From a35afc951dfae477106b6ddc9bbec08145e47c51 Mon Sep 17 00:00:00 2001 From: cmungall Date: Fri, 26 Aug 2022 15:33:14 -0700 Subject: [PATCH 1/2] bumping linkml version --- poetry.lock | 272 ++++++++++--------------------------------------- pyproject.toml | 2 +- 2 files changed, 54 insertions(+), 220 deletions(-) diff --git a/poetry.lock b/poetry.lock index e6ab7d0..07fff23 100644 --- a/poetry.lock +++ b/poetry.lock @@ -227,7 +227,7 @@ python-versions = "*" python-dateutil = ">=2.8.1" [package.extras] -dev = ["twine", "markdown", "flake8", "wheel"] +dev = ["wheel", "flake8", "markdown", "twine"] [[package]] name = "google" @@ -542,7 +542,7 @@ format_nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "linkml" -version = "1.2.16" +version = "1.3.2" description = "Linked Open Data Modeling Language" category = "main" optional = false @@ -559,7 +559,7 @@ jinja2 = "*" jsonasobj2 = ">=1.0.3,<2.0.0" jsonschema = ">=3.0.1" linkml-dataops = "*" -linkml-runtime = "1.2.21" +linkml-runtime = ">=1.3.0,<2.0.0" myst-parser = "*" openpyxl = "*" parse = "*" @@ -596,7 +596,7 @@ linkml-runtime = ">=1.1.6" [[package]] name = "linkml-runtime" -version = "1.2.21" +version = "1.3.2" description = "Runtime environment for LinkML, the Linked open data modeling language" category = "main" optional = false @@ -641,13 +641,13 @@ attrs = ">=19,<22" mdurl = ">=0.1,<1.0" [package.extras] -benchmarking = ["psutil", "pytest", "pytest-benchmark (>=3.2,<4.0)"] -code_style = ["pre-commit (==2.6)"] -compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.2.2,<3.3.0)", "mistletoe-ebp (>=0.10.0,<0.11.0)", "mistune (>=0.8.4,<0.9.0)", "panflute (>=1.12,<2.0)"] -linkify = ["linkify-it-py (>=1.0,<2.0)"] +testing = ["pytest-regressions", "pytest-cov", "pytest", "coverage"] +rtd = ["sphinx-book-theme", "sphinx-panels (>=0.4.0,<0.5.0)", "sphinx-copybutton", "sphinx (>=2,<4)", "pyyaml", "myst-nb (==0.13.0a1)"] plugins = ["mdit-py-plugins"] -rtd = ["myst-nb (==0.13.0a1)", "pyyaml", "sphinx (>=2,<4)", "sphinx-copybutton", "sphinx-panels (>=0.4.0,<0.5.0)", "sphinx-book-theme"] -testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] +linkify = ["linkify-it-py (>=1.0,<2.0)"] +compare = ["panflute (>=1.12,<2.0)", "mistune (>=0.8.4,<0.9.0)", "mistletoe-ebp (>=0.10.0,<0.11.0)", "markdown (>=3.2.2,<3.3.0)", "commonmark (>=0.9.1,<0.10.0)"] +code_style = ["pre-commit (==2.6)"] +benchmarking = ["pytest-benchmark (>=3.2,<4.0)", "pytest", "psutil"] [[package]] name = "markupsafe" @@ -984,11 +984,11 @@ requests = "*" tqdm = "*" [package.extras] -aws = ["boto3"] -docs = ["sphinx", "sphinx-rtd-theme", "sphinx-click", "sphinx-autodoc-typehints", "sphinx-automodapi"] -pandas = ["pandas"] -rdf = ["rdflib"] xml = ["lxml"] +rdf = ["rdflib"] +pandas = ["pandas"] +docs = ["sphinx-automodapi", "sphinx-autodoc-typehints", "sphinx-click", "sphinx-rtd-theme", "sphinx"] +aws = ["boto3"] [[package]] name = "pytest" @@ -1496,18 +1496,12 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest- [metadata] lock-version = "1.1" python-versions = "^3.9" -content-hash = "8dbfe73d5284fb8564abd1cc3dda7331716ba0267c504ad5463600ec33a776fa" +content-hash = "285dc735643ee2239a6c774016aa36061f102230ef151636a3b49c8d73a702c5" [metadata.files] -alabaster = [ - 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schemasheets/schemasheet_datamodel.py | 6 +- tests/test_headers.py | 121 ++++++++++++++++++++++++++ 3 files changed, 126 insertions(+), 2 deletions(-) create mode 100644 tests/test_headers.py diff --git a/schemasheets/schemamaker.py b/schemasheets/schemamaker.py index edf0c1c..edff3fa 100644 --- a/schemasheets/schemamaker.py +++ b/schemasheets/schemamaker.py @@ -144,7 +144,6 @@ def add_row(self, row: Dict[str, Any], table_config: TableConfig): for ann_key, ann_val in anns.items(): actual_element.annotations[ann_key] = ann_val elif isinstance(v, list): - #print(f'SETTING {k} to {v}') setattr(actual_element, cc.maps_to, getattr(actual_element, cc.maps_to, []) + v) elif