }, + "snv_tg_gt": { + "type": "integer" + }, + "snv_tg_ta": { + "type": "integer" + }, + "snv_tg_tc": { + "type": "integer" + }, + "snv_tg_tg": { + "type": "integer" + }, + "snv_tg_tt": { + "type": "integer" + }, + "dsbr_snv_load": { + "type": "integer" + }, + "dsbr_ct_ratio": { + "type": "float" + }, + "dsbr_del4_load": { + "type": "integer" + }, + "dsbr_del4_ratio": { + "type": "float" + }, + "dsbr_delsv_load": { + "type": "integer" + }, + "dsbr_delsv_ratio": { + "type": "float" + }, + "dsbr_dup_load": { + "type": "integer" + }, + "dsbr_sv_load": { + "type": "integer" + }, + "dsbr_first_genes": { + "type": "keyword", + "null_value": "No Data" + }, + "dsbr_second_genes": { + "type": "keyword", + "null_value": "No Data" + }, + "dsbr_score": { + "type": "integer" + }, + "dsbr_snv_load_cut": { + "type": "integer" + }, + "dsbr_ct_ratio_cut": { + "type": "float" + }, + "dsbr_del4_load_cut": { + "type": "integer" + }, + "dsbr_del4_ratio_cut": { + "type": "float" + }, + "dsbr_delsv_load_cut": { + "type": "integer" + }, + "dsbr_delsv_ratio_cut": { + "type": "float" + }, + "dsbr_dup_load_cut": { + "type": "integer" + }, + "dsbr_sv_load_cut": { + "type": "integer" + }, + "mmr_snv_load": { + "type": "integer" + }, + "mmr_indel_load": { + "type": "integer" + }, + "mmr_first_genes": { + "type": "keyword" + }, + "mmr_second_genes": { + "type": "keyword" + }, + "mmr_score": { + "type": "integer" + }, + "mmr_snv_load_cut": { + "type": "integer" + }, + "mmr_indel_load_cut": { + "type": "integer" + }, + "tdp_score": { + "type": "float" + }, + "hrdetect_score": { + "type": "keyword", + "null_value": "No Data" + }, + "hrdetect_myriad_score": { + "type": "keyword", + "null_value": "No Data" + }, + "hrdetect_deletion_microhomology_proportion": { + "type": "keyword", + "null_value": "No Data" + }, + "hrdetect_snv_signature_3": { + "type": "keyword", + "null_value": "No Data" + }, + "hrdetect_snv_signature_8": { + "type": "keyword", + "null_value": "No Data" + }, + "hrdetect_rearrangement_signature_3": { + "type": "keyword", + "null_value": "No Data" + }, + "hrdetect_rearrangement_signature_5": { + "type": "keyword", + "null_value": "No Data" + }, + "hrdetect_loh": { + "type": "keyword", + "null_value": "No Data" + }, + "hrdetect_tai": { + "type": "keyword", + "null_value": "No Data" + }, + "hrdetect_lst": { + "type": "keyword", + "null_value": "No Data" + }, + "snv_file": { + "type": "keyword" + }, + "indel_file": { + "type": "keyword" + }, + "sgv_file": { + "type": "keyword" + }, + "sv_file": { + "type": "keyword" + }, + "param_file": { + "type": "keyword" + }, + "seg_file": { + "type": "keyword" + }, + "neo_files": { + "type": "keyword", + "null_value": "No Data" + }, + "xenome_logs": { + "type": "keyword", + "null_value": "No Data" + }, + "rna_sig_file": { + "type": "keyword" + }, + "alexandrov_file": { + "type": "keyword" + }, + "json_files": { + "type": "keyword", + "null_value": "No Data" + }, + "genotype_files": { + "type": "keyword" + } + } + } + } + }, + "settings": { + "number_of_shards": 1, + "number_of_replicas": 0 + } +} \ No newline at end of file diff --git a/apps/conductor/configs/lecternDictionaries/dictionary.json b/apps/conductor/configs/lecternDictionaries/dictionary.json deleted file mode 100644 index 01348ec9..00000000 --- a/apps/conductor/configs/lecternDictionaries/dictionary.json +++ /dev/null @@ -1,338 +0,0 @@ -{ - "name": "example-dictionary", - "description": "A Lectern dictionary for Overture's Phase Two Prelude guide focused on clinical cancer data", - "version": "1.0", - "meta": { - "createdAt": "2025-03-20T10:30:00.000Z", - "createdBy": "Mitchell Shiell", - "primaryContact": "mshiell@oicr.on.ca" - }, - "schemas": [ - { - "name": "donor", - "description": "Core demographic information about donors. One donor can have multiple diagnoses, treatments, and followups.", - "fields": [ - { - "name": "donor_id", - "description": "Unique identifier for a donor across the system", - "valueType": "string", - "unique": true, - "restrictions": { - "required": true, - "regex": "^DO\\d{4}$" - }, - "meta": { - "displayName": "Donor ID", - "examples": ["DO0599", "DO0600"] - } - }, - { - "name": "gender", - "description": "Gender of the donor", - "valueType": "string", - "restrictions": { - "required": true, - "codeList": ["Male", "Female"] - }, - "meta": { - "displayName": "Gender" - } - }, - { - "name": "vital_status", - "description": "Current vital status of the donor", - "valueType": "string", - "restrictions": { - "required": true, - "codeList": ["Alive", "Deceased"] - }, - "meta": { - "displayName": "Vital Status" - } - } - ], - "restrictions": { - "primaryKey": ["donor_id"] - }, - "meta": { - "createdAt": "2025-03-20T16:11:06.493Z", - "sourceFile": "donor.csv" - } - }, - { - "name": "diagnosis", - "description": "Clinical diagnosis details linked to a donor via donor_id. Each diagnosis belongs to exactly one donor.", - "fields": [ - { - "name": "diagnosis_id", - "description": "Unique identifier for a diagnosis record", - "valueType": "string", - "unique": true, - "restrictions": { - "required": true, - "regex": "^PD\\d{6}$" - }, - "meta": { - "displayName": "Diagnosis ID", - "examples": ["PD059901", "PD059902"] - } - }, - { - "name": "donor_id", - "description": "Reference to the donor this diagnosis belongs to", - "valueType": "string", - "restrictions": { - "required": true, - "regex": "^DO\\d{4}$" - }, - "meta": { - "displayName": "Donor ID", - "examples": ["DO0599", "DO0600"] - } - }, - { - "name": "primary_site", - "description": "Primary anatomical site of the diagnosed condition", - "valueType": "string", - "restrictions": { - "required": true - }, - "meta": { - "displayName": "Primary Site", - "examples": ["Breast", "Lung", "Prostate gland"] - } - }, - { - "name": "age_at_diagnosis", - "description": "Age of the donor at the time of diagnosis in years", - "valueType": "integer", - "restrictions": { - "required": true, - "range": {"min": 0, "max": 120} - }, - "meta": { - "displayName": "Age at Diagnosis", - "units": "years" - } - }, - { - "name": "cancer_type", - "description": "Type of cancer diagnosed using ICD-O-3 topography codes", - "valueType": "string", - "restrictions": { - "required": true, - "regex": "^C[0-9]{2}(\\.[0-9])?$" - }, - "meta": { - "displayName": "Cancer Type", - "examples": ["C50.1", "C34.1", "C61"] - } - }, - { - "name": "staging_system", - "description": "Staging system used for cancer classification", - "valueType": "string", - "restrictions": { - "required": true - }, - "meta": { - "displayName": "Staging System", - "examples": ["AJCC 8th edition", "FIGO staging system", "Gleason grade group system"] - } - }, - { - "name": "stage", - "description": "Stage of cancer according to the specified staging system", - "valueType": "string", - "restrictions": { - "required": true - }, - "meta": { - "displayName": "Stage", - "examples": ["Stage I", "Stage IV", "Grade Group 2"] - } - } - ], - "restrictions": { - "primaryKey": ["diagnosis_id"], - "foreignKey": [ - { - "schema": "donor", - "mappings": [{ "local": "donor_id", "foreign": "donor_id" }] - } - ] - }, - "meta": { - "createdAt": "2025-03-20T16:11:06.491Z", - "sourceFile": "diagnosis.csv" - } - }, - { - "name": "treatment", - "description": "Treatment information linked to a donor and diagnosis. Each treatment belongs to exactly one donor.", - "fields": [ - { - "name": "donor_id", - "description": "Reference to the donor receiving this treatment", - "valueType": "string", - "restrictions": { - "required": true, - "regex": "^DO\\d{4}$" - }, - "meta": { - "displayName": "Donor ID", - "examples": ["DO0599", "DO0600"] - } - }, - { - "name": "treatment_id", - "description": "Unique identifier for a treatment record", - "valueType": "string", - "unique": true, - "restrictions": { - "required": true, - "regex": "^TR\\d{6}$" - }, - "meta": { - "displayName": "Treatment ID", - "examples": ["TR059901", "TR059902"] - } - }, - { - "name": "treatment_type", - "description": "Type of treatment administered", - "valueType": "string", - "restrictions": { - "required": true, - "codeList": ["Surgery", "Radiation therapy", "Chemotherapy", "Hormonal therapy"] - }, - "meta": { - "displayName": "Treatment Type" - } - }, - { - "name": "treatment_start", - "description": "Days since diagnosis when treatment started", - "valueType": "integer", - "restrictions": { - "required": true, - "range": {"min": 0} - }, - "meta": { - "displayName": "Treatment Start", - "units": "days" - } - }, - { - "name": "treatment_duration", - "description": "Duration of the treatment in days", - "valueType": "integer", - "restrictions": { - "required": true, - "range": {"min": 1} - }, - "meta": { - "displayName": "Treatment Duration", - "units": "days" - } - }, - { - "name": "treatment_response", - "description": "Response to the treatment", - "valueType": "string", - "restrictions": { - "required": true, - "codeList": ["Complete response", "Partial response", "Disease progression"] - }, - "meta": { - "displayName": "Treatment Response" - } - } - ], - "restrictions": { - "primaryKey": ["treatment_id"], - "foreignKey": [ - { - "schema": "donor", - "mappings": [{ "local": "donor_id", "foreign": "donor_id" }] - } - ] - }, - "meta": { - "createdAt": "2025-03-20T16:11:06.495Z", - "sourceFile": "treatment.csv" - } - }, - { - "name": "followup", - "description": "Follow-up assessment information linked to treatments and donors. Each followup is associated with exactly one treatment.", - "fields": [ - { - "name": "treatment_id", - "description": "Reference to the treatment this followup is associated with", - "valueType": "string", - "restrictions": { - "required": true, - "regex": "^TR\\d{6}$" - }, - "meta": { - "displayName": "Treatment ID", - "examples": ["TR059901", "TR059902"] - } - }, - { - "name": "followup_id", - "description": "Unique identifier for a followup record", - "valueType": "string", - "unique": true, - "restrictions": { - "required": true, - "regex": "^FO\\d{6}$" - }, - "meta": { - "displayName": "Followup ID", - "examples": ["FO059901", "FO059902"] - } - }, - { - "name": "followup_interval", - "description": "Time since treatment completion in days", - "valueType": "integer", - "restrictions": { - "required": true, - "range": {"min": 0} - }, - "meta": { - "displayName": "Followup Interval", - "units": "days" - } - }, - { - "name": "disease_status", - "description": "Status of the disease at followup", - "valueType": "string", - "restrictions": { - "required": true, - "codeList": ["No evidence of disease", "Complete remission", "Stable", "Progression NOS"] - }, - "meta": { - "displayName": "Disease Status" - } - } - ], - "restrictions": { - "primaryKey": ["followup_id"], - "foreignKey": [ - { - "schema": "treatment", - "mappings": [{ "local": "treatment_id", "foreign": "treatment_id" }] - } - ] - }, - "meta": { - "createdAt": "2025-03-20T16:11:06.494Z", - "sourceFile": "followup.csv" - } - } - ] -} \ No newline at end of file diff --git a/apps/conductor/configs/lecternDictionaries/lbr-dictionary.json b/apps/conductor/configs/lecternDictionaries/lbr-dictionary.json new file mode 100644 index 00000000..eb398d36 --- /dev/null +++ b/apps/conductor/configs/lecternDictionaries/lbr-dictionary.json @@ -0,0 +1,2678 @@ +{ + "name": "lbr-dictionary", + "description": "Generated dictionary from CSV files", + "version": "1.0", + "meta": {}, + "schemas": [ + { + "name": "idmapping", + "description": "Schema generated from idmapping.csv", + "fields": [ + { + "name": "external_id", + "description": "Field containing external_id data", + "valueType": "string", + "meta": { + "displayName": "external_id" + } + }, + { + "name": "donor", + "description": "Field containing donor data", + "valueType": "string", + "meta": { + "displayName": "donor" + } + }, + { + "name": "Age_at_diagnosis", + "description": "Field containing Age_at_diagnosis data", + "valueType": "integer", + "meta": { + "displayName": "Age_at_diagnosis" + } + }, + { + "name": "Sex", + "description": "Field containing Sex data", + "valueType": "string", + "meta": { + "displayName": "Sex" + } + }, + { + "name": "Date_of_Tissue", + "description": "Field containing Date_of_Tissue data", + "valueType": "string", + "meta": { + "displayName": "Date_of_Tissue" + } + }, + { + "name": "Sample", + "description": "Field containing Sample data", + "valueType": "string", + "meta": { + "displayName": "Sample" + } + }, + { + "name": "PPID", + "description": "Field containing PPID data", + "valueType": "string", + "meta": { + "displayName": "PPID" + } + }, + { + "name": "PDO_available", + "description": "Field containing PDO_available data", + "valueType": "string", + "meta": { + "displayName": "PDO_available" + } + }, + { + "name": "PDO_ID_Notta", + "description": "Field containing PDO_ID_Notta data", + "valueType": "string", + "meta": { + "displayName": "PDO_ID_Notta" + } + }, + { + "name": "PDO_ID_PMLB", + "description": "Field containing PDO_ID_PMLB data", + "valueType": "integer", + "meta": { + "displayName": "PDO_ID_PMLB" + } + }, + { + "name": "PDO_WT_RNAseq", + "description": "Field containing PDO_WT_RNAseq data", + "valueType": "string", + "meta": { + "displayName": "PDO_WT_RNAseq" + } + }, + { + "name": "PDO_WGS", + "description": "Field containing PDO_WGS data", + "valueType": "string", + "meta": { + "displayName": "PDO_WGS" + } + }, + { + "name": "PDO_Exome", + "description": "Field containing PDO_Exome data", + "valueType": "string", + "meta": { + "displayName": "PDO_Exome" + } + }, + { + "name": "PDO_drugscreen", + "description": "Field containing PDO_drugscreen data", + "valueType": "string", + "meta": { + "displayName": "PDO_drugscreen" + } + }, + { + "name": "Tumour_scRNAseq", + "description": "Field containing Tumour_scRNAseq data", + "valueType": "string", + "meta": { + "displayName": "Tumour_scRNAseq" + } + }, + { + "name": "Tumour_scCNV", + "description": "Field containing Tumour_scCNV data", + "valueType": "string", + "meta": { + "displayName": "Tumour_scCNV" + } + }, + { + "name": "Tumour_multiome", + "description": "Field containing Tumour_multiome data", + "valueType": "string", + "meta": { + "displayName": "Tumour_multiome" + } + }, + { + "name": "Tumour_spatial", + "description": "Field containing Tumour_spatial data", + "valueType": "string", + "meta": { + "displayName": "Tumour_spatial" + } + }, + { + "name": "Plasma_WGS", + "description": "Field containing Plasma_WGS data", + "valueType": "string", + "meta": { + "displayName": "Plasma_WGS" + } + }, + { + "name": "Plasma_cfRNA", + "description": "Field containing Plasma_cfRNA data", + "valueType": "string", + "meta": { + "displayName": "Plasma_cfRNA" + } + }, + { + "name": "Histology", + "description": "Field containing Histology data", + "valueType": "string", + "meta": { + "displayName": "Histology" + } + }, + { + "name": "Staging_at_Diagnosis_T", + "description": "Field containing Staging_at_Diagnosis_T data", + "valueType": "string", + "meta": { + "displayName": "Staging_at_Diagnosis_T" + } + }, + { + "name": "Staging_at_Diagnosis_N", + "description": "Field containing Staging_at_Diagnosis_N data", + "valueType": "string", + "meta": { + "displayName": "Staging_at_Diagnosis_N" + } + }, + { + "name": "Staging_at_Diagnosis_M", + "description": "Field containing Staging_at_Diagnosis_M data", + "valueType": "string", + "meta": { + "displayName": "Staging_at_Diagnosis_M" + } + }, + { + "name": "Biopsy_at_Diagnosis", + "description": "Field containing Biopsy_at_Diagnosis data", + "valueType": "string", + "meta": { + "displayName": "Biopsy_at_Diagnosis" + } + }, + { + "name": "Date_of_Rx", + "description": "Field containing Date_of_Rx data", + "valueType": "string", + "meta": { + "displayName": "Date_of_Rx" + } + }, + { + "name": "Systemic_Tx", + "description": "Field containing Systemic_Tx data", + "valueType": "string", + "meta": { + "displayName": "Systemic_Tx" + } + }, + { + "name": "Tx_Type", + "description": "Field containing Tx_Type data", + "valueType": "string", + "meta": { + "displayName": "Tx_Type" + } + }, + { + "name": "Biopsy_at_Progression", + "description": "Field containing Biopsy_at_Progression data", + "valueType": "string", + "meta": { + "displayName": "Biopsy_at_Progression" + } + }, + { + "name": "CRUK", + "description": "Field containing CRUK data", + "valueType": "string", + "meta": { + "displayName": "CRUK" + } + }, + { + "name": "PIMO", + "description": "Field containing PIMO data", + "valueType": "string", + "meta": { + "displayName": "PIMO" + } + }, + { + "name": "COMPASS", + "description": "Field containing COMPASS data", + "valueType": "string", + "meta": { + "displayName": "COMPASS" + } + }, + { + "name": "NeoPancONE", + "description": "Field containing NeoPancONE data", + "valueType": "string", + "meta": { + "displayName": "NeoPancONE" + } + }, + { + "name": "PASS", + "description": "Field containing PASS data", + "valueType": "string", + "meta": { + "displayName": "PASS" + } + }, + { + "name": "ARCAP", + "description": "Field containing ARCAP data", + "valueType": "string", + "meta": { + "displayName": "ARCAP" + } + }, + { + "name": "PA7", + "description": "Field containing PA7 data", + "valueType": "string", + "meta": { + "displayName": "PA7" + } + }, + { + "name": "PA6", + "description": "Field containing PA6 data", + "valueType": "string", + "meta": { + "displayName": "PA6" + } + }, + { + "name": "Prosper_Panc", + "description": "Field containing