From ba4eff16b0a2f378e9fde6ec850ed15d3480052d Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Wed, 13 Nov 2019 10:30:17 -0500 Subject: [PATCH 1/3] add optional build variables for git repo versions --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index bad02c964..e80c54634 100644 --- a/Dockerfile +++ b/Dockerfile @@ -60,8 +60,8 @@ RUN rm /quip/config-update/tac_lite.settings.yml COPY content/* /quip/content/ # download caMicroscope WORKDIR /quip/web -RUN git clone https://github.com/camicroscope/caMicroscope.git --branch=v3.5.9 -RUN git clone https://github.com/SBU-BMI/FeatureMap --branch=2.0.3 +RUN if [ -z ${viewer} ]; then git clone https://github.com/camicroscope/caMicroscope.git --branch=v3.5.10; else git clone https://github.com/camicroscope/caMicroscope.git --branch=$viewer; fi +RUN if [ -z ${featureMap} ]; then git clone https://github.com/SBU-BMI/FeatureMap --branch=2.0.3; else git clone https://github.com/SBU-BMI/FeatureMap --branch=$featureMap; fi RUN rm /etc/httpd/conf.d/ssl.conf RUN chmod 755 /root/run.sh RUN yum update -y && yum clean all From 9802953061e184bfd82a70137e4f6cd662a1fab1 Mon Sep 17 00:00:00 2001 From: Ryan Birmingham Date: Wed, 13 Nov 2019 10:57:01 -0500 Subject: [PATCH 2/3] Update Dockerfile --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index e80c54634..98e0f1df5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -60,7 +60,9 @@ RUN rm /quip/config-update/tac_lite.settings.yml COPY content/* /quip/content/ # download caMicroscope WORKDIR /quip/web +ARG viewer RUN if [ -z ${viewer} ]; then git clone https://github.com/camicroscope/caMicroscope.git --branch=v3.5.10; else git clone https://github.com/camicroscope/caMicroscope.git --branch=$viewer; fi +ARG featureMap RUN if [ -z ${featureMap} ]; then git clone https://github.com/SBU-BMI/FeatureMap --branch=2.0.3; else git clone https://github.com/SBU-BMI/FeatureMap --branch=$featureMap; fi RUN rm /etc/httpd/conf.d/ssl.conf RUN chmod 755 /root/run.sh From 4ede0ac43983e55896b3635889711a3c5691fb6d Mon Sep 17 00:00:00 2001 From: ebremer Date: Thu, 14 Nov 2019 18:57:49 -0500 Subject: [PATCH 3/3] fix links on list of images make collection facet alphabetical --- config/facets.facet.collection.yml | 6 -- config/views.view.listofimages.yml | 130 ++++++++++++++--------------- 2 files changed, 65 insertions(+), 71 deletions(-) diff --git a/config/facets.facet.collection.yml b/config/facets.facet.collection.yml index 4c607a99a..0e2166f3c 100644 --- a/config/facets.facet.collection.yml +++ b/config/facets.facet.collection.yml @@ -40,12 +40,6 @@ processor_configs: sort: 20 settings: sort: DESC - count_widget_order: - processor_id: count_widget_order - weights: - sort: 30 - settings: - sort: DESC display_value_widget_order: processor_id: display_value_widget_order weights: diff --git a/config/views.view.listofimages.yml b/config/views.view.listofimages.yml index 848f0484f..d20290e29 100644 --- a/config/views.view.listofimages.yml +++ b/config/views.view.listofimages.yml @@ -162,18 +162,18 @@ display: options: view_mode: teaser fields: - field_collection_1: - id: field_collection_1 - table: node__field_collection - field: field_collection + nid_3: + id: nid_3 + table: node_field_data + field: nid relationship: none group_type: group admin_label: '' - label: CollectionID + label: ID exclude: true alter: - alter_text: true - text: '{{ field_collection_1__target_id }}' + alter_text: false + text: '' make_link: false path: '' absolute: false @@ -210,11 +210,12 @@ display: hide_empty: false empty_zero: false hide_alter_empty: true - click_sort_column: target_id - type: entity_reference_label + click_sort_column: value + type: number_integer settings: - link: false - group_column: target_id + thousand_separator: '' + prefix_suffix: true + group_column: value group_columns: { } group_rows: true delta_limit: 0 @@ -224,19 +225,21 @@ display: multi_type: separator separator: ', ' field_api_classes: false + entity_type: node + entity_field: nid plugin_id: field - field_collection: - id: field_collection + field_collection_1: + id: field_collection_1 table: node__field_collection field: field_collection relationship: none group_type: group - admin_label: Collection - label: Collection - exclude: false + admin_label: '' + label: CollectionID + exclude: true alter: - alter_text: false - text: '' + alter_text: true + text: '{{ field_collection_1__target_id }}' make_link: false path: '' absolute: false @@ -288,14 +291,14 @@ display: separator: ', ' field_api_classes: false plugin_id: field - studyid: - id: studyid - table: node__studyid - field: studyid + field_collection: + id: field_collection + table: node__field_collection + field: field_collection relationship: none group_type: group - admin_label: '' - label: 'Study ID' + admin_label: Collection + label: Collection exclude: false alter: alter_text: false @@ -336,11 +339,11 @@ display: hide_empty: false empty_zero: false hide_alter_empty: true - click_sort_column: value - type: string + click_sort_column: target_id + type: entity_reference_label settings: - link_to_entity: false - group_column: value + link: false + group_column: target_id group_columns: { } group_rows: true delta_limit: 0 @@ -351,14 +354,14 @@ display: separator: ', ' field_api_classes: false plugin_id: field - clinicaltrialsubjectid: - id: clinicaltrialsubjectid - table: node__clinicaltrialsubjectid - field: clinicaltrialsubjectid + studyid: + id: studyid + table: node__studyid + field: studyid relationship: none group_type: group admin_label: '' - label: 'Subject ID' + label: 'Study ID' exclude: false alter: alter_text: false @@ -414,14 +417,14 @@ display: separator: ', ' field_api_classes: false plugin_id: field - imageid: - id: imageid - table: node__imageid - field: imageid + clinicaltrialsubjectid: + id: clinicaltrialsubjectid + table: node__clinicaltrialsubjectid + field: clinicaltrialsubjectid relationship: none group_type: group admin_label: '' - label: 'Image ID' + label: 'Subject ID' exclude: false alter: alter_text: false @@ -465,7 +468,7 @@ display: click_sort_column: value type: string settings: - link_to_entity: true + link_to_entity: false group_column: value group_columns: { } group_rows: true @@ -477,21 +480,21 @@ display: separator: ', ' field_api_classes: false plugin_id: field - nid: - id: nid - table: node_field_data - field: nid + imageid: + id: imageid + table: node__imageid + field: imageid relationship: none group_type: group admin_label: '' - label: View + label: 'Image ID' exclude: false alter: - alter_text: true - text: caMic + alter_text: false + text: '' make_link: true - path: '/caMicroscope/apps/viewer/viewer.html?slideId={{nid}}&mode=pathdb' - absolute: true + path: '/caMicroscope/apps/viewer/viewer.html?slideId={{nid_3}}&mode=pathdb' + absolute: false external: false replace_spaces: false path_case: none @@ -526,10 +529,9 @@ display: empty_zero: false hide_alter_empty: true click_sort_column: value - type: number_integer + type: string settings: - thousand_separator: '' - prefix_suffix: true + link_to_entity: false group_column: value group_columns: { } group_rows: true @@ -540,23 +542,21 @@ display: multi_type: separator separator: ', ' field_api_classes: false - entity_type: node - entity_field: nid plugin_id: field - nid_1: - id: nid_1 + nid: + id: nid table: node_field_data field: nid relationship: none group_type: group admin_label: '' - label: Map - exclude: true + label: '' + exclude: false alter: alter_text: true - text: 'Add Map' + text: Meta make_link: true - path: '/node/add/map?edit[field_wsi][widget][0][target_id]={{nid_1}}' + path: '/node/{{nid}}' absolute: true external: false replace_spaces: false @@ -583,7 +583,7 @@ display: element_class: '' element_label_type: '' element_label_class: '' - element_label_colon: true + element_label_colon: false element_wrapper_type: '' element_wrapper_class: '' element_default_classes: true @@ -594,8 +594,8 @@ display: click_sort_column: value type: number_integer settings: - thousand_separator: '' - prefix_suffix: true + thousand_separator: . + prefix_suffix: false group_column: value group_columns: { } group_rows: true @@ -616,13 +616,13 @@ display: relationship: none group_type: group admin_label: '' - label: Maps + label: '' exclude: false alter: alter_text: true text: Maps make_link: true - path: '/maps/{{ nid_1 }}' + path: '/maps/{{ nid_2 }}' absolute: false external: false replace_spaces: false @@ -649,7 +649,7 @@ display: element_class: '' element_label_type: '' element_label_class: '' - element_label_colon: true + element_label_colon: false element_wrapper_type: '' element_wrapper_class: '' element_default_classes: true