isinstance(v, dict): for v_k, v_v in v.items(): diff --git a/schemasheets/schemasheet_datamodel.py b/schemasheets/schemasheet_datamodel.py index fcd11ac..d6f6364 100644 --- a/schemasheets/schemasheet_datamodel.py +++ b/schemasheets/schemasheet_datamodel.py @@ -95,7 +95,11 @@ def add_info(self, info: Union[Dict, DESCRIPTOR]) -> None: snmap = mm.slot_name_mappings() # TODO: use alias snmap['uri'] = snmap['type_uri'] - if self.maps_to in snmap: + if self.maps_to.startswith("metaslot."): + maps_to = self.maps_to.replace("metaslot.", "") + self.metaslot = snmap[maps_to] + self.maps_to = maps_to + elif self.maps_to in snmap and self.maps_to != 'type': self.metaslot = snmap[self.maps_to] else: if self.maps_to not in tmap and self.maps_to not in Shortcuts: diff --git a/tests/test_headers.py b/tests/test_headers.py new file mode 100644 index 0000000..1eadd68 --- /dev/null +++ b/tests/test_headers.py @@ -0,0 +1,121 @@ +from schemasheets.schemasheet_datamodel import SchemaSheet + +RECORD = "Record" +FIELD = "Field" +METATYPE = "MetaType" +INFO = "Info" +CV = "CV" +PV = "PV" +SDO_MAPPINGS = "schema.org" +WD_MAPPINGS = "wikidata" +DATATYPE = "Datatype" + +CASES = [ + (1, + [ + { + RECORD: "> class", + INFO: " description", + SDO_MAPPINGS: "exact_mappings: {curie_prefix: sdo}", + WD_MAPPINGS: "exact_mappings" + }, + { + RECORD: ">", + WD_MAPPINGS: "curie_prefix: wd" + }, + ] + ), + (2, + [ + {RECORD: "> class", FIELD: " slot", INFO: " description"}, + ] + ), + (3, + [ + {METATYPE: "> metatype", INFO: " description"}, + ] + ), + (4, + [ + {CV: "> enum", PV: "permissible_value", INFO: " description"}, + ] + ), + (5, + [ + {DATATYPE: "> type", INFO: " description"}, + ] + ), + (6, + [ + {DATATYPE: "> metaslot.type", INFO: " description"}, + ] + ), +] + +def test_parse_header(): + print() + for case_id, case in CASES: + ss = SchemaSheet.from_dictreader(case) + tc = ss.table_config + info_cc = tc.columns[INFO] + assert info_cc.name == INFO + assert info_cc.maps_to == "description" + assert info_cc.metaslot is not None + assert info_cc.metaslot.name == "description" + if case_id == 1 or case_id == 2: + assert tc.metatype_column is None + record_cc = tc.columns[RECORD] + assert record_cc.name == RECORD + assert record_cc.maps_to == "class" + assert record_cc.metaslot is None + if case_id == 2: + field_cc = tc.columns[FIELD] + assert field_cc.name == FIELD + assert field_cc.maps_to == "slot" + assert field_cc.metaslot is None + if case_id == 1: + sdo_cc = tc.columns[SDO_MAPPINGS] + assert sdo_cc.name == SDO_MAPPINGS + assert sdo_cc.maps_to == "exact_mappings" + assert sdo_cc.metaslot is not None + assert sdo_cc.metaslot.name == "exact mappings" or\ + sdo_cc.metaslot.name == "exact_mappings" + assert sdo_cc.settings.curie_prefix == "sdo" + wd_cc = tc.columns[WD_MAPPINGS] + assert wd_cc.name == WD_MAPPINGS + assert wd_cc.maps_to == "exact_mappings" + assert wd_cc.metaslot is not None + assert wd_cc.metaslot.name == "exact mappings" or \ + wd_cc.metaslot.name == "exact_mappings" + assert wd_cc.settings.curie_prefix == "wd" + if case_id == 3: + assert tc.metatype_column == METATYPE + record_cc = tc.columns[METATYPE] + assert record_cc.name == METATYPE + assert record_cc.maps_to == "metatype" + assert record_cc.metaslot is None + if case_id == 4: + cv_cc = tc.columns[CV] + assert cv_cc.name == CV + assert cv_cc.maps_to == "enum" + assert cv_cc.metaslot is None + pv_cc = tc.columns[PV] + assert pv_cc.name == PV + assert pv_cc.maps_to == "permissible_value" + assert pv_cc.metaslot is None + if case_id == 5: + dt_cc = tc.columns[DATATYPE] + #print(dt_cc) + assert dt_cc.name == DATATYPE + assert dt_cc.maps_to == "type" + assert dt_cc.metaslot is None + if case_id == 6: + # See https://github.com/linkml/schemasheets/issues/75 + dt_cc = tc.columns[DATATYPE] + assert dt_cc.name == DATATYPE + assert dt_cc.maps_to == "type" + assert dt_cc.metaslot is not None + assert dt_cc.metaslot.name == "type" + + +