Prosper_Panc data", + "valueType": "string", + "meta": { + "displayName": "Prosper_Panc" + } + }, + { + "name": "HPB_Banking", + "description": "Field containing HPB_Banking data", + "valueType": "string", + "meta": { + "displayName": "HPB_Banking" + } + }, + { + "name": "OPCS", + "description": "Field containing OPCS data", + "valueType": "string", + "meta": { + "displayName": "OPCS" + } + }, + { + "name": "Surgical_DB", + "description": "Field containing Surgical_DB data", + "valueType": "string", + "meta": { + "displayName": "Surgical_DB" + } + }, + { + "name": "TMA_1", + "description": "Field containing TMA_1 data", + "valueType": "string", + "meta": { + "displayName": "TMA_1" + } + }, + { + "name": "TMA_2", + "description": "Field containing TMA_2 data", + "valueType": "string", + "meta": { + "displayName": "TMA_2" + } + }, + { + "name": "Rapid_Autopsy", + "description": "Field containing Rapid_Autopsy data", + "valueType": "string", + "meta": { + "displayName": "Rapid_Autopsy" + } + }, + { + "name": "Jackson_Lab_ID", + "description": "Field containing Jackson_Lab_ID data", + "valueType": "string", + "meta": { + "displayName": "Jackson_Lab_ID" + } + }, + { + "name": "McGaha_Lab_ID", + "description": "Field containing McGaha_Lab_ID data", + "valueType": "string", + "meta": { + "displayName": "McGaha_Lab_ID" + } + }, + { + "name": "Sheba_SPC", + "description": "Field containing Sheba_SPC data", + "valueType": "string", + "meta": { + "displayName": "Sheba_SPC" + } + }, + { + "name": "QPCS_ID", + "description": "Field containing QPCS_ID data", + "valueType": "string", + "meta": { + "displayName": "QPCS_ID" + } + }, + { + "name": "OCIP_ID", + "description": "Field containing OCIP_ID data", + "valueType": "string", + "meta": { + "displayName": "OCIP_ID" + } + }, + { + "name": "PCD_ID", + "description": "Field containing PCD_ID data", + "valueType": "string", + "meta": { + "displayName": "PCD_ID" + } + }, + { + "name": "RB_xxxx", + "description": "Field containing RB_xxxx data", + "valueType": "string", + "meta": { + "displayName": "RB_xxxx" + } + }, + { + "name": "GPxx", + "description": "Field containing GPxx data", + "valueType": "string", + "meta": { + "displayName": "GPxx" + } + } + ], + "meta": { + "createdAt": "2025-05-23T19:08:46.352Z", + "sourceFile": "idmapping.csv" + } + }, + { + "name": "sample", + "description": "Schema generated from sample.csv", + "fields": [ + { + "name": "donor_name", + "description": "Field containing donor_name data", + "valueType": "string", + "meta": { + "displayName": "donor_name" + } + }, + { + "name": "sample_name", + "description": "Field containing sample_name data", + "valueType": "string", + "meta": { + "displayName": "sample_name" + } + }, + { + "name": "seq_type", + "description": "Field containing seq_type data", + "valueType": "string", + "meta": { + "displayName": "seq_type" + } + }, + { + "name": "case_id", + "description": "Field containing case_id data", + "valueType": "string", + "meta": { + "displayName": "case_id" + } + }, + { + "name": "test_id", + "description": "Field containing test_id data", + "valueType": "string", + "meta": { + "displayName": "test_id" + } + }, + { + "name": "req_id", + "description": "Field containing req_id data", + "valueType": "string", + "meta": { + "displayName": "req_id" + } + }, + { + "name": "project", + "description": "Field containing project data", + "valueType": "string", + "meta": { + "displayName": "project" + } + }, + { + "name": "external_id", + "description": "Field containing external_id data", + "valueType": "string", + "meta": { + "displayName": "external_id" + } + }, + { + "name": "tissue_origin", + "description": "Field containing tissue_origin data", + "valueType": "string", + "meta": { + "displayName": "tissue_origin" + } + }, + { + "name": "tissue_type", + "description": "Field containing tissue_type data", + "valueType": "string", + "meta": { + "displayName": "tissue_type" + } + }, + { + "name": "group_id", + "description": "Field containing group_id data", + "valueType": "string", + "meta": { + "displayName": "group_id" + } + }, + { + "name": "library_design", + "description": "Field containing library_design data", + "valueType": "string", + "meta": { + "displayName": "library_design" + } + }, + { + "name": "library_name", + "description": "Field containing library_name data", + "valueType": "string", + "meta": { + "displayName": "library_name" + } + }, + { + "name": "sequencer_run", + "description": "Field containing sequencer_run data", + "valueType": "string", + "meta": { + "displayName": "sequencer_run" + } + }, + { + "name": "sequencing_id", + "description": "Field containing sequencing_id data", + "valueType": "string", + "meta": { + "displayName": "sequencing_id" + } + }, + { + "name": "instrument_model", + "description": "Field containing instrument_model data", + "valueType": "string", + "meta": { + "displayName": "instrument_model" + } + }, + { + "name": "gsi_workflow_run_id", + "description": "Field containing gsi_workflow_run_id data", + "valueType": "string", + "meta": { + "displayName": "gsi_workflow_run_id" + } + }, + { + "name": "gsi_workflow", + "description": "Field containing gsi_workflow data", + "valueType": "string", + "meta": { + "displayName": "gsi_workflow" + } + }, + { + "name": "gsi_workflow_version", + "description": "Field containing gsi_workflow_version data", + "valueType": "string", + "meta": { + "displayName": "gsi_workflow_version" + } + }, + { + "name": "gsi_md5sum", + "description": "Field containing gsi_md5sum data", + "valueType": "string", + "meta": { + "displayName": "gsi_md5sum" + } + }, + { + "name": "gsi_time", + "description": "Field containing gsi_time data", + "valueType": "string", + "meta": { + "displayName": "gsi_time" + } + }, + { + "name": "fastq_path", + "description": "Field containing fastq_path data", + "valueType": "string", + "meta": { + "displayName": "fastq_path" + } + }, + { + "name": "modification_date", + "description": "Field containing modification_date data", + "valueType": "string", + "meta": { + "displayName": "modification_date" + } + }, + { + "name": "linked_file", + "description": "Field containing linked_file data", + "valueType": "string", + "meta": { + "displayName": "linked_file" + } + }, + { + "name": "linked_file_time", + "description": "Field containing linked_file_time data", + "valueType": "string", + "meta": { + "displayName": "linked_file_time" + } + } + ], + "meta": { + "createdAt": "2025-05-23T19:08:46.381Z", + "sourceFile": "sample.csv" + } + }, + { + "name": "summary", + "description": "Schema generated from summary.csv", + "fields": [ + { + "name": "donor", + "description": "Field containing donor data", + "valueType": "string", + "meta": { + "displayName": "donor" + } + }, + { + "name": "tumour", + "description": "Field containing tumour data", + "valueType": "string", + "meta": { + "displayName": "tumour" + } + }, + { + "name": "normal", + "description": "Field containing normal data", + "valueType": "string", + "meta": { + "displayName": "normal" + } + }, + { + "name": "external_id", + "description": "Field containing external_id data", + "valueType": "string", + "meta": { + "displayName": "external_id" + } + }, + { + "name": "seq_type", + "description": "Field containing seq_type data", + "valueType": "string", + "meta": { + "displayName": "seq_type" + } + }, + { + "name": "tumour_coverage", + "description": "Field containing tumour_coverage data", + "valueType": "number", + "meta": { + "displayName": "tumour_coverage" + } + }, + { + "name": "normal_coverage", + "description": "Field containing normal_coverage data", + "valueType": "integer", + "meta": { + "displayName": "normal_coverage" + } + }, + { + "name": "mouse_content", + "description": "Field containing mouse_content data", + "valueType": "string", + "meta": { + "displayName": "mouse_content" + } + }, + { + "name": "tumour_reads_per_sp", + "description": "Field containing tumour_reads_per_sp data", + "valueType": "string", + "meta": { + "displayName": "tumour_reads_per_sp" + } + }, + { + "name": "normal_reads_per_sp", + "description": "Field containing normal_reads_per_sp data", + "valueType": "string", + "meta": { + "displayName": "normal_reads_per_sp" + } + }, + { + "name": "tumour_error_rate", + "description": "Field containing tumour_error_rate data", + "valueType": "string", + "meta": { + "displayName": "tumour_error_rate" + } + }, + { + "name": "normal_error_rate", + "description": "Field containing normal_error_rate data", + "valueType": "string", + "meta": { + "displayName": "normal_error_rate" + } + }, + { + "name": "tumour_soft_clip", + "description": "Field containing tumour_soft_clip data", + "valueType": "string", + "meta": { + "displayName": "tumour_soft_clip" + } + }, + { + "name": "normal_soft_clip", + "description": "Field containing normal_soft_clip data", + "valueType": "string", + "meta": { + "displayName": "normal_soft_clip" + } + }, + { + "name": "inferred_sex", + "description": "Field containing inferred_sex data", + "valueType": "string", + "meta": { + "displayName": "inferred_sex" + } + }, + { + "name": "genotype_concordance", + "description": "Field containing genotype_concordance data", + "valueType": "string", + "meta": { + "displayName": "genotype_concordance" + } + }, + { + "name": "snv_count", + "description": "Field containing snv_count data", + "valueType": "integer", + "meta": { + "displayName": "snv_count" + } + }, + { + "name": "del_count", + "description": "Field containing del_count data", + "valueType": "integer", + "meta": { + "displayName": "del_count" + } + }, + { + "name": "ins_count", + "description": "Field containing ins_count data", + "valueType": "integer", + "meta": { + "displayName": "ins_count" + } + }, + { + "name": "indel_count", + "description": "Field containing indel_count data", + "valueType": "integer", + "meta": { + "displayName": "indel_count" + } + }, + { + "name": "deleterious_count", + "description": "Field containing deleterious_count data", + "valueType": "integer", + "meta": { + "displayName": "deleterious_count" + } + }, + { + "name": "nonsyn_count", + "description": "Field containing nonsyn_count data", + "valueType": "integer", + "meta": { + "displayName": "nonsyn_count" + } + }, + { + "name": "stopgain_count", + "description": "Field containing stopgain_count data", + "valueType": "integer", + "meta": { + "displayName": "stopgain_count" + } + }, + { + "name": "stoploss_count", + "description": "Field containing stoploss_count data", + "valueType": "string", + "meta": { + "displayName": "stoploss_count" + } + }, + { + "name": "splice_count", + "description": "Field containing splice_count data", + "valueType": "integer", + "meta": { + "displayName": "splice_count" + } + }, + { + "name": "noncoding_count", + "description": "Field containing noncoding_count data", + "valueType": "string", + "meta": { + "displayName": "noncoding_count" + } + }, + { + "name": "frameshift_count", + "description": "Field containing frameshift_count data", + "valueType": "integer", + "meta": { + "displayName": "frameshift_count" + } + }, + { + "name": "nonframeshift_count", + "description": "Field containing nonframeshift_count data", + "valueType": "string", + "meta": { + "displayName": "nonframeshift_count" + } + }, + { + "name": "del_frameshift_count", + "description": "Field containing del_frameshift_count data", + "valueType": "integer", + "meta": { + "displayName": "del_frameshift_count" + } + }, + { + "name": "del_nonframeshift_count", + "description": "Field containing del_nonframeshift_count data", + "valueType": "string", + "meta": { + "displayName": "del_nonframeshift_count" + } + }, + { + "name": "ins_frameshift_count", + "description": "Field containing ins_frameshift_count data", + "valueType": "string", + "meta": { + "displayName": "ins_frameshift_count" + } + }, + { + "name": "ins_nonframeshift_count", + "description": "Field containing ins_nonframeshift_count data", + "valueType": "string", + "meta": { + "displayName": "ins_nonframeshift_count" + } + }, + { + "name": "sv_count", + "description": "Field containing sv_count data", + "valueType": "integer", + "meta": { + "displayName": "sv_count" + } + }, + { + "name": "sv_del_count", + "description": "Field containing sv_del_count data", + "valueType": "integer", + "meta": { + "displayName": "sv_del_count" + } + }, + { + "name": "sv_dup_count", + "description": "Field containing sv_dup_count data", + "valueType": "integer", + "meta": { + "displayName": "sv_dup_count" + } + }, + { + "name": "sv_inv_count", + "description": "Field containing sv_inv_count data", + "valueType": "integer", + "meta": { + "displayName": "sv_inv_count" + } + }, + { + "name": "sv_tra_count", + "description": "Field containing sv_tra_count data", + "valueType": "string", + "meta": { + "displayName": "sv_tra_count" + } + }, + { + "name": "sv_del_bp_gene_count", + "description": "Field containing sv_del_bp_gene_count data", + "valueType": "integer", + "meta": { + "displayName": "sv_del_bp_gene_count" + } + }, + { + "name": "sv_dup_bp_gene_count", + "description": "Field containing sv_dup_bp_gene_count data", + "valueType": "integer", + "meta": { + "displayName": "sv_dup_bp_gene_count" + } + }, + { + "name": "sv_inv_bp_gene_count", + "description": "Field containing sv_inv_bp_gene_count data", + "valueType": "integer", + "meta": { + "displayName": "sv_inv_bp_gene_count" + } + }, + { + "name": "sv_tra_bp_gene_count", + "description": "Field containing sv_tra_bp_gene_count data", + "valueType": "string", + "meta": { + "displayName": "sv_tra_bp_gene_count" + } + }, + { + "name": "waddell", + "description": "Field containing waddell data", + "valueType": "string", + "meta": { + "displayName": "waddell" + } + }, + { + "name": "neo_antigens", + "description": "Field containing neo_antigens data", + "valueType": "string", + "meta": { + "displayName": "neo_antigens" + } + }, + { + "name": "neo_antigens_weak", + "description": "Field containing neo_antigens_weak data", + "valueType": "string", + "meta": { + "displayName": "neo_antigens_weak" + } + }, + { + "name": "neo_antigens_strong", + "description": "Field containing neo_antigens_strong data", + "valueType": "string", + "meta": { + "displayName": "neo_antigens_strong" + } + }, + { + "name": "hla_types", + "description": "Field containing hla_types data", + "valueType": "string", + "meta": { + "displayName": "hla_types" + } + }, + { + "name": "cellularity", + "description": "Field containing cellularity data", + "valueType": "number", + "meta": { + "displayName": "cellularity" + } + }, + { + "name": "ploidy", + "description": "Field containing ploidy data", + "valueType": "number", + "meta": { + "displayName": "ploidy" + } + }, + { + "name": "alexandrov_class", + "description": "Field containing alexandrov_class data", + "valueType": "string", + "meta": { + "displayName": "alexandrov_class" + } + }, + { + "name": "alexandrov_etiology", + "description": "Field containing alexandrov_etiology data", + "valueType": "string", + "meta": { + "displayName": "alexandrov_etiology" + } + }, + { + "name": "moffitt", + "description": "Field containing moffitt data", + "valueType": "string", + "meta": { + "displayName": "moffitt" + } + }, + { + "name": "collisson", + "description": "Field containing collisson data", + "valueType": "string", + "meta": { + "displayName": "collisson" + } + }, + { + "name": "bailey", + "description": "Field containing bailey data", + "valueType": "string", + "meta": { + "displayName": "bailey" + } + }, + { + "name": "dsbr_deficient", + "description": "Field containing dsbr_deficient data", + "valueType": "string", + "meta": { + "displayName": "dsbr_deficient" + } + }, + { + "name": "dsbr_first_hit", + "description": "Field containing dsbr_first_hit data", + "valueType": "string", + "meta": { + "displayName": "dsbr_first_hit" + } + }, + { + "name": "dsbr_second_hit", + "description": "Field containing dsbr_second_hit data", + "valueType": "string", + "meta": { + "displayName": "dsbr_second_hit" + } + }, + { + "name": "mmr_deficient", + "description": "Field containing mmr_deficient data", + "valueType": "string", + "meta": { + "displayName": "mmr_deficient" + } + }, + { + "name": "mmr_first_hit", + "description": "Field containing mmr_first_hit data", + "valueType": "string", + "meta": { + "displayName": "mmr_first_hit" + } + }, + { + "name": "mmr_second_hit", + "description": "Field containing mmr_second_hit data", + "valueType": "string", + "meta": { + "displayName": "mmr_second_hit" + } + }, + { + "name": "csnnls_sig1", + "description": "Field containing csnnls_sig1 data", + "valueType": "number", + "meta": { + "displayName": "csnnls_sig1" + } + }, + { + "name": "csnnls_sig2", + "description": "Field containing csnnls_sig2 data", + "valueType": "number", + "meta": { + "displayName": "csnnls_sig2" + } + }, + { + "name": "csnnls_sig3", + "description": "Field containing csnnls_sig3 data", + "valueType": "string", + "meta": { + "displayName": "csnnls_sig3" + } + }, + { + "name": "csnnls_sig5", + "description": "Field containing csnnls_sig5 data", + "valueType": "number", + "meta": { + "displayName": "csnnls_sig5" + } + }, + { + "name": "csnnls_sig6", + "description": "Field containing csnnls_sig6 data", + "valueType": "string", + "meta": { + "displayName": "csnnls_sig6" + } + }, + { + "name": "csnnls_sig8", + "description": "Field containing csnnls_sig8 data", + "valueType": "number", + "meta": { + "displayName": "csnnls_sig8" + } + }, + { + "name": "csnnls_sig13", + "description": "Field containing csnnls_sig13 data", + "valueType": "string", + "meta": { + "displayName": "csnnls_sig13" + } + }, + { + "name": "csnnls_sig17", + "description": "Field containing csnnls_sig17 data", + "valueType": "string", + "meta": { + "displayName": "csnnls_sig17" + } + }, + { + "name": "csnnls_sig18", + "description": "Field containing csnnls_sig18 data", + "valueType": "string", + "meta": { + "displayName": "csnnls_sig18" + } + }, + { + "name": "csnnls_sig20", + "description": "Field containing csnnls_sig20 data", + "valueType": "string", + "meta": { + "displayName": "csnnls_sig20" + } + }, + { + "name": "csnnls_sig26", + "description": "Field containing csnnls_sig26 data", + "valueType": "string", + "meta": { + "displayName": "csnnls_sig26" + } + }, + { + "name": "csnnls_residuals", + "description": "Field containing csnnls_residuals data", + "valueType": "number", + "meta": { + "displayName": "csnnls_residuals" + } + }, + { + "name": "csnnls_n_mutations", + "description": "Field containing csnnls_n_mutations data", + "valueType": "string", + "meta": { + "displayName": "csnnls_n_mutations" + } + }, + { + "name": "germline_snv_count", + "description": "Field containing germline_snv_count data", + "valueType": "integer", + "meta": { + "displayName": "germline_snv_count" + } + }, + { + "name": "germline_indel_count", + "description": "Field containing germline_indel_count data", + "valueType": "integer", + "meta": { + "displayName": "germline_indel_count" + } + }, + { + "name": "germline_titv_ratio", + "description": "Field containing germline_titv_ratio data", + "valueType": "number", + "meta": { + "displayName": "germline_titv_ratio" + } + }, + { + "name": "germline_missense_count", + "description": "Field containing germline_missense_count data", + "valueType": "integer", + "meta": { + "displayName": "germline_missense_count" + } + }, + { + "name": "germline_nonsense_count", + "description": "Field containing germline_nonsense_count data", + "valueType": "integer", + "meta": { + "displayName": "germline_nonsense_count" + } + }, + { + "name": "snv_ca", + "description": "Field containing snv_ca data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca" + } + }, + { + "name": "snv_cg", + "description": "Field containing snv_cg data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg" + } + }, + { + "name": "snv_ct", + "description": "Field containing snv_ct data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct" + } + }, + { + "name": "snv_ta", + "description": "Field containing snv_ta data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta" + } + }, + { + "name": "snv_tc", + "description": "Field containing snv_tc data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc" + } + }, + { + "name": "snv_tg", + "description": "Field containing snv_tg data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg" + } + }, + { + "name": "del_1_count", + "description": "Field containing del_1_count data", + "valueType": "integer", + "meta": { + "displayName": "del_1_count" + } + }, + { + "name": "del_4_count", + "description": "Field containing del_4_count data", + "valueType": "integer", + "meta": { + "displayName": "del_4_count" + } + }, + { + "name": "ins_1_count", + "description": "Field containing ins_1_count data", + "valueType": "integer", + "meta": { + "displayName": "ins_1_count" + } + }, + { + "name": "ins_4_count", + "description": "Field containing ins_4_count data", + "valueType": "integer", + "meta": { + "displayName": "ins_4_count" + } + }, + { + "name": "DEL_100", + "description": "Field containing DEL_100 data", + "valueType": "integer", + "meta": { + "displayName": "DEL_100" + } + }, + { + "name": "DEL_1k", + "description": "Field containing DEL_1k data", + "valueType": "integer", + "meta": { + "displayName": "DEL_1k" + } + }, + { + "name": "DEL_10k", + "description": "Field containing DEL_10k data", + "valueType": "integer", + "meta": { + "displayName": "DEL_10k" + } + }, + { + "name": "DEL_100k", + "description": "Field containing DEL_100k data", + "valueType": "string", + "meta": { + "displayName": "DEL_100k" + } + }, + { + "name": "DEL_1m", + "description": "Field containing DEL_1m data", + "valueType": "string", + "meta": { + "displayName": "DEL_1m" + } + }, + { + "name": "DEL_10m", + "description": "Field containing DEL_10m data", + "valueType": "integer", + "meta": { + "displayName": "DEL_10m" + } + }, + { + "name": "DEL_GREATER_THAN_10m", + "description": "Field containing DEL_GREATER_THAN_10m data", + "valueType": "string", + "meta": { + "displayName": "DEL_GREATER_THAN_10m" + } + }, + { + "name": "DUP_100", + "description": "Field containing DUP_100 data", + "valueType": "string", + "meta": { + "displayName": "DUP_100" + } + }, + { + "name": "DUP_1k", + "description": "Field containing DUP_1k data", + "valueType": "string", + "meta": { + "displayName": "DUP_1k" + } + }, + { + "name": "DUP_10k", + "description": "Field containing DUP_10k data", + "valueType": "string", + "meta": { + "displayName": "DUP_10k" + } + }, + { + "name": "DUP_100k", + "description": "Field containing DUP_100k data", + "valueType": "string", + "meta": { + "displayName": "DUP_100k" + } + }, + { + "name": "DUP_1m", + "description": "Field containing DUP_1m data", + "valueType": "string", + "meta": { + "displayName": "DUP_1m" + } + }, + { + "name": "DUP_10m", + "description": "Field containing DUP_10m data", + "valueType": "integer", + "meta": { + "displayName": "DUP_10m" + } + }, + { + "name": "DUP_GREATER_THAN_10m", + "description": "Field containing DUP_GREATER_THAN_10m data", + "valueType": "integer", + "meta": { + "displayName": "DUP_GREATER_THAN_10m" + } + }, + { + "name": "INV_100", + "description": "Field containing INV_100 data", + "valueType": "string", + "meta": { + "displayName": "INV_100" + } + }, + { + "name": "INV_1k", + "description": "Field containing INV_1k data", + "valueType": "string", + "meta": { + "displayName": "INV_1k" + } + }, + { + "name": "INV_10k", + "description": "Field containing INV_10k data", + "valueType": "integer", + "meta": { + "displayName": "INV_10k" + } + }, + { + "name": "INV_100k", + "description": "Field containing INV_100k data", + "valueType": "string", + "meta": { + "displayName": "INV_100k" + } + }, + { + "name": "INV_1m", + "description": "Field containing INV_1m data", + "valueType": "string", + "meta": { + "displayName": "INV_1m" + } + }, + { + "name": "INV_10m", + "description": "Field containing INV_10m data", + "valueType": "string", + "meta": { + "displayName": "INV_10m" + } + }, + { + "name": "INV_GREATER_THAN_10m", + "description": "Field containing INV_GREATER_THAN_10m data", + "valueType": "integer", + "meta": { + "displayName": "INV_GREATER_THAN_10m" + } + }, + { + "name": "snv_ca_aa", + "description": "Field containing snv_ca_aa data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_aa" + } + }, + { + "name": "snv_ca_ac", + "description": "Field containing snv_ca_ac data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_ac" + } + }, + { + "name": "snv_ca_ag", + "description": "Field containing snv_ca_ag data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_ag" + } + }, + { + "name": "snv_ca_at", + "description": "Field containing snv_ca_at data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_at" + } + }, + { + "name": "snv_ca_ca", + "description": "Field containing snv_ca_ca data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_ca" + } + }, + { + "name": "snv_ca_cc", + "description": "Field containing snv_ca_cc data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_cc" + } + }, + { + "name": "snv_ca_cg", + "description": "Field containing snv_ca_cg data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_cg" + } + }, + { + "name": "snv_ca_ct", + "description": "Field containing snv_ca_ct data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_ct" + } + }, + { + "name": "snv_ca_ga", + "description": "Field containing snv_ca_ga data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_ga" + } + }, + { + "name": "snv_ca_gc", + "description": "Field containing snv_ca_gc data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_gc" + } + }, + { + "name": "snv_ca_gg", + "description": "Field containing snv_ca_gg data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_gg" + } + }, + { + "name": "snv_ca_gt", + "description": "Field containing snv_ca_gt data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_gt" + } + }, + { + "name": "snv_ca_ta", + "description": "Field containing snv_ca_ta data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_ta" + } + }, + { + "name": "snv_ca_tc", + "description": "Field containing snv_ca_tc data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_tc" + } + }, + { + "name": "snv_ca_tg", + "description": "Field containing snv_ca_tg data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_tg" + } + }, + { + "name": "snv_ca_tt", + "description": "Field containing snv_ca_tt data", + "valueType": "integer", + "meta": { + "displayName": "snv_ca_tt" + } + }, + { + "name": "snv_cg_aa", + "description": "Field containing snv_cg_aa data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_aa" + } + }, + { + "name": "snv_cg_ac", + "description": "Field containing snv_cg_ac data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_ac" + } + }, + { + "name": "snv_cg_ag", + "description": "Field containing snv_cg_ag data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_ag" + } + }, + { + "name": "snv_cg_at", + "description": "Field containing snv_cg_at data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_at" + } + }, + { + "name": "snv_cg_ca", + "description": "Field containing snv_cg_ca data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_ca" + } + }, + { + "name": "snv_cg_cc", + "description": "Field containing snv_cg_cc data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_cc" + } + }, + { + "name": "snv_cg_cg", + "description": "Field containing snv_cg_cg data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_cg" + } + }, + { + "name": "snv_cg_ct", + "description": "Field containing snv_cg_ct data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_ct" + } + }, + { + "name": "snv_cg_ga", + "description": "Field containing snv_cg_ga data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_ga" + } + }, + { + "name": "snv_cg_gc", + "description": "Field containing snv_cg_gc data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_gc" + } + }, + { + "name": "snv_cg_gg", + "description": "Field containing snv_cg_gg data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_gg" + } + }, + { + "name": "snv_cg_gt", + "description": "Field containing snv_cg_gt data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_gt" + } + }, + { + "name": "snv_cg_ta", + "description": "Field containing snv_cg_ta data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_ta" + } + }, + { + "name": "snv_cg_tc", + "description": "Field containing snv_cg_tc data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_tc" + } + }, + { + "name": "snv_cg_tg", + "description": "Field containing snv_cg_tg data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_tg" + } + }, + { + "name": "snv_cg_tt", + "description": "Field containing snv_cg_tt data", + "valueType": "integer", + "meta": { + "displayName": "snv_cg_tt" + } + }, + { + "name": "snv_ct_aa", + "description": "Field containing snv_ct_aa data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_aa" + } + }, + { + "name": "snv_ct_ac", + "description": "Field containing snv_ct_ac data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_ac" + } + }, + { + "name": "snv_ct_ag", + "description": "Field containing snv_ct_ag data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_ag" + } + }, + { + "name": "snv_ct_at", + "description": "Field containing snv_ct_at data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_at" + } + }, + { + "name": "snv_ct_ca", + "description": "Field containing snv_ct_ca data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_ca" + } + }, + { + "name": "snv_ct_cc", + "description": "Field containing snv_ct_cc data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_cc" + } + }, + { + "name": "snv_ct_cg", + "description": "Field containing snv_ct_cg data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_cg" + } + }, + { + "name": "snv_ct_ct", + "description": "Field containing snv_ct_ct data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_ct" + } + }, + { + "name": "snv_ct_ga", + "description": "Field containing snv_ct_ga data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_ga" + } + }, + { + "name": "snv_ct_gc", + "description": "Field containing snv_ct_gc data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_gc" + } + }, + { + "name": "snv_ct_gg", + "description": "Field containing snv_ct_gg data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_gg" + } + }, + { + "name": "snv_ct_gt", + "description": "Field containing snv_ct_gt data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_gt" + } + }, + { + "name": "snv_ct_ta", + "description": "Field containing snv_ct_ta data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_ta" + } + }, + { + "name": "snv_ct_tc", + "description": "Field containing snv_ct_tc data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_tc" + } + }, + { + "name": "snv_ct_tg", + "description": "Field containing snv_ct_tg data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_tg" + } + }, + { + "name": "snv_ct_tt", + "description": "Field containing snv_ct_tt data", + "valueType": "integer", + "meta": { + "displayName": "snv_ct_tt" + } + }, + { + "name": "snv_ta_aa", + "description": "Field containing snv_ta_aa data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_aa" + } + }, + { + "name": "snv_ta_ac", + "description": "Field containing snv_ta_ac data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_ac" + } + }, + { + "name": "snv_ta_ag", + "description": "Field containing snv_ta_ag data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_ag" + } + }, + { + "name": "snv_ta_at", + "description": "Field containing snv_ta_at data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_at" + } + }, + { + "name": "snv_ta_ca", + "description": "Field containing snv_ta_ca data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_ca" + } + }, + { + "name": "snv_ta_cc", + "description": "Field containing snv_ta_cc data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_cc" + } + }, + { + "name": "snv_ta_cg", + "description": "Field containing snv_ta_cg data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_cg" + } + }, + { + "name": "snv_ta_ct", + "description": "Field containing snv_ta_ct data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_ct" + } + }, + { + "name": "snv_ta_ga", + "description": "Field containing snv_ta_ga data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_ga" + } + }, + { + "name": "snv_ta_gc", + "description": "Field containing snv_ta_gc data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_gc" + } + }, + { + "name": "snv_ta_gg", + "description": "Field containing snv_ta_gg data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_gg" + } + }, + { + "name": "snv_ta_gt", + "description": "Field containing snv_ta_gt data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_gt" + } + }, + { + "name": "snv_ta_ta", + "description": "Field containing snv_ta_ta data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_ta" + } + }, + { + "name": "snv_ta_tc", + "description": "Field containing snv_ta_tc data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_tc" + } + }, + { + "name": "snv_ta_tg", + "description": "Field containing snv_ta_tg data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_tg" + } + }, + { + "name": "snv_ta_tt", + "description": "Field containing snv_ta_tt data", + "valueType": "integer", + "meta": { + "displayName": "snv_ta_tt" + } + }, + { + "name": "snv_tc_aa", + "description": "Field containing snv_tc_aa data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_aa" + } + }, + { + "name": "snv_tc_ac", + "description": "Field containing snv_tc_ac data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_ac" + } + }, + { + "name": "snv_tc_ag", + "description": "Field containing snv_tc_ag data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_ag" + } + }, + { + "name": "snv_tc_at", + "description": "Field containing snv_tc_at data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_at" + } + }, + { + "name": "snv_tc_ca", + "description": "Field containing snv_tc_ca data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_ca" + } + }, + { + "name": "snv_tc_cc", + "description": "Field containing snv_tc_cc data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_cc" + } + }, + { + "name": "snv_tc_cg", + "description": "Field containing snv_tc_cg data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_cg" + } + }, + { + "name": "snv_tc_ct", + "description": "Field containing snv_tc_ct data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_ct" + } + }, + { + "name": "snv_tc_ga", + "description": "Field containing snv_tc_ga data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_ga" + } + }, + { + "name": "snv_tc_gc", + "description": "Field containing snv_tc_gc data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_gc" + } + }, + { + "name": "snv_tc_gg", + "description": "Field containing snv_tc_gg data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_gg" + } + }, + { + "name": "snv_tc_gt", + "description": "Field containing snv_tc_gt data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_gt" + } + }, + { + "name": "snv_tc_ta", + "description": "Field containing snv_tc_ta data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_ta" + } + }, + { + "name": "snv_tc_tc", + "description": "Field containing snv_tc_tc data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_tc" + } + }, + { + "name": "snv_tc_tg", + "description": "Field containing snv_tc_tg data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_tg" + } + }, + { + "name": "snv_tc_tt", + "description": "Field containing snv_tc_tt data", + "valueType": "integer", + "meta": { + "displayName": "snv_tc_tt" + } + }, + { + "name": "snv_tg_aa", + "description": "Field containing snv_tg_aa data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_aa" + } + }, + { + "name": "snv_tg_ac", + "description": "Field containing snv_tg_ac data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_ac" + } + }, + { + "name": "snv_tg_ag", + "description": "Field containing snv_tg_ag data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_ag" + } + }, + { + "name": "snv_tg_at", + "description": "Field containing snv_tg_at data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_at" + } + }, + { + "name": "snv_tg_ca", + "description": "Field containing snv_tg_ca data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_ca" + } + }, + { + "name": "snv_tg_cc", + "description": "Field containing snv_tg_cc data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_cc" + } + }, + { + "name": "snv_tg_cg", + "description": "Field containing snv_tg_cg data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_cg" + } + }, + { + "name": "snv_tg_ct", + "description": "Field containing snv_tg_ct data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_ct" + } + }, + { + "name": "snv_tg_ga", + "description": "Field containing snv_tg_ga data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_ga" + } + }, + { + "name": "snv_tg_gc", + "description": "Field containing snv_tg_gc data", + "valueType": "string", + "meta": { + "displayName": "snv_tg_gc" + } + }, + { + "name": "snv_tg_gg", + "description": "Field containing snv_tg_gg data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_gg" + } + }, + { + "name": "snv_tg_gt", + "description": "Field containing snv_tg_gt data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_gt" + } + }, + { + "name": "snv_tg_ta", + "description": "Field containing snv_tg_ta data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_ta" + } + }, + { + "name": "snv_tg_tc", + "description": "Field containing snv_tg_tc data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_tc" + } + }, + { + "name": "snv_tg_tg", + "description": "Field containing snv_tg_tg data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_tg" + } + }, + { + "name": "snv_tg_tt", + "description": "Field containing snv_tg_tt data", + "valueType": "integer", + "meta": { + "displayName": "snv_tg_tt" + } + }, + { + "name": "dsbr_snv_load", + "description": "Field containing dsbr_snv_load data", + "valueType": "integer", + "meta": { + "displayName": "dsbr_snv_load" + } + }, + { + "name": "dsbr_ct_ratio", + "description": "Field containing dsbr_ct_ratio data", + "valueType": "number", + "meta": { + "displayName": "dsbr_ct_ratio" + } + }, + { + "name": "dsbr_del4_load", + "description": "Field containing dsbr_del4_load data", + "valueType": "integer", + "meta": { + "displayName": "dsbr_del4_load" + } + }, + { + "name": "dsbr_del4_ratio", + "description": "Field containing dsbr_del4_ratio data", + "valueType": "number", + "meta": { + "displayName": "dsbr_del4_ratio" + } + }, + { + "name": "dsbr_delsv_load", + "description": "Field containing dsbr_delsv_load data", + "valueType": "integer", + "meta": { + "displayName": "dsbr_delsv_load" + } + }, + { + "name": "dsbr_delsv_ratio", + "description": "Field containing dsbr_delsv_ratio data", + "valueType": "number", + "meta": { + "displayName": "dsbr_delsv_ratio" + } + }, + { + "name": "dsbr_dup_load", + "description": "Field containing dsbr_dup_load data", + "valueType": "string", + "meta": { + "displayName": "dsbr_dup_load" + } + }, + { + "name": "dsbr_sv_load", + "description": "Field containing dsbr_sv_load data", + "valueType": "integer", + "meta": { + "displayName": "dsbr_sv_load" + } + }, + { + "name": "dsbr_first_genes", + "description": "Field containing dsbr_first_genes data", + "valueType": "string", + "meta": { + "displayName": "dsbr_first_genes" + } + }, + { + "name": "dsbr_second_genes", + "description": "Field containing dsbr_second_genes data", + "valueType": "string", + "meta": { + "displayName": "dsbr_second_genes" + } + }, + { + "name": "dsbr_score", + "description": "Field containing dsbr_score data", + "valueType": "string", + "meta": { + "displayName": "dsbr_score" + } + }, + { + "name": "dsbr_snv_load_cut", + "description": "Field containing dsbr_snv_load_cut data", + "valueType": "integer", + "meta": { + "displayName": "dsbr_snv_load_cut" + } + }, + { + "name": "dsbr_ct_ratio_cut", + "description": "Field containing dsbr_ct_ratio_cut data", + "valueType": "number", + "meta": { + "displayName": "dsbr_ct_ratio_cut" + } + }, + { + "name": "dsbr_del4_load_cut", + "description": "Field containing dsbr_del4_load_cut data", + "valueType": "integer", + "meta": { + "displayName": "dsbr_del4_load_cut" + } + }, + { + "name": "dsbr_del4_ratio_cut", + "description": "Field containing dsbr_del4_ratio_cut data", + "valueType": "number", + "meta": { + "displayName": "dsbr_del4_ratio_cut" + } + }, + { + "name": "dsbr_delsv_load_cut", + "description": "Field containing dsbr_delsv_load_cut data", + "valueType": "integer", + "meta": { + "displayName": "dsbr_delsv_load_cut" + } + }, + { + "name": "dsbr_delsv_ratio_cut", + "description": "Field containing dsbr_delsv_ratio_cut data", + "valueType": "number", + "meta": { + "displayName": "dsbr_delsv_ratio_cut" + } + }, + { + "name": "dsbr_dup_load_cut", + "description": "Field containing dsbr_dup_load_cut data", + "valueType": "integer", + "meta": { + "displayName": "dsbr_dup_load_cut" + } + }, + { + "name": "dsbr_sv_load_cut", + "description": "Field containing dsbr_sv_load_cut data", + "valueType": "integer", + "meta": { + "displayName": "dsbr_sv_load_cut" + } + }, + { + "name": "mmr_snv_load", + "description": "Field containing mmr_snv_load data", + "valueType": "integer", + "meta": { + "displayName": "mmr_snv_load" + } + }, + { + "name": "mmr_indel_load", + "description": "Field containing mmr_indel_load data", + "valueType": "integer", + "meta": { + "displayName": "mmr_indel_load" + } + }, + { + "name": "mmr_first_genes", + "description": "Field containing mmr_first_genes data", + "valueType": "string", + "meta": { + "displayName": "mmr_first_genes" + } + }, + { + "name": "mmr_second_genes", + "description": "Field containing mmr_second_genes data", + "valueType": "string", + "meta": { + "displayName": "mmr_second_genes" + } + }, + { + "name": "mmr_score", + "description": "Field containing mmr_score data", + "valueType": "integer", + "meta": { + "displayName": "mmr_score" + } + }, + { + "name": "mmr_snv_load_cut", + "description": "Field containing mmr_snv_load_cut data", + "valueType": "integer", + "meta": { + "displayName": "mmr_snv_load_cut" + } + }, + { + "name": "mmr_indel_load_cut", + "description": "Field containing mmr_indel_load_cut data", + "valueType": "integer", + "meta": { + "displayName": "mmr_indel_load_cut" + } + }, + { + "name": "tdp_score", + "description": "Field containing tdp_score data", + "valueType": "number", + "meta": { + "displayName": "tdp_score" + } + }, + { + "name": "hrdetect_score", + "description": "Field containing hrdetect_score data", + "valueType": "string", + "meta": { + "displayName": "hrdetect_score" + } + }, + { + "name": "hrdetect_myriad_score", + "description": "Field containing hrdetect_myriad_score data", + "valueType": "string", + "meta": { + "displayName": "hrdetect_myriad_score" + } + }, + { + "name": "hrdetect_deletion_microhomology_proportion", + "description": "Field containing hrdetect_deletion_microhomology_proportion data", + "valueType": "string", + "meta": { + "displayName": "hrdetect_deletion_microhomology_proportion" + } + }, + { + "name": "hrdetect_snv_signature_3", + "description": "Field containing hrdetect_snv_signature_3 data", + "valueType": "string", + "meta": { + "displayName": "hrdetect_snv_signature_3" + } + }, + { + "name": "hrdetect_snv_signature_8", + "description": "Field containing hrdetect_snv_signature_8 data", + "valueType": "string", + "meta": { + "displayName": "hrdetect_snv_signature_8" + } + }, + { + "name": "hrdetect_rearrangement_signature_3", + "description": "Field containing hrdetect_rearrangement_signature_3 data", + "valueType": "string", + "meta": { + "displayName": "hrdetect_rearrangement_signature_3" + } + }, + { + "name": "hrdetect_rearrangement_signature_5", + "description": "Field containing hrdetect_rearrangement_signature_5 data", + "valueType": "string", + "meta": { + "displayName": "hrdetect_rearrangement_signature_5" + } + }, + { + "name": "hrdetect_loh", + "description": "Field containing hrdetect_loh data", + "valueType": "string", + "meta": { + "displayName": "hrdetect_loh" + } + }, + { + "name": "hrdetect_tai", + "description": "Field containing hrdetect_tai data", + "valueType": "string", + "meta": { + "displayName": "hrdetect_tai" + } + }, + { + "name": "hrdetect_lst", + "description": "Field containing hrdetect_lst data", + "valueType": "string", + "meta": { + "displayName": "hrdetect_lst" + } + }, + { + "name": "snv_file", + "description": "Field containing snv_file data", + "valueType": "string", + "meta": { + "displayName": "snv_file" + } + }, + { + "name": "indel_file", + "description": "Field containing indel_file data", + "valueType": "string", + "meta": { + "displayName": "indel_file" + } + }, + { + "name": "sgv_file", + "description": "Field containing sgv_file data", + "valueType": "string", + "meta": { + "displayName": "sgv_file" + } + }, + { + "name": "sv_file", + "description": "Field containing sv_file data", + "valueType": "string", + "meta": { + "displayName": "sv_file" + } + }, + { + "name": "param_file", + "description": "Field containing param_file data", + "valueType": "string", + "meta": { + "displayName": "param_file" + } + }, + { + "name": "seg_file", + "description": "Field containing seg_file data", + "valueType": "string", + "meta": { + "displayName": "seg_file" + } + }, + { + "name": "neo_files", + "description": "Field containing neo_files data", + "valueType": "string", + "meta": { + "displayName": "neo_files" + } + }, + { + "name": "xenome_logs", + "description": "Field containing xenome_logs data", + "valueType": "string", + "meta": { + "displayName": "xenome_logs" + } + }, + { + "name": "rna_sig_file", + "description": "Field containing rna_sig_file data", + "valueType": "string", + "meta": { + "displayName": "rna_sig_file" + } + }, + { + "name": "alexandrov_file", + "description": "Field containing alexandrov_file data", + "valueType": "string", + "meta": { + "displayName": "alexandrov_file" + } + }, + { + "name": "json_files", + "description": "Field containing json_files data", + "valueType": "string", + "meta": { + "displayName": "json_files" + } + }, + { + "name": "genotype_files", + "description": "Field containing genotype_files data", + "valueType": "string", + "meta": { + "displayName": "genotype_files" + } + } + ], + "meta": { + "createdAt": "2025-05-23T19:08:46.384Z", + "sourceFile": "summary.csv" + } + } + ] +} \ No newline at end of file diff --git a/apps/conductor/package-lock.json b/apps/conductor/package-lock.json index 26dec66b..0d03e0f0 100644 --- a/apps/conductor/package-lock.json +++ b/apps/conductor/package-lock.json @@ -33,7 +33,6 @@ "version": "0.8.1", "resolved": "https://registry.npmjs.org/@cspotcode/source-map-support/-/source-map-support-0.8.1.tgz", "integrity": "sha512-IchNf6dN4tHoMFIn/7OE8LWZ19Y6q/67Bmf6vnGREv8RSbBVb9LPJxEcnwrcwX6ixSvaiGoomAUvu4YSxXrVgw==", - "license": "MIT", "dependencies": { "@jridgewell/trace-mapping": "0.3.9" }, @@ -45,7 +44,6 @@ "version": "7.17.14", "resolved": "https://registry.npmjs.org/@elastic/elasticsearch/-/elasticsearch-7.17.14.tgz", "integrity": "sha512-6uQ1pVXutwz1Krwooo67W+3K8BwH1ASMh1WoHTpomUzw8EXecXN5lHIJ9EPqTHuv1WqR2LKkSJyagcq0HYUJpg==", - "license": 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"MIT", "dependencies": { "es-errors": "^1.3.0", "function-bind": "^1.1.2" @@ -224,7 +204,6 @@ "version": "4.1.2", "resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.2.tgz", "integrity": "sha512-oKnbhFyRIXpUuez8iBMmyEa4nbj4IOQyuhc/wy9kY7/WVPcwIO9VA668Pu8RkO7+0G76SLROeyw9CpQ061i4mA==", - "license": "MIT", "dependencies": { "ansi-styles": "^4.1.0", "supports-color": "^7.1.0" @@ -240,7 +219,6 @@ "version": "2.0.1", "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz", "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==", - "license": "MIT", "dependencies": { "color-name": "~1.1.4" }, @@ -251,14 +229,12 @@ "node_modules/color-name": { "version": "1.1.4", "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz", - "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==", - "license": "MIT" + "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==" }, "node_modules/combined-stream": { "version": "1.0.8", "resolved": "https://registry.npmjs.org/combined-stream/-/combined-stream-1.0.8.tgz", "integrity": "sha512-FQN4MRfuJeHf7cBbBMJFXhKSDq+2kAArBlmRBvcvFE5BB1HZKXtSFASDhdlz9zOYwxh8lDdnvmMOe/+5cdoEdg==", - "license": "MIT", "dependencies": { "delayed-stream": "~1.0.0" }, @@ -270,7 +246,6 @@ "version": "12.1.0", "resolved": "https://registry.npmjs.org/commander/-/commander-12.1.0.tgz", "integrity": "sha512-Vw8qHK3bZM9y/P10u3Vib8o/DdkvA2OtPtZvD871QKjy74Wj1WSKFILMPRPSdUSx5RFK1arlJzEtA4PkFgnbuA==", - "license": "MIT", "engines": { "node": ">=18" } @@ -278,20 +253,17 @@ "node_modules/create-require": { "version": "1.1.1", "resolved": "https://registry.npmjs.org/create-require/-/create-require-1.1.1.tgz", - "integrity": "sha512-dcKFX3jn0MpIaXjisoRvexIJVEKzaq7z2rZKxf+MSr9TkdmHmsU4m2lcLojrj/FHl8mk5VxMmYA+ftRkP/3oKQ==", - "license": "MIT" + 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"license": "MIT", "engines": { "node": ">=0.4.0" } @@ -317,7 +288,6 @@ "version": "4.0.2", "resolved": "https://registry.npmjs.org/diff/-/diff-4.0.2.tgz", "integrity": "sha512-58lmxKSA4BNyLz+HHMUzlOEpg09FV+ev6ZMe3vJihgdxzgcwZ8VoEEPmALCZG9LmqfVoNMMKpttIYTVG6uDY7A==", - "license": "BSD-3-Clause", "engines": { "node": ">=0.3.1" } @@ -326,7 +296,6 @@ "version": "1.0.1", "resolved": "https://registry.npmjs.org/dunder-proto/-/dunder-proto-1.0.1.tgz", "integrity": "sha512-KIN/nDJBQRcXw0MLVhZE9iQHmG68qAVIBg9CqmUYjmQIhgij9U5MFvrqkUL5FbtyyzZuOeOt0zdeRe4UY7ct+A==", - "license": "MIT", "dependencies": { "call-bind-apply-helpers": "^1.0.1", "es-errors": "^1.3.0", @@ -340,7 +309,6 @@ "version": "1.0.1", "resolved": "https://registry.npmjs.org/es-define-property/-/es-define-property-1.0.1.tgz", "integrity": "sha512-e3nRfgfUZ4rNGL232gUgX06QNyyez04KdjFrF+LTRoOXmrOgFKDg4BCdsjW8EnT69eqdYGmRpJwiPVYNrCaW3g==", - "license": "MIT", "engines": { "node": ">= 0.4" } @@ -349,7 +317,6 @@ "version": "1.3.0", "resolved": "https://registry.npmjs.org/es-errors/-/es-errors-1.3.0.tgz", "integrity": "sha512-Zf5H2Kxt2xjTvbJvP2ZWLEICxA6j+hAmMzIlypy4xcBg1vKVnx89Wy0GbS+kf5cwCVFFzdCFh2XSCFNULS6csw==", - "license": "MIT", "engines": { "node": ">= 0.4" } @@ -358,7 +325,6 @@ "version": "1.1.1", "resolved": "https://registry.npmjs.org/es-object-atoms/-/es-object-atoms-1.1.1.tgz", "integrity": "sha512-FGgH2h8zKNim9ljj7dankFPcICIK9Cp5bm+c2gQSYePhpaG5+esrLODihIorn+Pe6FGJzWhXQotPv73jTaldXA==", - "license": "MIT", "dependencies": { "es-errors": "^1.3.0" }, @@ -370,7 +336,6 @@ "version": "2.1.0", "resolved": "https://registry.npmjs.org/es-set-tostringtag/-/es-set-tostringtag-2.1.0.tgz", "integrity": "sha512-j6vWzfrGVfyXxge+O0x5sh6cvxAog0a/4Rdd2K36zCMV5eJ+/+tOAngRO8cODMNWbVRdVlmGZQL2YS3yR8bIUA==", - "license": "MIT", "dependencies": { "es-errors": "^1.3.0", "get-intrinsic": "^1.2.6", @@ -391,7 +356,6 @@ "url": "https://github.com/sponsors/RubenVerborgh" } ], - "license": "MIT", "engines": { "node": ">=4.0" }, @@ -405,7 +369,6 @@ "version": "4.0.2", "resolved": "https://registry.npmjs.org/form-data/-/form-data-4.0.2.tgz", "integrity": "sha512-hGfm/slu0ZabnNt4oaRZ6uREyfCj6P4fT/n6A1rGV+Z0VdGXjfOhVUpkn6qVQONHGIFwmveGXyDs75+nr6FM8w==", - "license": "MIT", "dependencies": { "asynckit": "^0.4.0", "combined-stream": "^1.0.8", @@ -420,7 +383,6 @@ "version": "1.1.2", "resolved": "https://registry.npmjs.org/function-bind/-/function-bind-1.1.2.tgz", "integrity": "sha512-7XHNxH7qX9xG5mIwxkhumTox/MIRNcOgDrxWsMt2pAr23WHp6MrRlN7FBSFpCpr+oVO0F744iUgR82nJMfG2SA==", - "license": "MIT", "funding": { "url": "https://github.com/sponsors/ljharb" } @@ -429,7 +391,6 @@ "version": "1.3.0", "resolved": "https://registry.npmjs.org/get-intrinsic/-/get-intrinsic-1.3.0.tgz", "integrity": "sha512-9fSjSaos/fRIVIp+xSJlE6lfwhES7LNtKaCBIamHsjr2na1BiABJPo0mOjjz8GJDURarmCPGqaiVg5mfjb98CQ==", - "license": "MIT", "dependencies": { "call-bind-apply-helpers": "^1.0.2", "es-define-property": "^1.0.1", @@ -453,7 +414,6 @@ "version": 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"sha512-1cDNdwJ2Jaohmb3sg4OmKaMBwuC48sYni5HUw2DvsC8LjGTLK9h+eb1X6RyuOHe4hT0ULCW68iomhjUoKUqlPQ==", - "license": "MIT", "engines": { "node": ">= 0.4" }, @@ -499,7 +456,6 @@ "version": "1.0.2", "resolved": "https://registry.npmjs.org/has-tostringtag/-/has-tostringtag-1.0.2.tgz", "integrity": "sha512-NqADB8VjPFLM2V0VvHUewwwsw0ZWBaIdgo+ieHtK3hasLz4qeCRjYcqfB6AQrBggRKppKF8L52/VqdVsO47Dlw==", - "license": "MIT", "dependencies": { "has-symbols": "^1.0.3" }, @@ -514,7 +470,6 @@ "version": "2.0.2", "resolved": "https://registry.npmjs.org/hasown/-/hasown-2.0.2.tgz", "integrity": "sha512-0hJU9SCPvmMzIBdZFqNPXWa6dqh7WdH0cII9y+CyS8rG3nL48Bclra9HmKhVVUHyPWNH5Y7xDwAB7bfgSjkUMQ==", - "license": "MIT", "dependencies": { "function-bind": "^1.1.2" }, @@ -525,20 +480,17 @@ "node_modules/hpagent": { "version": "0.1.2", "resolved": "https://registry.npmjs.org/hpagent/-/hpagent-0.1.2.tgz", - "integrity": "sha512-ePqFXHtSQWAFXYmj+JtOTHr84iNrII4/QRlAAPPE+zqnKy4xJo7Ie1Y4kC7AdB+LxLxSTTzBMASsEcy0q8YyvQ==", - "license": "MIT" + "integrity": "sha512-ePqFXHtSQWAFXYmj+JtOTHr84iNrII4/QRlAAPPE+zqnKy4xJo7Ie1Y4kC7AdB+LxLxSTTzBMASsEcy0q8YyvQ==" }, "node_modules/make-error": { "version": "1.3.6", "resolved": "https://registry.npmjs.org/make-error/-/make-error-1.3.6.tgz", - "integrity": "sha512-s8UhlNe7vPKomQhC1qFelMokr/Sc3AgNbso3n74mVPA5LTZwkB9NlXf4XPamLxJE8h0gh73rM94xvwRT2CVInw==", - "license": "ISC" + "integrity": "sha512-s8UhlNe7vPKomQhC1qFelMokr/Sc3AgNbso3n74mVPA5LTZwkB9NlXf4XPamLxJE8h0gh73rM94xvwRT2CVInw==" }, "node_modules/math-intrinsics": { "version": "1.1.0", "resolved": "https://registry.npmjs.org/math-intrinsics/-/math-intrinsics-1.1.0.tgz", "integrity": "sha512-/IXtbwEk5HTPyEwyKX6hGkYXxM9nbj64B+ilVJnC/R6B0pH5G4V3b0pVbL7DBj4tkhBAppbQUlf6F6Xl9LHu1g==", - "license": "MIT", "engines": { "node": ">= 0.4" } @@ -547,7 +499,6 @@ "version": "1.52.0", "resolved": "https://registry.npmjs.org/mime-db/-/mime-db-1.52.0.tgz", "integrity": "sha512-sPU4uV7dYlvtWJxwwxHD0PuihVNiE7TyAbQ5SWxDCB9mUYvOgroQOwYQQOKPJ8CIbE+1ETVlOoK1UC2nU3gYvg==", - "license": "MIT", "engines": { "node": ">= 0.6" } @@ -556,7 +507,6 @@ "version": "2.1.35", "resolved": "https://registry.npmjs.org/mime-types/-/mime-types-2.1.35.tgz", "integrity": "sha512-ZDY+bPm5zTTF+YpCrAU9nK0UgICYPT0QtT1NZWFv4s++TNkcgVaT0g6+4R2uI4MjQjzysHB1zxuWL50hzaeXiw==", - "license": "MIT", "dependencies": { "mime-db": "1.52.0" }, @@ -567,26 +517,22 @@ "node_modules/ms": { "version": "2.1.3", "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz", - "integrity": "sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA==", - "license": "MIT" + "integrity": "sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA==" }, "node_modules/proxy-from-env": { "version": "1.1.0", "resolved": "https://registry.npmjs.org/proxy-from-env/-/proxy-from-env-1.1.0.tgz", - "integrity": "sha512-D+zkORCbA9f1tdWRK0RaCR3GPv50cMxcrz4X8k5LTSUD1Dkw47mKJEZQNunItRTkWwgtaUSo1RVFRIG9ZXiFYg==", - "license": "MIT" + "integrity": "sha512-D+zkORCbA9f1tdWRK0RaCR3GPv50cMxcrz4X8k5LTSUD1Dkw47mKJEZQNunItRTkWwgtaUSo1RVFRIG9ZXiFYg==" }, "node_modules/secure-json-parse": { "version": "2.7.0", "resolved": "https://registry.npmjs.org/secure-json-parse/-/secure-json-parse-2.7.0.tgz", - "integrity": "sha512-6aU+Rwsezw7VR8/nyvKTx8QpWH9FrcYiXXlqC4z5d5XQBDRqtbfsRjnwGyqbi3gddNtWHuEk9OANUotL26qKUw==", - "license": "BSD-3-Clause" + "integrity": "sha512-6aU+Rwsezw7VR8/nyvKTx8QpWH9FrcYiXXlqC4z5d5XQBDRqtbfsRjnwGyqbi3gddNtWHuEk9OANUotL26qKUw==" }, "node_modules/supports-color": { "version": "7.2.0", "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz", "integrity": "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw==", - "license": "MIT", "dependencies": { "has-flag": "^4.0.0" }, @@ -598,7 +544,6 @@ "version": "10.9.2", "resolved": "https://registry.npmjs.org/ts-node/-/ts-node-10.9.2.tgz", "integrity": "sha512-f0FFpIdcHgn8zcPSbf1dRevwt047YMnaiJM3u2w2RewrB+fob/zePZcrOyQoLMMO7aBIddLcQIEK5dYjkLnGrQ==", - "license": "MIT", "dependencies": { "@cspotcode/source-map-support": "^0.8.0", "@tsconfig/node10": "^1.0.7", @@ -641,7 +586,6 @@ "version": "5.7.3", "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.7.3.tgz", "integrity": "sha512-84MVSjMEHP+FQRPy3pX9sTVV/INIex71s9TL2Gm5FG/WG1SqXeKyZ0k7/blY/4FdOzI12CBy1vGc4og/eus0fw==", - "license": "Apache-2.0", "bin": { "tsc": "bin/tsc", "tsserver": "bin/tsserver" @@ -653,8 +597,7 @@ "node_modules/undici-types": { "version": "6.20.0", "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.20.0.tgz", - "integrity": "sha512-Ny6QZ2Nju20vw1SRHe3d9jVu6gJ+4e3+MMpqu7pqE5HT6WsTSlce++GQmK5UXS8mzV8DSYHrQH+Xrf2jVcuKNg==", - "license": "MIT" + "integrity": "sha512-Ny6QZ2Nju20vw1SRHe3d9jVu6gJ+4e3+MMpqu7pqE5HT6WsTSlce++GQmK5UXS8mzV8DSYHrQH+Xrf2jVcuKNg==" }, "node_modules/uuid": { "version": "11.0.5", @@ -664,7 +607,6 @@ "https://github.com/sponsors/broofa", "https://github.com/sponsors/ctavan" ], - "license": "MIT", "bin": { "uuid": "dist/esm/bin/uuid" } @@ -672,14 +614,12 @@ "node_modules/v8-compile-cache-lib": { "version": "3.0.1", "resolved": "https://registry.npmjs.org/v8-compile-cache-lib/-/v8-compile-cache-lib-3.0.1.tgz", - "integrity": "sha512-wa7YjyUGfNZngI/vtK0UHAN+lgDCxBPCylVXGp0zu59Fz5aiGtNXaq3DhIov063MorB+VfufLh3JlF2KdTK3xg==", - "license": "MIT" + "integrity": "sha512-wa7YjyUGfNZngI/vtK0UHAN+lgDCxBPCylVXGp0zu59Fz5aiGtNXaq3DhIov063MorB+VfufLh3JlF2KdTK3xg==" }, "node_modules/yn": { "version": "3.1.1", "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz", "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==", - "license": "MIT", "engines": { "node": ">=6" } diff --git a/apps/conductor/scripts/services/upload-data.sh b/apps/conductor/scripts/services/upload-data.sh new file mode 100755 index 00000000..3eb45810 --- /dev/null +++ b/apps/conductor/scripts/services/upload-data.sh @@ -0,0 +1,60 @@ +#!/bin/sh +set -e + +echo "=== Data Setup Deployment Starting ===" + +# Install curl (needed for health checks) +echo "Installing curl..." +apk add --no-cache curl + +# Install conductor CLI +echo "Installing Conductor CLI..." +cd /conductor +npm ci +npm install -g . + +# Wait for services to be ready +echo "Waiting for services to be ready..." +timeout=0 +until curl -f $LECTERN_URL/health 2>/dev/null || [ $timeout -eq 30 ]; do + echo "Waiting for Lectern to be ready... ($timeout/30)" + sleep 2 + timeout=$((timeout + 1)) +done + +timeout=0 +until curl -f $LYRIC_URL/health 2>/dev/null || [ $timeout -eq 30 ]; do + echo "Waiting for Lyric to be ready... ($timeout/30)" + sleep 2 + timeout=$((timeout + 1)) +done + +echo "Services are ready, starting data setup..." + +# Upload consolidated dictionary to Lectern +echo "Uploading dictionary to Lectern..." +conductor lecternUpload -s /conductor/configs/lecternDictionaries/lbr-dictionary.json + +# Register entities with Lyric schema +echo "Registering entities with Lyric..." +conductor lyricRegister -c idmapping --dict-name lbr-dictionary -v 1.0 -e idmapping +conductor lyricRegister -c sample --dict-name lbr-dictionary -v 1.0 -e sample +conductor lyricRegister -c summary --dict-name lbr-dictionary -v 1.0 -e summary + +# Upload tabular data to Lyric +echo "Uploading tabular data to Lyric..." +conductor lyricUpload -d /data/idmapping -c 1 --max-retries 100 +conductor lyricUpload -d /data/sample -c 2 --max-retries 100 +conductor lyricUpload -d /data/summary -c 3 --max-retries 100 + +# Index data with Maestro +echo "Indexing data with Maestro..." +conductor maestroIndex --repository-code idmapping +conductor maestroIndex --repository-code sample +conductor maestroIndex --repository-code summary + +# Create health check file +echo "Creating health check file..." +touch /health/data_setup_health + +echo "=== Data Setup Deployment Completed Successfully ===" \ No newline at end of file diff --git a/apps/stage/components/inactiveDataTables/dataTableFive/RepoTable/index.tsx b/apps/stage/components/inactiveDataTables/dataTableFive/RepoTable/index.tsx index 5d40d89e..f38c9a4a 100644 --- a/apps/stage/components/inactiveDataTables/dataTableFive/RepoTable/index.tsx +++ b/apps/stage/components/inactiveDataTables/dataTableFive/RepoTable/index.tsx @@ -53,7 +53,7 @@ const getTableConfigs = ({ // appearance background: theme.colors.white, - borderColor: theme.colors.grey_5, // Updated from grey_3 to grey_5 for more contrast + borderColor: theme.colors.grey_3, css: css` ${theme.shadow.default} `, @@ -82,8 +82,8 @@ const getTableConfigs = ({ }, DownloadButton: { customExporters, - exportSelectedRowsField: 'submission_metadata.submitter_id', - downloadUrl: urlJoin(apiHost, 'download'), + exportSelectedRowsField: 'id', + downloadUrl: urlJoin(apiHost, 'download'), label: () => ( <> ( <> { + if (!sqon) return false; + + // Check if sqon has a content array with at least one item + if (sqon.content && Array.isArray(sqon.content) && sqon.content.length > 0) { + return true; + } + + return false; +}; + +/** + * A generic button component that applies filters from one table to another + * Only becomes active when filters are selected + */ +const CrossTableFilterButton = withData(({ + sqon, + targetPath = INTERNAL_PATHS.DATATABLE_2, + disabledText = 'Apply filters to target table', + enabledText = 'Apply filter(s) to target table', +}: CrossTableFilterButtonProps) => { + const hasFilters = hasActiveFilters(sqon); + const urlParams = hasFilters ? new URLSearchParams({ filters: stringify(sqon) }).toString() : ''; + const theme = useTheme(); + + // Common styles for both states + const commonStyles = css` + background-color: ${theme.colors.primary_dark || '#043565'}; + padding: 10px 20px; + margin-bottom: 8px; + font-size: 14px; + font-weight: 500; + border-radius: 8px; + display: flex; + align-items: center; + justify-content: center; + white-space: nowrap; + border: none; + box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1); + height: 20px; + `; + + // If no filters are selected, render a disabled button + if (!hasFilters) { + return ( +
+ {disabledText} +
+ ); + } + + // If filters are selected, render an active button + return ( + + + {enabledText} + + + ); +}); + +export default CrossTableFilterButton; \ No newline at end of file diff --git a/apps/stage/components/pages/activeDataTables/dataTableOne/Facets.tsx b/apps/stage/components/pages/activeDataTables/idMappings/Facets.tsx similarity index 100% rename from apps/stage/components/pages/activeDataTables/dataTableOne/Facets.tsx rename to apps/stage/components/pages/activeDataTables/idMappings/Facets.tsx diff --git a/apps/stage/components/pages/activeDataTables/dataTableOne/PageContent.tsx b/apps/stage/components/pages/activeDataTables/idMappings/PageContent.tsx similarity index 100% rename from apps/stage/components/pages/activeDataTables/dataTableOne/PageContent.tsx rename to apps/stage/components/pages/activeDataTables/idMappings/PageContent.tsx diff --git a/apps/stage/components/inactiveDataTables/dataTableThree/QueryBar.tsx b/apps/stage/components/pages/activeDataTables/idMappings/QueryBar.tsx similarity index 84% rename from apps/stage/components/inactiveDataTables/dataTableThree/QueryBar.tsx rename to apps/stage/components/pages/activeDataTables/idMappings/QueryBar.tsx index 4520e3dc..03f5dcb8 100644 --- a/apps/stage/components/inactiveDataTables/dataTableThree/QueryBar.tsx +++ b/apps/stage/components/pages/activeDataTables/idMappings/QueryBar.tsx @@ -23,6 +23,9 @@ import { css, useTheme } from '@emotion/react'; import { SQONViewer, useArrangerTheme } from '@overture-stack/arranger-components'; import { UseThemeContextProps } from '@overture-stack/arranger-components/dist/types'; import { Row } from 'react-grid-system'; +import CrossTableFilterButton from '../CrossTableFilterButton'; +import { INTERNAL_PATHS } from '@/global/utils/constants'; + const getThemeCustomisations = (theme: StageThemeInterface): UseThemeContextProps => ({ callerName: 'DataSetOne-QueryBar', components: { @@ -96,10 +99,12 @@ const getThemeCustomisations = (theme: StageThemeInterface): UseThemeContextProp }, }, }); + const QueryBar = () => { const theme = useTheme(); useArrangerTheme(getThemeCustomisations(theme)); return ( + <> css` @@ -112,6 +117,32 @@ const QueryBar = () => { > + + {/* Flex container for buttons */} +
+
+ +
+
+ +
+
+ ); }; -export default QueryBar; + +export default QueryBar; \ No newline at end of file diff --git a/apps/stage/components/pages/activeDataTables/dataTableOne/RepoTable/helper.ts b/apps/stage/components/pages/activeDataTables/idMappings/RepoTable/helper.ts similarity index 100% rename from apps/stage/components/pages/activeDataTables/dataTableOne/RepoTable/helper.ts rename to apps/stage/components/pages/activeDataTables/idMappings/RepoTable/helper.ts diff --git a/apps/stage/components/pages/activeDataTables/dataTableOne/RepoTable/index.tsx b/apps/stage/components/pages/activeDataTables/idMappings/RepoTable/index.tsx similarity index 91% rename from apps/stage/components/pages/activeDataTables/dataTableOne/RepoTable/index.tsx rename to apps/stage/components/pages/activeDataTables/idMappings/RepoTable/index.tsx index 773b2c41..aba0a233 100644 --- a/apps/stage/components/pages/activeDataTables/dataTableOne/RepoTable/index.tsx +++ b/apps/stage/components/pages/activeDataTables/idMappings/RepoTable/index.tsx @@ -53,7 +53,7 @@ const getTableConfigs = ({ // appearance background: theme.colors.white, - borderColor: theme.colors.grey_5, // Updated from grey_3 to grey_5 for more contrast + borderColor: theme.colors.grey_3, css: css` ${theme.shadow.default} `, @@ -82,8 +82,8 @@ const getTableConfigs = ({ }, DownloadButton: { customExporters, - exportSelectedRowsField: 'submission_metadata.submitter_id', - downloadUrl: urlJoin(apiHost, 'download'), + exportSelectedRowsField: 'id', + downloadUrl: urlJoin(apiHost, 'download'), label: () => ( <> { const theme = useTheme(); const today = new Date().toISOString().slice(0, 10).replace(/-/g, ''); const customExporters = [ - { label: 'Download', fileName: `dataset-2-data-export.${today}.tsv` }, // exports a TSV with what is displayed on the table (columns selected, etc.) + { label: 'Download', fileName: `dataset-1-data-export.${today}.tsv` }, // exports a TSV with what is displayed on the table (columns selected, etc.) ]; useArrangerTheme(getTableConfigs({ apiHost: INTERNAL_API_PROXY.DATATABLE_1_ARRANGER, customExporters, theme })); diff --git a/apps/stage/components/pages/activeDataTables/dataTableOne/getConfigError.tsx b/apps/stage/components/pages/activeDataTables/idMappings/getConfigError.tsx similarity index 100% rename from apps/stage/components/pages/activeDataTables/dataTableOne/getConfigError.tsx rename to apps/stage/components/pages/activeDataTables/idMappings/getConfigError.tsx diff --git a/apps/stage/components/pages/activeDataTables/dataTableOne/index.tsx b/apps/stage/components/pages/activeDataTables/idMappings/index.tsx similarity index 100% rename from apps/stage/components/pages/activeDataTables/dataTableOne/index.tsx rename to apps/stage/components/pages/activeDataTables/idMappings/index.tsx diff --git a/apps/stage/components/pages/activeDataTables/sampleTable/CrossTableFilterButton.tsx b/apps/stage/components/pages/activeDataTables/sampleTable/CrossTableFilterButton.tsx new file mode 100644 index 00000000..4b54e74c --- /dev/null +++ b/apps/stage/components/pages/activeDataTables/sampleTable/CrossTableFilterButton.tsx @@ -0,0 +1,96 @@ +import React from 'react'; +import { css, useTheme } from '@emotion/react'; +import { SQON } from '@overture-stack/sqon-builder'; +import { withData } from '@overture-stack/arranger-components/dist/DataContext'; +import stringify from 'fast-json-stable-stringify'; +import { InternalLink, StyledLinkAsButton } from '@/components/Link'; +import { INTERNAL_PATHS } from '@/global/utils/constants'; + +interface CrossTableFilterButtonProps { + sqon?: SQON; + targetPath?: string; + disabledText?: string; + enabledText?: string; +} + +// Helper function to check if SQON has active filters +const hasActiveFilters = (sqon?: SQON): boolean => { + if (!sqon) return false; + + // Check if sqon has a content array with at least one item + if (sqon.content && Array.isArray(sqon.content) && sqon.content.length > 0) { + return true; + } + + return false; +}; + +/** + * A generic button component that applies filters from one table to another + * Only becomes active when filters are selected + */ +const CrossTableFilterButton = withData(({ + sqon, + targetPath = INTERNAL_PATHS.DATATABLE_2, + disabledText = 'Apply filters to target table', + enabledText = 'Apply filter(s) to target table', +}: CrossTableFilterButtonProps) => { + const hasFilters = hasActiveFilters(sqon); + const urlParams = hasFilters ? new URLSearchParams({ filters: stringify(sqon) }).toString() : ''; + const theme = useTheme(); + + // Common styles for both states + const commonStyles = css` + background-color: ${theme.colors.primary_dark || '#043565'}; + padding: 10px 20px; + margin-bottom: 8px; + font-size: 14px; + font-weight: 500; + border-radius: 8px; + display: flex; + align-items: center; + justify-content: center; + white-space: nowrap; + border: none; + box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1); + height: 20px; + `; + + // If no filters are selected, render a disabled button + if (!hasFilters) { + return ( +
+ {disabledText} +
+ ); + } + + // If filters are selected, render an active button + return ( + + + {enabledText} + + + ); +}); + +export default CrossTableFilterButton; \ No newline at end of file diff --git a/apps/stage/components/pages/activeDataTables/dataTableTwo/Facets.tsx b/apps/stage/components/pages/activeDataTables/sampleTable/Facets.tsx similarity index 100% rename from apps/stage/components/pages/activeDataTables/dataTableTwo/Facets.tsx rename to apps/stage/components/pages/activeDataTables/sampleTable/Facets.tsx diff --git a/apps/stage/components/inactiveDataTables/dataTableThree/PageContent.tsx b/apps/stage/components/pages/activeDataTables/sampleTable/PageContent.tsx similarity index 100% rename from apps/stage/components/inactiveDataTables/dataTableThree/PageContent.tsx rename to apps/stage/components/pages/activeDataTables/sampleTable/PageContent.tsx diff --git a/apps/stage/components/pages/activeDataTables/dataTableOne/QueryBar.tsx b/apps/stage/components/pages/activeDataTables/sampleTable/QueryBar.tsx similarity index 83% rename from apps/stage/components/pages/activeDataTables/dataTableOne/QueryBar.tsx rename to apps/stage/components/pages/activeDataTables/sampleTable/QueryBar.tsx index 4520e3dc..5aaeb3fd 100644 --- a/apps/stage/components/pages/activeDataTables/dataTableOne/QueryBar.tsx +++ b/apps/stage/components/pages/activeDataTables/sampleTable/QueryBar.tsx @@ -23,8 +23,10 @@ import { css, useTheme } from '@emotion/react'; import { SQONViewer, useArrangerTheme } from '@overture-stack/arranger-components'; import { UseThemeContextProps } from '@overture-stack/arranger-components/dist/types'; import { Row } from 'react-grid-system'; +import CrossTableFilterButton from '../CrossTableFilterButton'; +import { INTERNAL_PATHS } from '@/global/utils/constants'; const getThemeCustomisations = (theme: StageThemeInterface): UseThemeContextProps => ({ - callerName: 'DataSetOne-QueryBar', + callerName: 'DataSetTwo-QueryBar', components: { SQONViewer: { EmptyMessage: { @@ -100,6 +102,7 @@ const QueryBar = () => { const theme = useTheme(); useArrangerTheme(getThemeCustomisations(theme)); return ( + <> css` @@ -112,6 +115,30 @@ const QueryBar = () => { > + {/* Flex container for buttons */} +
+
+ +
+
+ +
+
+ ); }; export default QueryBar; diff --git a/apps/stage/components/pages/activeDataTables/dataTableTwo/RepoTable/helper.ts b/apps/stage/components/pages/activeDataTables/sampleTable/RepoTable/helper.ts similarity index 100% rename from apps/stage/components/pages/activeDataTables/dataTableTwo/RepoTable/helper.ts rename to apps/stage/components/pages/activeDataTables/sampleTable/RepoTable/helper.ts diff --git a/apps/stage/components/pages/activeDataTables/dataTableTwo/RepoTable/index.tsx b/apps/stage/components/pages/activeDataTables/sampleTable/RepoTable/index.tsx similarity index 93% rename from apps/stage/components/pages/activeDataTables/dataTableTwo/RepoTable/index.tsx rename to apps/stage/components/pages/activeDataTables/sampleTable/RepoTable/index.tsx index 7ea42d67..4e719104 100644 --- a/apps/stage/components/pages/activeDataTables/dataTableTwo/RepoTable/index.tsx +++ b/apps/stage/components/pages/activeDataTables/sampleTable/RepoTable/index.tsx @@ -53,7 +53,7 @@ const getTableConfigs = ({ // appearance background: theme.colors.white, - borderColor: theme.colors.grey_5, // Updated from grey_3 to grey_5 for more contrast + borderColor: theme.colors.grey_3, css: css` ${theme.shadow.default} `, @@ -82,7 +82,7 @@ const getTableConfigs = ({ }, DownloadButton: { customExporters, - exportSelectedRowsField: 'submission_metadata.submitter_id', + exportSelectedRowsField: 'id', downloadUrl: urlJoin(apiHost, 'download'), label: () => ( <> @@ -127,7 +127,7 @@ const getTableConfigs = ({ }, }, HeaderRow: { - borderColor: theme.colors.grey_5, // Updated from grey_3 to grey_5 for more contrast + borderColor: theme.colors.grey_3, css: css` ${theme.typography.data} `, @@ -148,7 +148,7 @@ const getTableConfigs = ({ hoverBackground: theme.colors.grey_highlight, lineHeight: '1.5rem', selectedBackground: theme.colors.accent_highlight, - verticalBorderColor: theme.colors.grey_5, // Updated from grey_3 to grey_5 for more contrast + verticalBorderColor: theme.colors.grey_3, }, TableWrapper: { margin: '0.5rem 0', diff --git a/apps/stage/components/pages/activeDataTables/dataTableTwo/getConfigError.tsx b/apps/stage/components/pages/activeDataTables/sampleTable/getConfigError.tsx similarity index 100% rename from apps/stage/components/pages/activeDataTables/dataTableTwo/getConfigError.tsx rename to apps/stage/components/pages/activeDataTables/sampleTable/getConfigError.tsx diff --git a/apps/stage/components/pages/activeDataTables/dataTableTwo/index.tsx b/apps/stage/components/pages/activeDataTables/sampleTable/index.tsx similarity index 100% rename from apps/stage/components/pages/activeDataTables/dataTableTwo/index.tsx rename to apps/stage/components/pages/activeDataTables/sampleTable/index.tsx diff --git a/apps/stage/components/inactiveDataTables/dataTableThree/Facets.tsx b/apps/stage/components/pages/activeDataTables/summaryTable/Facets.tsx similarity index 100% rename from apps/stage/components/inactiveDataTables/dataTableThree/Facets.tsx rename to apps/stage/components/pages/activeDataTables/summaryTable/Facets.tsx diff --git a/apps/stage/components/pages/activeDataTables/dataTableTwo/PageContent.tsx b/apps/stage/components/pages/activeDataTables/summaryTable/PageContent.tsx similarity index 100% rename from apps/stage/components/pages/activeDataTables/dataTableTwo/PageContent.tsx rename to apps/stage/components/pages/activeDataTables/summaryTable/PageContent.tsx diff --git a/apps/stage/components/pages/activeDataTables/dataTableTwo/QueryBar.tsx b/apps/stage/components/pages/activeDataTables/summaryTable/QueryBar.tsx similarity index 83% rename from apps/stage/components/pages/activeDataTables/dataTableTwo/QueryBar.tsx rename to apps/stage/components/pages/activeDataTables/summaryTable/QueryBar.tsx index 4520e3dc..554d3eee 100644 --- a/apps/stage/components/pages/activeDataTables/dataTableTwo/QueryBar.tsx +++ b/apps/stage/components/pages/activeDataTables/summaryTable/QueryBar.tsx @@ -23,8 +23,10 @@ import { css, useTheme } from '@emotion/react'; import { SQONViewer, useArrangerTheme } from '@overture-stack/arranger-components'; import { UseThemeContextProps } from '@overture-stack/arranger-components/dist/types'; import { Row } from 'react-grid-system'; +import CrossTableFilterButton from '../CrossTableFilterButton'; +import { INTERNAL_PATHS } from '@/global/utils/constants'; const getThemeCustomisations = (theme: StageThemeInterface): UseThemeContextProps => ({ - callerName: 'DataSetOne-QueryBar', + callerName: 'DataSetThree-QueryBar', components: { SQONViewer: { EmptyMessage: { @@ -100,6 +102,7 @@ const QueryBar = () => { const theme = useTheme(); useArrangerTheme(getThemeCustomisations(theme)); return ( + <> css` @@ -112,6 +115,30 @@ const QueryBar = () => { > + {/* Flex container for buttons */} +
+
+ +
+
+ +
+
+ ); }; export default QueryBar; diff --git a/apps/stage/components/inactiveDataTables/dataTableThree/RepoTable/helper.ts b/apps/stage/components/pages/activeDataTables/summaryTable/RepoTable/helper.ts similarity index 100% rename from apps/stage/components/inactiveDataTables/dataTableThree/RepoTable/helper.ts rename to apps/stage/components/pages/activeDataTables/summaryTable/RepoTable/helper.ts diff --git a/apps/stage/components/inactiveDataTables/dataTableThree/RepoTable/index.tsx b/apps/stage/components/pages/activeDataTables/summaryTable/RepoTable/index.tsx similarity index 92% rename from apps/stage/components/inactiveDataTables/dataTableThree/RepoTable/index.tsx rename to apps/stage/components/pages/activeDataTables/summaryTable/RepoTable/index.tsx index 020841cd..fefd8e6c 100644 --- a/apps/stage/components/inactiveDataTables/dataTableThree/RepoTable/index.tsx +++ b/apps/stage/components/pages/activeDataTables/summaryTable/RepoTable/index.tsx @@ -53,7 +53,7 @@ const getTableConfigs = ({ // appearance background: theme.colors.white, - borderColor: theme.colors.grey_5, // Updated from grey_3 to grey_5 for more contrast + borderColor: theme.colors.grey_3, css: css` ${theme.shadow.default} `, @@ -82,7 +82,7 @@ const getTableConfigs = ({ }, DownloadButton: { customExporters, - exportSelectedRowsField: 'submission_metadata.submitter_id', + exportSelectedRowsField: 'id', downloadUrl: urlJoin(apiHost, 'download'), label: () => ( <> @@ -127,7 +127,7 @@ const getTableConfigs = ({ }, }, HeaderRow: { - borderColor: theme.colors.grey_5, // Updated from grey_3 to grey_5 for more contrast + borderColor: theme.colors.grey_3, css: css` ${theme.typography.data} `, @@ -148,7 +148,7 @@ const getTableConfigs = ({ hoverBackground: theme.colors.grey_highlight, lineHeight: '1.5rem', selectedBackground: theme.colors.accent_highlight, - verticalBorderColor: theme.colors.grey_5, // Updated from grey_3 to grey_5 for more contrast + verticalBorderColor: theme.colors.grey_3, }, TableWrapper: { margin: '0.5rem 0', @@ -161,7 +161,7 @@ const RepoTable = () => { const theme = useTheme(); const today = new Date().toISOString().slice(0, 10).replace(/-/g, ''); const customExporters = [ - { label: 'Download', fileName: `dataset-2-data-export.${today}.tsv` }, // exports a TSV with what is displayed on the table (columns selected, etc.) + { label: 'Download', fileName: `dataset-3-data-export.${today}.tsv` }, // exports a TSV with what is displayed on the table (columns selected, etc.) ]; useArrangerTheme(getTableConfigs({ apiHost: INTERNAL_API_PROXY.DATATABLE_3_ARRANGER, customExporters, theme })); diff --git a/apps/stage/components/inactiveDataTables/dataTableThree/getConfigError.tsx b/apps/stage/components/pages/activeDataTables/summaryTable/getConfigError.tsx similarity index 100% rename from apps/stage/components/inactiveDataTables/dataTableThree/getConfigError.tsx rename to apps/stage/components/pages/activeDataTables/summaryTable/getConfigError.tsx diff --git a/apps/stage/components/inactiveDataTables/dataTableThree/index.tsx b/apps/stage/components/pages/activeDataTables/summaryTable/index.tsx similarity index 95% rename from apps/stage/components/inactiveDataTables/dataTableThree/index.tsx rename to apps/stage/components/pages/activeDataTables/summaryTable/index.tsx index c7a960dc..42999ad7 100644 --- a/apps/stage/components/inactiveDataTables/dataTableThree/index.tsx +++ b/apps/stage/components/pages/activeDataTables/summaryTable/index.tsx @@ -66,7 +66,7 @@ const configsQuery = ` } `; -const DataSetTwoRepositoryPage = (): ReactElement => { +const DataSetThreeRepositoryPage = (): ReactElement => { const theme = useTheme(); const [arrangerHasConfig, setArrangerHasConfig] = useState(false); const [loadingArrangerConfig, setLoadingArrangerConfig] = useState(true); @@ -91,7 +91,7 @@ const DataSetTwoRepositoryPage = (): ReactElement => { return setLoadingArrangerConfig(false); } - throw new Error('Could not validate Arranger Dataset2 server configuration!'); + throw new Error('Could not validate Arranger Dataset3 server configuration!'); }) .catch(async (err) => { console.warn(err); @@ -108,7 +108,7 @@ const DataSetTwoRepositoryPage = (): ReactElement => { }); return ( - + {loadingArrangerConfig ? (
{ ); }; -export default DataSetTwoRepositoryPage; +export default DataSetThreeRepositoryPage; diff --git a/apps/stage/components/pages/home/HomeContent.tsx b/apps/stage/components/pages/home/HomeContent.tsx index f36cc861..8b3fde9b 100644 --- a/apps/stage/components/pages/home/HomeContent.tsx +++ b/apps/stage/components/pages/home/HomeContent.tsx @@ -13,8 +13,8 @@ const HomeContent = (): ReactElement => { `} > diff --git a/apps/stage/global/utils/constants.ts b/apps/stage/global/utils/constants.ts index cb48244d..a6dfef2f 100644 --- a/apps/stage/global/utils/constants.ts +++ b/apps/stage/global/utils/constants.ts @@ -32,10 +32,9 @@ export const LOGIN_PATH = '/login'; export const ROOT_PATH = '/'; export enum INTERNAL_PATHS { - MOLECULAR = '/molecular', - DATATABLE_1 = '/dataTableOne', - DATATABLE_2 = '/dataTableTwo', - DATATABLE_3 = '/dataTableThree', + DATATABLE_1 = '/idMappings', + DATATABLE_2 = '/sampleTable', + DATATABLE_3 = '/summaryTable', DATATABLE_4 = '/dataTableFour', DATATABLE_5 = '/dataTableFive', HOME = '/home', diff --git a/apps/stage/inactivePages/dataTableThree/index.tsx b/apps/stage/inactivePages/dataTableThree/index.tsx deleted file mode 100644 index 0525d611..00000000 --- a/apps/stage/inactivePages/dataTableThree/index.tsx +++ /dev/null @@ -1,13 +0,0 @@ -// import DataTableThree from '../../compThreents/pages/activeDataTables/dataTableThree'; -// import { createPage } from '../../global/utils/pages'; - -// const DataSetThreeExplorationPage = createPage({ -// getInitialProps: async ({ query, egoJwt }) => { -// return { query, egoJwt }; -// }, -// isPublic: true, -// })(() => { -// return ; -// }); - -// export default DataSetThreeExplorationPage; diff --git a/apps/stage/pages/dataTableOne/index.tsx b/apps/stage/pages/idMappings/index.tsx similarity index 95% rename from apps/stage/pages/dataTableOne/index.tsx rename to apps/stage/pages/idMappings/index.tsx index 72d1ab5c..37037ee8 100644 --- a/apps/stage/pages/dataTableOne/index.tsx +++ b/apps/stage/pages/idMappings/index.tsx @@ -1,4 +1,4 @@ -import DataTableOne from '../../components/pages/activeDataTables/dataTableOne'; +import DataTableOne from '../../components/pages/activeDataTables/idMappings'; import { createPage } from '../../global/utils/pages'; const DataSetOneExplorationPage = createPage({ diff --git a/apps/stage/pages/dataTableTwo/index.tsx b/apps/stage/pages/sampleTable/index.tsx similarity index 95% rename from apps/stage/pages/dataTableTwo/index.tsx rename to apps/stage/pages/sampleTable/index.tsx index 2721e3cb..f9a1d056 100644 --- a/apps/stage/pages/dataTableTwo/index.tsx +++ b/apps/stage/pages/sampleTable/index.tsx @@ -1,4 +1,4 @@ -import DataTableTwo from '../../components/pages/activeDataTables/dataTableTwo'; +import DataTableTwo from '../../components/pages/activeDataTables/sampleTable'; import { createPage } from '../../global/utils/pages'; const DataSetTwoExplorationPage = createPage({ diff --git a/apps/stage/pages/summaryTable/index.tsx b/apps/stage/pages/summaryTable/index.tsx new file mode 100644 index 00000000..2b5f835c --- /dev/null +++ b/apps/stage/pages/summaryTable/index.tsx @@ -0,0 +1,13 @@ +import DataTableThree from '@/components/pages/activeDataTables/summaryTable'; +import { createPage } from '../../global/utils/pages'; + +const DataSetThreeExplorationPage = createPage({ + getInitialProps: async ({ query, egoJwt }) => { + return { query, egoJwt }; + }, + isPublic: true, +})(() => { + return ; +}); + +export default DataSetThreeExplorationPage; diff --git a/data/datatable1.csv b/data/datatable1.csv deleted file mode 100644 index a552eae4..00000000 --- a/data/datatable1.csv +++ /dev/null @@ -1,52 +0,0 @@ -donor_id,gender,primary_site,vital_status,diagnosis_id,age_at_diagnosis,cancer_type,staging_system,stage,specimen_id,specimen_type,tissue_source,sample_id,sample_type,treatment_id,treatment_type,treatment_start,treatment_duration,treatment_response,drug_name,followup_id,followup_interval,disease_status -DO0599,Female,Trachea,Alive,PD059901,50,C34.2,Binet staging system,Stage A,SP059902,Normal - tissue adjacent to primary tumour,Blood derived - bone marrow,SP059902,Total DNA,TR059901,Chemotherapy,58,52,Complete response,Tamoxifen,FO059901,45,Stable -DO0600,Male,Brain,Alive,PD059902,45,C71.0,AJCC 8th edition,Stage II,SP059903,Primary tumour,Solid tissue,SP059903,Total RNA,TR059902,Radiation therapy,30,45,Partial response,None,FO059902,60,Stable -DO0601,Female,Breast,Alive,PD059903,62,C50.1,AJCC 8th edition,Stage IIA,SP059904,Primary tumour,Solid tissue,SP059904,Total DNA,TR059903,Chemotherapy,45,90,Complete response,Doxorubicin,FO059903,90,Complete remission -DO0602,Male,Prostate gland,Alive,PD059904,71,C61,Gleason grade group system,Grade Group 2,SP059905,Primary tumour,Solid tissue,SP059905,Total DNA,TR059904,Hormonal therapy,15,180,Partial response,Leuprolide,FO059904,120,Stable -DO0603,Female,Ovary,Deceased,PD059905,58,C56,FIGO staging system,Stage IIIC,SP059906,Primary tumour,Solid tissue,SP059906,Total DNA,TR059905,Chemotherapy,20,120,Disease progression,Carboplatin,FO059905,150,Progression NOS -DO0604,Male,Lung,Alive,PD059906,67,C34.1,AJCC 8th edition,Stage IIIA,SP059907,Primary tumour,Solid tissue,SP059907,Total DNA,TR059906,Chemotherapy,40,60,Partial response,Cisplatin,FO059906,80,Stable -DO0605,Female,Thyroid gland,Alive,PD059907,43,C73,AJCC 8th edition,Stage I,SP059908,Primary tumour,Solid tissue,SP059908,Total DNA,TR059907,Surgery,10,1,Complete response,None,FO059907,180,No evidence of disease -DO0606,Male,Colon,Alive,PD059908,59,C18.2,AJCC 8th edition,Stage IIB,SP059909,Primary tumour,Solid tissue,SP059909,Total DNA,TR059908,Chemotherapy,25,84,Complete response,FOLFOX,FO059908,120,Stable -DO0607,Female,Pancreas,Deceased,PD059909,64,C25.0,AJCC 8th edition,Stage IV,SP059910,Primary tumour,Solid tissue,SP059910,Total DNA,TR059909,Chemotherapy,15,45,Disease progression,Gemcitabine,FO059909,60,Progression NOS -DO0608,Male,Liver,Alive,PD059910,55,C22.0,AJCC 8th edition,Stage II,SP059911,Primary tumour,Solid tissue,SP059911,Total DNA,TR059910,Surgery,5,1,Complete response,None,FO059910,90,Stable -DO0609,Female,Cervix uteri,Alive,PD059911,48,C53.0,FIGO staging system,Stage IB,SP059912,Primary tumour,Solid tissue,SP059912,Total DNA,TR059911,Radiation therapy,20,40,Complete response,None,FO059911,150,No evidence of disease -DO0610,Male,Bladder,Alive,PD059912,72,C67.0,AJCC 8th edition,Stage I,SP059913,Primary tumour,Solid tissue,SP059913,Total DNA,TR059912,Surgery,0,1,Complete response,None,FO059912,120,Stable -DO0611,Female,Breast,Alive,PD059913,51,C50.2,AJCC 8th edition,Stage IIA,SP059914,Primary tumour,Solid tissue,SP059914,Total DNA,TR059913,Chemotherapy,30,120,Complete response,Paclitaxel,FO059913,180,Complete remission -DO0612,Male,Prostate gland,Alive,PD059914,68,C61,Gleason grade group system,Grade Group 3,SP059915,Primary tumour,Solid tissue,SP059915,Total DNA,TR059914,Hormonal therapy,10,240,Partial response,Enzalutamide,FO059914,150,Stable -DO0613,Female,Ovary,Deceased,PD059915,61,C56,FIGO staging system,Stage IV,SP059916,Primary tumour,Solid tissue,SP059916,Total DNA,TR059915,Chemotherapy,25,90,Disease progression,Paclitaxel,FO059915,120,Progression NOS -DO0614,Male,Kidney,Alive,PD059916,57,C64.9,AJCC 8th edition,Stage II,SP059917,Primary tumour,Solid tissue,SP059917,Total DNA,TR059916,Surgery,15,1,Complete response,None,FO059916,90,No evidence of disease -DO0615,Female,Thyroid gland,Alive,PD059917,39,C73,AJCC 8th edition,Stage I,SP059918,Primary tumour,Solid tissue,SP059918,Total DNA,TR059917,Surgery,5,1,Complete response,None,FO059917,240,Stable -DO0616,Male,Stomach,Deceased,PD059918,70,C16.0,AJCC 8th edition,Stage IIIB,SP059919,Primary tumour,Solid tissue,SP059919,Total DNA,TR059918,Chemotherapy,20,60,Partial response,FLOT,FO059918,90,Progression NOS -DO0617,Female,Lung,Alive,PD059919,63,C34.3,AJCC 8th edition,Stage IIB,SP059920,Primary tumour,Solid tissue,SP059920,Total DNA,TR059919,Chemotherapy,35,75,Complete response,Pemetrexed,FO059919,120,Stable -DO0618,Male,Brain,Deceased,PD059920,52,C71.2,AJCC 8th edition,Stage IV,SP059921,Primary tumour,Solid tissue,SP059921,Total DNA,TR059920,Radiation therapy,15,30,Disease progression,None,FO059920,45,Progression NOS -DO0619,Female,Breast,Alive,PD059921,47,C50.4,AJCC 8th edition,Stage I,SP059922,Primary tumour,Solid tissue,SP059922,Total DNA,TR059921,Surgery,0,1,Complete response,None,FO059921,180,No evidence of disease -DO0620,Male,Colon,Alive,PD059922,66,C18.7,AJCC 8th edition,Stage IIIA,SP059923,Primary tumour,Solid tissue,SP059923,Total DNA,TR059922,Chemotherapy,25,120,Partial response,CAPOX,FO059922,150,Stable -DO0621,Female,Pancreas,Deceased,PD059923,69,C25.1,AJCC 8th edition,Stage IV,SP059924,Primary tumour,Solid tissue,SP059924,Total DNA,TR059923,Chemotherapy,10,60,Disease progression,FOLFIRINOX,FO059923,75,Progression NOS -DO0622,Male,Liver,Alive,PD059924,58,C22.0,AJCC 8th edition,Stage II,SP059925,Primary tumour,Solid tissue,SP059925,Total DNA,TR059924,Surgery,5,1,Complete response,None,FO059924,120,Stable -DO0623,Female,Cervix uteri,Alive,PD059925,44,C53.1,FIGO staging system,Stage IIA,SP059926,Primary tumour,Solid tissue,SP059926,Total DNA,TR059925,Radiation therapy,20,45,Complete response,None,FO059925,180,No evidence of disease -DO0624,Male,Bladder,Alive,PD059926,73,C67.1,AJCC 8th edition,Stage I,SP059927,Primary tumour,Solid tissue,SP059927,Total DNA,TR059926,Surgery,0,1,Complete response,None,FO059926,90,Stable -DO0625,Female,Breast,Alive,PD059927,54,C50.1,AJCC 8th edition,Stage IIB,SP059928,Primary tumour,Solid tissue,SP059928,Total DNA,TR059927,Chemotherapy,30,90,Complete response,AC-T,FO059927,150,Complete remission -DO0626,Male,Prostate gland,Alive,PD059928,65,C61,Gleason grade group system,Grade Group 2,SP059929,Primary tumour,Solid tissue,SP059929,Total DNA,TR059928,Hormonal therapy,15,180,Partial response,Abiraterone,FO059928,120,Stable -DO0627,Female,Ovary,Deceased,PD059929,60,C56,FIGO staging system,Stage IIIC,SP059930,Primary tumour,Solid tissue,SP059930,Total DNA,TR059929,Chemotherapy,25,120,Disease progression,Carboplatin,FO059929,90,Progression NOS -DO0628,Male,Kidney,Alive,PD059930,56,C64.9,AJCC 8th edition,Stage I,SP059931,Primary tumour,Solid tissue,SP059931,Total DNA,TR059930,Surgery,10,1,Complete response,None,FO059930,180,No evidence of disease -DO0629,Female,Thyroid gland,Alive,PD059931,41,C73,AJCC 8th edition,Stage I,SP059932,Primary tumour,Solid tissue,SP059932,Total DNA,TR059931,Surgery,5,1,Complete response,None,FO059931,240,Stable -DO0630,Male,Stomach,Deceased,PD059932,71,C16.3,AJCC 8th edition,Stage IV,SP059933,Primary tumour,Solid tissue,SP059933,Total DNA,TR059932,Chemotherapy,20,45,Disease progression,FLOT,FO059932,60,Progression NOS -DO0631,Female,Lung,Alive,PD059933,62,C34.1,AJCC 8th edition,Stage IIIA,SP059934,Primary tumour,Solid tissue,SP059934,Total DNA,TR059933,Chemotherapy,35,60,Partial response,Cisplatin,FO059933,120,Stable -DO0632,Male,Brain,Deceased,PD059934,53,C71.6,AJCC 8th edition,Stage IV,SP059935,Primary tumour,Solid tissue,SP059935,Total DNA,TR059934,Radiation therapy,15,30,Disease progression,None,FO059934,45,Progression NOS -DO0633,Female,Breast,Alive,PD059935,49,C50.2,AJCC 8th edition,Stage I,SP059936,Primary tumour,Solid tissue,SP059936,Total DNA,TR059935,Surgery,0,1,Complete response,None,FO059935,180,No evidence of disease -DO0634,Male,Colon,Alive,PD059936,67,C18.5,AJCC 8th edition,Stage IIIB,SP059937,Primary tumour,Solid tissue,SP059937,Total DNA,TR059936,Chemotherapy,25,120,Partial response,FOLFOX,FO059936,150,Stable -DO0635,Female,Pancreas,Deceased,PD059937,68,C25.2,AJCC 8th edition,Stage IV,SP059938,Primary tumour,Solid tissue,SP059938,Total DNA,TR059937,Chemotherapy,10,45,Disease progression,Gemcitabine,FO059937,60,Progression NOS -DO0636,Male,Liver,Alive,PD059938,57,C22.0,AJCC 8th edition,Stage II,SP059939,Primary tumour,Solid tissue,SP059939,Total DNA,TR059938,Surgery,5,1,Complete response,None,FO059938,120,Stable -DO0637,Female,Cervix uteri,Alive,PD059939,46,C53.0,FIGO staging system,Stage IB,SP059940,Primary tumour,Solid tissue,SP059940,Total DNA,TR059939,Radiation therapy,20,40,Complete response,None,FO059939,180,No evidence of disease -DO0638,Male,Bladder,Alive,PD059940,74,C67.2,AJCC 8th edition,Stage I,SP059941,Primary tumour,Solid tissue,SP059941,Total DNA,TR059940,Surgery,0,1,Complete response,None,FO059940,90,Stable -DO0639,Female,Breast,Alive,PD059941,52,C50.3,AJCC 8th edition,Stage IIA,SP059942,Primary tumour,Solid tissue,SP059942,Total DNA,TR059941,Chemotherapy,30,90,Complete response,TC,FO059941,150,Complete remission -DO0640,Male,Prostate gland,Alive,PD059942,69,C61,Gleason grade group system,Grade Group 3,SP059943,Primary tumour,Solid tissue,SP059943,Total DNA,TR059942,Hormonal therapy,15,240,Partial response,Enzalutamide,FO059942,120,Stable -DO0641,Female,Ovary,Deceased,PD059943,59,C56,FIGO staging system,Stage IV,SP059944,Primary tumour,Solid tissue,SP059944,Total DNA,TR059943,Chemotherapy,25,90,Disease progression,Paclitaxel,FO059943,75,Progression NOS -DO0642,Male,Kidney,Alive,PD059944,55,C64.9,AJCC 8th edition,Stage II,SP059945,Primary tumour,Solid tissue,SP059945,Total DNA,TR059944,Surgery,10,1,Complete response,None,FO059944,180,No evidence of disease -DO0643,Female,Thyroid gland,Alive,PD059945,40,C73,AJCC 8th edition,Stage I,SP059946,Primary tumour,Solid tissue,SP059946,Total DNA,TR059945,Surgery,5,1,Complete response,None,FO059945,240,Stable -DO0644,Male,Stomach,Deceased,PD059946,72,C16.4,AJCC 8th edition,Stage IIIB,SP059947,Primary tumour,Solid tissue,SP059947,Total DNA,TR059946,Chemotherapy,20,60,Disease progression,FLOT,FO059946,90,Progression NOS -DO0645,Female,Lung,Alive,PD059947,61,C34.3,AJCC 8th edition,Stage IIB,SP059948,Primary tumour,Solid tissue,SP059948,Total DNA,TR059947,Chemotherapy,35,75,Partial response,Pemetrexed,FO059947,120,Stable -DO0646,Male,Brain,Deceased,PD059948,54,C71.2,AJCC 8th edition,Stage IV,SP059949,Primary tumour,Solid tissue,SP059949,Total DNA,TR059948,Radiation therapy,15,30,Disease progression,None,FO059948,45,Progression NOS -DO0647,Female,Breast,Alive,PD059949,48,C50.4,AJCC 8th edition,Stage I,SP059950,Primary tumour,Solid tissue,SP059950,Total DNA,TR059949,Surgery,0,1,Complete response,None,FO059949,180,No evidence of disease -DO0648,Male,Colon,Alive,PD059950,65,C18.7,AJCC 8th edition,Stage IIIA,SP059951,Primary tumour,Solid tissue,SP059951,Total DNA,TR059950,Chemotherapy,25,120,Complete response,CAPOX,FO059950,150,Stable -DO0649,Female,Pancreas,Deceased,PD059951,70,C25.1,AJCC 8th edition,Stage IV,SP059952,Primary tumour,Solid tissue,SP059952,Total DNA,TR059951,Chemotherapy,10,60,Disease progression,FOLFIRINOX,FO059951,75,Progression NOS \ No newline at end of file diff --git a/data/esDoc.json b/data/esDoc.json deleted file mode 100644 index bae73f9e..00000000 --- a/data/esDoc.json +++ /dev/null @@ -1,40 +0,0 @@ -{ - "entityName": "donor", - "data": { - "gender": "Male", - "donor_id": "DO0608", - "vital_status": "Alive", - "diagnosis": [ - { - "stage": "Stage II", - "donor_id": "DO0608", - "cancer_type": "C22.0", - "diagnosis_id": "PD059910", - "primary_site": "Liver", - "staging_system": "AJCC 8th edition", - "age_at_diagnosis": 55 - } - ], - "treatment": [ - { - "donor_id": "DO0608", - "treatment_id": "TR059942", - "treatment_type": "Hormonal therapy", - "treatment_start": 15, - "treatment_duration": 240, - "treatment_response": "Partial response", - "followup": [ - { - "followup_id": "FO059910", - "treatment_id": "TR059942", - "disease_status": "Stable", - "followup_interval": 90 - } - ] - } - ] - }, - "organization": "OICR", - "isValid": true, - "systemId": "UZE1VP2KVT5SGCE2UJL2Z" - } \ No newline at end of file diff --git a/data/fileData/SP059902.snv.vcf.gz b/data/fileData/SP059902.snv.vcf.gz deleted file mode 100644 index 731ae2b4..00000000 Binary files a/data/fileData/SP059902.snv.vcf.gz and /dev/null differ diff --git a/data/fileData/SP059902.snv.vcf.gz.tbi b/data/fileData/SP059902.snv.vcf.gz.tbi deleted file mode 100644 index 28eb7822..00000000 Binary files a/data/fileData/SP059902.snv.vcf.gz.tbi and /dev/null differ diff --git a/data/fileData/file-metadata.json b/data/fileData/file-metadata.json deleted file mode 100644 index cf31c685..00000000 --- a/data/fileData/file-metadata.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "studyId": "demo", - "analysisType": { - "name": "MyNewSchema" - }, - "files": [ - { - "dataType": "Raw SV Calls", - "fileName": "SP059902.snv.vcf.gz", - "fileSize": 17246, - "fileMd5sum": "94b790078d8e98ad08ffc42389e2fa68", - "fileAccess": "open", - "fileType": "VCF", - "info": { - "dataCategory": "Simple Nucelotide Variation", - "jbrowseCoordinates": "hg38:chr1:100000-200000" - } - }, - { - "dataType": "Raw SV Calls", - "fileName": "SP059902.snv.vcf.gz.tbi", - "fileSize": 141, - "fileMd5sum": "f5cca6ace25d076d1f76cebf4ce3defd", - "fileAccess": "open", - "fileType": "TBI", - "info": { - "dataCategory": "Simple Nucelotide Variation", - "jbrowseCoordinates": "hg38:chr1:100000-200000" - } - } - ], - "workflow": { - "workflowName": "Mutect2 Variant Calling", - "workflowShortName": "Mutect2Variant", - "workflowVersion": "0.1.1.1", - "inputs": [ - { - "analysisType": "sequencing_alignment", - "analysisId": "00000000-0000-0000-0000-0000000000599" - } - ], - "runId": "RI0599", - "sessionId": "SI0599" - }, - "experiment": { - "platform": "PacBio", - "experimentalStrategy": "WXS", - "sequencingCenter": "CGTA", - "sequencingDate": "2021-03-08T19:00:00.000Z" - } -} diff --git a/data/readme.md b/data/readme.md deleted file mode 100644 index 60034696..00000000 --- a/data/readme.md +++ /dev/null @@ -1,25 +0,0 @@ -# Data Folder - -This folder is for storing data files used in your project. Below are guidelines -for optimal data management: - -## File Format - -- The composer supports configurable delimiters, but CSV (Comma-Separated - Values) is the recommended format for tabular data -- Include headers in your CSV files for clear column identification your - elasticsearch index mapping should match these field names - -## Data Security - -- If storing sensitive data, add your data files to `.gitignore` before - committing to GitHub -- If pushing data files to github review them for any personally identifiable - information (PII) before committing - -## Dataset Size - -- Use representative sample datasets of approximately 500 records for - development and testing -- No strict minimum or maximum size limits exist beyond Docker and Elasticsearch - resource constraints diff --git a/data/segmentedData/diagnosis.csv b/data/segmentedData/diagnosis.csv deleted file mode 100644 index 6f481d03..00000000 --- a/data/segmentedData/diagnosis.csv +++ /dev/null @@ -1,52 +0,0 @@ -diagnosis_id,donor_id,primary_site,age_at_diagnosis,cancer_type,staging_system,stage -PD059901,DO0599,Trachea,50,C34.2,Binet staging system,Stage A -PD059902,DO0600,Brain,45,C71.0,AJCC 8th edition,Stage II -PD059903,DO0601,Breast,62,C50.1,AJCC 8th edition,Stage IIA -PD059904,DO0602,Prostate gland,71,C61,Gleason grade group system,Grade Group 2 -PD059905,DO0603,Ovary,58,C56,FIGO staging system,Stage IIIC -PD059906,DO0604,Lung,67,C34.1,AJCC 8th edition,Stage IIIA -PD059907,DO0605,Thyroid gland,43,C73,AJCC 8th edition,Stage I -PD059908,DO0606,Colon,59,C18.2,AJCC 8th edition,Stage IIB -PD059909,DO0607,Pancreas,64,C25.0,AJCC 8th edition,Stage IV -PD059910,DO0608,Liver,55,C22.0,AJCC 8th edition,Stage II -PD059911,DO0609,Cervix uteri,48,C53.0,FIGO staging system,Stage IB -PD059912,DO0610,Bladder,72,C67.0,AJCC 8th edition,Stage I -PD059913,DO0611,Breast,51,C50.2,AJCC 8th edition,Stage IIA -PD059914,DO0612,Prostate gland,68,C61,Gleason grade group system,Grade Group 3 -PD059915,DO0613,Ovary,61,C56,FIGO staging system,Stage IV -PD059916,DO0614,Kidney,57,C64.9,AJCC 8th edition,Stage II -PD059917,DO0615,Thyroid gland,39,C73,AJCC 8th edition,Stage I -PD059918,DO0616,Stomach,70,C16.0,AJCC 8th edition,Stage IIIB -PD059919,DO0617,Lung,63,C34.3,AJCC 8th edition,Stage IIB -PD059920,DO0618,Brain,52,C71.2,AJCC 8th edition,Stage IV -PD059921,DO0619,Breast,47,C50.4,AJCC 8th edition,Stage I -PD059922,DO0620,Colon,66,C18.7,AJCC 8th edition,Stage IIIA -PD059923,DO0621,Pancreas,69,C25.1,AJCC 8th edition,Stage IV -PD059924,DO0622,Liver,58,C22.0,AJCC 8th edition,Stage II -PD059925,DO0623,Cervix uteri,44,C53.1,FIGO staging system,Stage IIA -PD059926,DO0624,Bladder,73,C67.1,AJCC 8th edition,Stage I -PD059927,DO0625,Breast,54,C50.1,AJCC 8th edition,Stage IIB -PD059928,DO0626,Prostate gland,65,C61,Gleason grade group system,Grade Group 2 -PD059929,DO0627,Ovary,60,C56,FIGO staging system,Stage IIIC -PD059930,DO0628,Kidney,56,C64.9,AJCC 8th edition,Stage I -PD059931,DO0629,Thyroid gland,41,C73,AJCC 8th edition,Stage I -PD059932,DO0630,Stomach,71,C16.3,AJCC 8th edition,Stage IV -PD059933,DO0631,Lung,62,C34.1,AJCC 8th edition,Stage IIIA -PD059934,DO0632,Brain,53,C71.6,AJCC 8th edition,Stage IV -PD059935,DO0633,Breast,49,C50.2,AJCC 8th edition,Stage I -PD059936,DO0634,Colon,67,C18.5,AJCC 8th edition,Stage IIIB -PD059937,DO0635,Pancreas,68,C25.2,AJCC 8th edition,Stage IV -PD059938,DO0636,Liver,57,C22.0,AJCC 8th edition,Stage II -PD059939,DO0637,Cervix uteri,46,C53.0,FIGO staging system,Stage IB -PD059940,DO0638,Bladder,74,C67.2,AJCC 8th edition,Stage I -PD059941,DO0639,Breast,52,C50.3,AJCC 8th edition,Stage IIA -PD059942,DO0640,Prostate gland,69,C61,Gleason grade group system,Grade Group 3 -PD059943,DO0641,Ovary,59,C56,FIGO staging system,Stage IV -PD059944,DO0642,Kidney,55,C64.9,AJCC 8th edition,Stage II -PD059945,DO0643,Thyroid gland,40,C73,AJCC 8th edition,Stage I -PD059946,DO0644,Stomach,72,C16.4,AJCC 8th edition,Stage IIIB -PD059947,DO0645,Lung,61,C34.3,AJCC 8th edition,Stage IIB -PD059948,DO0646,Brain,54,C71.2,AJCC 8th edition,Stage IV -PD059949,DO0647,Breast,48,C50.4,AJCC 8th edition,Stage I -PD059950,DO0648,Colon,65,C18.7,AJCC 8th edition,Stage IIIA -PD059951,DO0649,Pancreas,70,C25.1,AJCC 8th edition,Stage IV \ No newline at end of file diff --git a/data/segmentedData/donor.csv b/data/segmentedData/donor.csv deleted file mode 100644 index d9a49655..00000000 --- a/data/segmentedData/donor.csv +++ /dev/null @@ -1,52 +0,0 @@ -donor_id,gender,vital_status -DO0599,Female,Alive -DO0600,Male,Alive -DO0601,Female,Alive -DO0602,Male,Alive -DO0603,Female,Deceased -DO0604,Male,Alive -DO0605,Female,Alive -DO0606,Male,Alive -DO0607,Female,Deceased -DO0608,Male,Alive -DO0609,Female,Alive -DO0610,Male,Alive -DO0611,Female,Alive -DO0612,Male,Alive -DO0613,Female,Deceased -DO0614,Male,Alive -DO0615,Female,Alive -DO0616,Male,Deceased -DO0617,Female,Alive -DO0618,Male,Deceased -DO0619,Female,Alive -DO0620,Male,Alive -DO0621,Female,Deceased -DO0622,Male,Alive -DO0623,Female,Alive -DO0624,Male,Alive -DO0625,Female,Alive -DO0626,Male,Alive -DO0627,Female,Deceased -DO0628,Male,Alive -DO0629,Female,Alive -DO0630,Male,Deceased -DO0631,Female,Alive -DO0632,Male,Deceased -DO0633,Female,Alive -DO0634,Male,Alive -DO0635,Female,Deceased -DO0636,Male,Alive -DO0637,Female,Alive -DO0638,Male,Alive -DO0639,Female,Alive -DO0640,Male,Alive -DO0641,Female,Deceased -DO0642,Male,Alive -DO0643,Female,Alive -DO0644,Male,Deceased -DO0645,Female,Alive -DO0646,Male,Deceased -DO0647,Female,Alive -DO0648,Male,Alive -DO0649,Female,Deceased \ No newline at end of file diff --git a/data/segmentedData/followup.csv b/data/segmentedData/followup.csv deleted file mode 100644 index de0ec1aa..00000000 --- a/data/segmentedData/followup.csv +++ /dev/null @@ -1,52 +0,0 @@ -treatment_id,followup_id,followup_interval,disease_status -TR059951,FO059901,45,Stable -TR059950,FO059902,60,Stable -TR059949,FO059903,90,Complete remission -TR059948,FO059904,120,Stable -TR059947,FO059905,150,Progression NOS -TR059946,FO059906,80,Stable -TR059945,FO059907,180,No evidence of disease -TR059944,FO059908,120,Stable -TR059943,FO059909,60,Progression NOS -TR059942,FO059910,90,Stable -TR059941,FO059911,150,No evidence of disease -TR059940,FO059912,120,Stable -TR059939,FO059913,180,Complete remission -TR059938,FO059914,150,Stable -TR059937,FO059915,120,Progression NOS -TR059936,FO059916,90,No evidence of disease -TR059935,FO059917,240,Stable -TR059934,FO059918,90,Progression NOS -TR059933,FO059919,120,Stable -TR059932,FO059920,45,Progression NOS -TR059931,FO059921,180,No evidence of disease -TR059930,FO059922,150,Stable -TR059929,FO059923,75,Progression NOS -TR059928,FO059924,120,Stable -TR059927,FO059925,180,No evidence of disease -TR059926,FO059926,90,Stable -TR059925,FO059927,150,Complete remission -TR059924,FO059928,120,Stable -TR059923,FO059929,90,Progression NOS -TR059922,FO059930,180,No evidence of disease -TR059921,FO059931,240,Stable -TR059920,FO059932,60,Progression NOS -TR059919,FO059933,120,Stable -TR059918,FO059934,45,Progression NOS -TR059917,FO059935,180,No evidence of disease -TR059916,FO059936,150,Stable -TR059915,FO059937,60,Progression NOS -TR059914,FO059938,120,Stable -TR059913,FO059939,180,No evidence of disease -TR059912,FO059940,90,Stable -TR059911,FO059941,150,Complete remission -TR059910,FO059942,120,Stable -TR059909,FO059943,75,Progression NOS -TR059908,FO059944,180,No evidence of disease -TR059907,FO059945,240,Stable -TR059906,FO059946,90,Progression NOS -TR059905,FO059947,120,Stable -TR059904,FO059948,45,Progression NOS -TR059903,FO059949,180,No evidence of disease -TR059902,FO059950,150,Stable -TR059901,FO059951,75,Progression NOS \ No newline at end of file diff --git a/data/segmentedData/treatment.csv b/data/segmentedData/treatment.csv deleted file mode 100644 index 41d750f9..00000000 --- a/data/segmentedData/treatment.csv +++ /dev/null @@ -1,52 +0,0 @@ -donor_id,treatment_id,treatment_type,treatment_start,treatment_duration,treatment_response -DO0649,TR059901,Chemotherapy,58,52,Complete response -DO0648,TR059902,Radiation therapy,30,45,Partial response -DO0647,TR059903,Chemotherapy,45,90,Complete response -DO0646,TR059904,Hormonal therapy,15,180,Partial response -DO0645,TR059905,Chemotherapy,20,120,Disease progression -DO0644,TR059906,Chemotherapy,40,60,Partial response -DO0643,TR059907,Surgery,10,1,Complete response -DO0642,TR059908,Chemotherapy,25,84,Complete response -DO0641,TR059909,Chemotherapy,15,45,Disease progression -DO0640,TR059910,Surgery,5,1,Complete response -DO0639,TR059911,Radiation therapy,20,40,Complete response -DO0638,TR059912,Surgery,0,1,Complete response -DO0637,TR059913,Chemotherapy,30,120,Complete response -DO0636,TR059914,Hormonal therapy,10,240,Partial response -DO0635,TR059915,Chemotherapy,25,90,Disease progression -DO0634,TR059916,Surgery,15,1,Complete response -DO0633,TR059917,Surgery,5,1,Complete response -DO0632,TR059918,Chemotherapy,20,60,Partial response -DO0631,TR059919,Chemotherapy,35,75,Complete response -DO0630,TR059920,Radiation therapy,15,30,Disease progression -DO0629,TR059921,Surgery,0,1,Complete response -DO0628,TR059922,Chemotherapy,25,120,Partial response -DO0627,TR059923,Chemotherapy,10,60,Disease progression -DO0626,TR059924,Surgery,5,1,Complete response -DO0625,TR059925,Radiation therapy,20,45,Complete response -DO0624,TR059926,Surgery,0,1,Complete response -DO0623,TR059927,Chemotherapy,30,90,Complete response -DO0622,TR059928,Hormonal therapy,15,180,Partial response -DO0621,TR059929,Chemotherapy,25,120,Disease progression -DO0620,TR059930,Surgery,10,1,Complete response -DO0619,TR059931,Surgery,5,1,Complete response -DO0618,TR059932,Chemotherapy,20,45,Disease progression -DO0617,TR059933,Chemotherapy,35,60,Partial response -DO0616,TR059934,Radiation therapy,15,30,Disease progression -DO0615,TR059935,Surgery,0,1,Complete response -DO0614,TR059936,Chemotherapy,25,120,Partial response -DO0613,TR059937,Chemotherapy,10,45,Disease progression -DO0612,TR059938,Surgery,5,1,Complete response -DO0611,TR059939,Radiation therapy,20,40,Complete response -DO0610,TR059940,Surgery,0,1,Complete response -DO0609,TR059941,Chemotherapy,30,90,Complete response -DO0608,TR059942,Hormonal therapy,15,240,Partial response -DO0607,TR059943,Chemotherapy,25,90,Disease progression -DO0606,TR059944,Surgery,10,1,Complete response -DO0605,TR059945,Surgery,5,1,Complete response -DO0604,TR059946,Chemotherapy,20,60,Disease progression -DO0603,TR059947,Chemotherapy,35,75,Partial response -DO0602,TR059948,Radiation therapy,15,30,Disease progression -DO0601,TR059949,Surgery,0,1,Complete response -DO0600,TR059950,Chemotherapy,25,120,Complete response -DO0599,TR059951,Chemotherapy,10,60,Disease progression \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index 1b3adef8..eb199374 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -21,23 +21,28 @@ services: DEBUG: false # Elasticsearch Index Configuration # Dynamic indices are configured with a count and indexed variables - ES_INDEX_COUNT: 1 + ES_INDEX_COUNT: 3 # First index - ES_INDEX_0_NAME: datatable1-index - ES_INDEX_0_TEMPLATE_FILE: conductor/configs/elasticsearchConfigs/datatable1-mapping.json - ES_INDEX_0_TEMPLATE_NAME: datatable1-index - ES_INDEX_0_ALIAS_NAME: datatable1_centric + ES_INDEX_0_NAME: idmapping-index + ES_INDEX_0_TEMPLATE_FILE: conductor/configs/elasticsearchConfigs/idmapping-mapping.json + ES_INDEX_0_TEMPLATE_NAME: idmapping-index + ES_INDEX_0_ALIAS_NAME: idmapping_centric # Second index - # ES_INDEX_1_NAME: file-index - # ES_INDEX_1_TEMPLATE_FILE: conductor/configs/elasticsearchConfigs/datatable2-mapping.json - # ES_INDEX_1_TEMPLATE_NAME: datatable2-index - # ES_INDEX_1_ALIAS_NAME: datatable2_centric + ES_INDEX_1_NAME: sample-index + ES_INDEX_1_TEMPLATE_FILE: conductor/configs/elasticsearchConfigs/sample-mapping.json + ES_INDEX_1_TEMPLATE_NAME: sample-index + ES_INDEX_1_ALIAS_NAME: sample_centric + # Third index + ES_INDEX_2_NAME: summary-index + ES_INDEX_2_TEMPLATE_FILE: conductor/configs/elasticsearchConfigs/summary-mapping.json + ES_INDEX_2_TEMPLATE_NAME: summary-index + ES_INDEX_2_ALIAS_NAME: summary_centric # Arranger Services Configuration # Dynamically configurable number of Arranger instances - ARRANGER_COUNT: 1 - ARRANGER_0_URL: http://arranger-datatable1:5050 - ARRANGER_1_URL: http://arranger-datatable2:5051 - # ARRANGER_2_URL: http://arranger-datatable3:5052 + ARRANGER_COUNT: 3 + ARRANGER_0_URL: http://arranger-idmapping:5050 + ARRANGER_1_URL: http://arranger-sampletable:5051 + ARRANGER_2_URL: http://arranger-summarytable:5052 # Add more ARRANGER_X_URL as needed, matching ARRANGER_COUNT # ARRANGER_X_URL: http://arranger-x:505X # Service Connections @@ -92,6 +97,52 @@ services: networks: - conductor-network + # ================================================================================== # + # Data Setup Container - Handles initial data loading and configuration # + # ================================================================================== # + data-setup: + # ================================================================================== # + # Runs scripts that automate data loading and configuration. # + # Handles dictionary upload, entity registration, data upload, and indexing # + # More information can be found within the docs folder # + # ================================================================================== # + profiles: ["dataSetup"] + image: node:18-alpine + container_name: data-setup + volumes: + - ./data:/data + - ./apps/conductor/:/conductor + environment: + # Global Configuration + PROFILE: ${PROFILE:-default} + # Service Connections + ES_USER: elastic + ES_PASS: myelasticpassword + ES_URL: http://elasticsearch:9200 + STAGE_URL: http://stage:3000 + LECTERN_URL: http://lectern:3031 + LYRIC_URL: http://lyric:3030 + MAESTRO_URL: http://maestro:11235 + command: > + sh -c ' + set -e + echo "Profile is set to: $PROFILE" + case "$PROFILE" in + "dataSetup") + echo "Running data setup deployment..." + chmod +x /conductor/scripts/services/upload-data.sh + /conductor/scripts/services/upload-data.sh + ;; + *) + echo "Invalid profile specified for data-setup container." + exit 1 + ;; + esac + exit 0 + ' + networks: + - conductor-network + # ================================================================================== # # ================================================================================== # # phase1: # @@ -147,10 +198,10 @@ services: # Search API generation with compatible search UI components # # https://docs.overture.bio/docs/core-software/Arranger/overview # # ------------------------------------------------------------------------------------# - arranger-datatable1: + arranger-idmapping: profiles: ["phase1", "phase2", "phase3", "stageDev", "default"] image: ghcr.io/overture-stack/arranger-server:3.0.0-beta.36 - container_name: arranger-datatable1 + container_name: arranger-idmapping platform: linux/amd64 depends_on: conductor: @@ -158,24 +209,24 @@ services: ports: - "5050:5050" volumes: - - ./apps/conductor/configs/arrangerConfigs/datatable1:/app/modules/server/configs + - ./apps/conductor/configs/arrangerConfigs/idmapping:/app/modules/server/configs environment: # Elasticsearch Variables ES_HOST: http://elasticsearch:9200 ES_USER: elastic ES_PASS: myelasticpassword - ES_ARRANGER_SET_INDEX: data_arranger_set + ES_ARRANGER_SET_INDEX: idmapping_arranger_set # Arranger Variables (Port required) PORT: 5050 - DEBUG: false - ENABLE_LOGS: false + DEBUG: true + ENABLE_LOGS: true networks: - conductor-network - arranger-datatable2: + arranger-sampletable: profiles: ["phase1", "phase2", "phase3", "stageDev", "default"] image: ghcr.io/overture-stack/arranger-server:3.0.0-beta.36 - container_name: arranger-datatable2 + container_name: arranger-sampletable platform: linux/amd64 depends_on: conductor: @@ -183,44 +234,44 @@ services: ports: - "5051:5051" # Use unique ports for each Arranger instance volumes: - - ./apps/conductor/configs/arrangerConfigs/datatable2:/app/modules/server/configs # Point to the relevant generated config + - ./apps/conductor/configs/arrangerConfigs/sample:/app/modules/server/configs # Point to the relevant generated config environment: # Elasticsearch Variables ES_HOST: http://elasticsearch:9200 ES_USER: elastic ES_PASS: myelasticpassword - ES_ARRANGER_SET_INDEX: datatable2_arranger_set + ES_ARRANGER_SET_INDEX: sampletable_arranger_set # Arranger Variables PORT: 5051 # Required - DEBUG: false - ENABLE_LOGS: false + DEBUG: true + ENABLE_LOGS: true networks: - conductor-network - # arranger-datatable3: - # profiles: ["phase1", "phase2", "phase3", "stageDev", "default"] - # image: ghcr.io/overture-stack/arranger-server:3.0.0-beta.36 - # container_name: arranger-datatable3 - # platform: linux/amd64 - # depends_on: - # conductor: - # condition: service_healthy - # ports: - # - "5052:5052" # Use unique ports for each Arranger instance - # volumes: - # - ./apps/conductor/configs/arrangerConfigs/datatable3:/app/modules/server/configs # Point to the relevant generated config - # environment: - # # Elasticsearch Variables - # ES_HOST: http://elasticsearch:9200 - # ES_USER: elastic - # ES_PASS: myelasticpassword - # ES_ARRANGER_SET_INDEX: datatable3_arranger_set - # # Arranger Variables - # PORT: 5052 # Required - # DEBUG: false - # ENABLE_LOGS: false - # networks: - # - conductor-network + arranger-summarytable: + profiles: ["phase1", "phase2", "phase3", "stageDev", "default"] + image: ghcr.io/overture-stack/arranger-server:3.0.0-beta.36 + container_name: arranger-summarytable + platform: linux/amd64 + depends_on: + conductor: + condition: service_healthy + ports: + - "5052:5052" # Use unique ports for each Arranger instance + volumes: + - ./apps/conductor/configs/arrangerConfigs/summary:/app/modules/server/configs # Point to the relevant generated config + environment: + # Elasticsearch Variables + ES_HOST: http://elasticsearch:9200 + ES_USER: elastic + ES_PASS: myelasticpassword + ES_ARRANGER_SET_INDEX: summarytable_arranger_set + # Arranger Variables + PORT: 5052 # Required + DEBUG: true + ENABLE_LOGS: true + networks: + - conductor-network # ------------------------------------------------------------------------------------# # Stage # @@ -233,7 +284,7 @@ services: image: stageimage:1.0 container_name: stage pull_policy: never - platform: linux/arm64/v8 + platform: linux/amd64 depends_on: conductor: condition: service_healthy @@ -242,23 +293,23 @@ services: environment: # Stage Variables NEXTAUTH_URL: http://localhost:3000/api/auth - NEXT_PUBLIC_LAB_NAME: Prelude + NEXT_PUBLIC_LAB_NAME: PanTracker Portal NEXT_PUBLIC_ADMIN_EMAIL: example@example.com NEXT_PUBLIC_DEBUG: false NEXT_PUBLIC_SHOW_MOBILE_WARNING: true NEXT_PUBLIC_ENABLE_DOWNLOADS: true - # Datatable1 Arranger Variables - NEXT_PUBLIC_ARRANGER_DATATABLE_1_API: http://arranger-datatable1:5050 + # idmapping Arranger Variables + NEXT_PUBLIC_ARRANGER_DATATABLE_1_API: http://pantrack.genomeinformatics.org/idmapping-api NEXT_PUBLIC_ARRANGER_DATATABLE_1_DOCUMENT_TYPE: file - NEXT_PUBLIC_ARRANGER_DATATABLE_1_INDEX: datatable1_centric - # Datatable2 Arranger Variables - NEXT_PUBLIC_ARRANGER_DATATABLE_2_API: http://arranger-datatable2:5051 + NEXT_PUBLIC_ARRANGER_DATATABLE_1_INDEX: idmapping_centric + # sampletable Arranger Variables + NEXT_PUBLIC_ARRANGER_DATATABLE_2_API: http://pantrack.genomeinformatics.org/sample-api NEXT_PUBLIC_ARRANGER_DATATABLE_2_DOCUMENT_TYPE: file - NEXT_PUBLIC_ARRANGER_DATATABLE_2_INDEX: datatable2_centric - # Datatable3 Arranger Variables - NEXT_PUBLIC_ARRANGER_DATATABLE_3_API: http://arranger-datatable3:5052 + NEXT_PUBLIC_ARRANGER_DATATABLE_2_INDEX: sample_centric + # summarytable Arranger Variables + NEXT_PUBLIC_ARRANGER_DATATABLE_3_API: http://pantrack.genomeinformatics.org/summary-api NEXT_PUBLIC_ARRANGER_DATATABLE_3_DOCUMENT_TYPE: file - NEXT_PUBLIC_ARRANGER_DATATABLE_3_INDEX: datatable3_centric + NEXT_PUBLIC_ARRANGER_DATATABLE_3_INDEX: summary_centric # Using localhost for client-side requests NEXT_PUBLIC_SONG_API: http://song:8080 NEXT_PUBLIC_SCORE_API: http://score:8087 @@ -424,7 +475,7 @@ services: # -----------------------------------------------------------------------------------# maestro: profiles: ["phase2", phase3, "default"] - image: ghcr.io/overture-stack/maestro:e868d03 + image: ghcr.io/overture-stack/maestro:7f05c8d container_name: maestro platform: linux/amd64 depends_on: @@ -438,18 +489,35 @@ services: # Maestro Base Variables MAESTRO_FAILURELOG_ENABLED: true MAESTRO_FAILURELOG_DIR: app/logs/maestro - MAESTRO_LOGGING_LEVEL_ROOT: INFO + MAESTRO_LOGGING_LEVEL_ROOT: DEBUG MAESTRO_DISABLEEVENTINDEXING: true - # Repository Configuration - Lyric + # idmapping MAESTRO_REPOSITORIES_0_BASE_URL: http://lyric:3030 - # in the old world we added these to each document in elasticsearch, - MAESTRO_REPOSITORIES_0_CODE: lyric.overture - MAESTRO_REPOSITORIES_0_NAME: Overture Lyric + MAESTRO_REPOSITORIES_0_CODE: sample + MAESTRO_REPOSITORIES_0_NAME: sample lyric MAESTRO_REPOSITORIES_0_PAGINATION_SIZE: 50 - MAESTRO_REPOSITORIES_0_INDEX_NAME: datatable1-index + MAESTRO_REPOSITORIES_0_INDEX_NAME: sample-index MAESTRO_REPOSITORIES_0_TYPE: LYRIC MAESTRO_REPOSITORIES_0_LYRIC_VALID_DATA_ONLY: true - MAESTRO_REPOSITORIES_0_LYRIC_CATEGORY_ID: 1 + MAESTRO_REPOSITORIES_0_LYRIC_CATEGORY_ID: 2 + # sample + MAESTRO_REPOSITORIES_1_BASE_URL: http://lyric:3030 + MAESTRO_REPOSITORIES_1_CODE: idmapping + MAESTRO_REPOSITORIES_1_NAME: idmapping Lyric + MAESTRO_REPOSITORIES_1_PAGINATION_SIZE: 50 + MAESTRO_REPOSITORIES_1_INDEX_NAME: idmapping-index + MAESTRO_REPOSITORIES_1_TYPE: LYRIC + MAESTRO_REPOSITORIES_1_LYRIC_VALID_DATA_ONLY: true + MAESTRO_REPOSITORIES_1_LYRIC_CATEGORY_ID: 1 + # summary + MAESTRO_REPOSITORIES_2_BASE_URL: http://lyric:3030 + MAESTRO_REPOSITORIES_2_CODE: summary + MAESTRO_REPOSITORIES_2_NAME: Summary Lyric + MAESTRO_REPOSITORIES_2_PAGINATION_SIZE: 50 + MAESTRO_REPOSITORIES_2_INDEX_NAME: summary-index + MAESTRO_REPOSITORIES_2_TYPE: LYRIC + MAESTRO_REPOSITORIES_2_LYRIC_VALID_DATA_ONLY: true + MAESTRO_REPOSITORIES_2_LYRIC_CATEGORY_ID: 3 # Elasticsearch Settings (Required) MAESTRO_ELASTICSEARCH_NODES: http://elasticsearch:9200 MAESTRO_ELASTICSEARCH_VERSION: 7 @@ -461,16 +529,16 @@ services: MAESTRO_ELASTICSEARCH_CLIENT_DOCS_PER_BULK_REQ_MAX: 5000 MAESTRO_ELASTICSEARCH_CLIENT_CONNECTION_TIMEOUT: 5000 # Repository Configuration - Song - MAESTRO_REPOSITORIES_1_BASE_URL: http://song:8080 - MAESTRO_REPOSITORIES_1_CODE: song.overture - MAESTRO_REPOSITORIES_1_NAME: Overture Song - MAESTRO_REPOSITORIES_1_PAGINATION_SIZE: 50 - MAESTRO_REPOSITORIES_1_INDEX_NAME: file-index - MAESTRO_REPOSITORIES_1_TYPE: SONG - MAESTRO_REPOSITORIES_1_SONG_INDEXABLE_STUDY_STATES: PUBLISHED - MAESTRO_REPOSITORIES_1_SONG_ANALYSIS_CENTRIC_ENABLED: true - MAESTRO_REPOSITORIES_1_SONG_ORGANIZATION: OICR - MAESTRO_REPOSITORIES_1_SONG_COUNTRY: CA + MAESTRO_REPOSITORIES_4_BASE_URL: http://song:8080 + MAESTRO_REPOSITORIES_4_CODE: song.overture + MAESTRO_REPOSITORIES_4_NAME: Overture Song + MAESTRO_REPOSITORIES_4_PAGINATION_SIZE: 50 + MAESTRO_REPOSITORIES_4_INDEX_NAME: file-index + MAESTRO_REPOSITORIES_4_TYPE: SONG + MAESTRO_REPOSITORIES_4_SONG_INDEXABLE_STUDY_STATES: PUBLISHED + MAESTRO_REPOSITORIES_4_SONG_ANALYSIS_CENTRIC_ENABLED: true + MAESTRO_REPOSITORIES_4_SONG_ORGANIZATION: OICR + MAESTRO_REPOSITORIES_4_SONG_COUNTRY: CA volumes: - maestro-data:/app/app-data networks: