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hash = "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96"}, + {file = "isodate-0.6.1.tar.gz", hash = "sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9"}, +] [package.dependencies] six = "*" @@ -928,24 +1671,33 @@ description = "Operations with ISO 8601 durations" category = "main" optional = false python-versions = ">=3.7" +files = [ + {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"}, + {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"}, +] [package.dependencies] arrow = ">=0.15.0" [[package]] name = "jedi" -version = "0.18.1" +version = "0.18.2" description = "An autocompletion tool for Python that can be used for text editors." category = "dev" optional = false python-versions = ">=3.6" +files = [ + {file = "jedi-0.18.2-py2.py3-none-any.whl", hash = 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click = "*" @@ -975,14 +1735,15 @@ pyyaml = "*" [[package]] name = "jsonasobj" -version = "2.0.1" +version = "1.3.1" description = "JSON as python objects" category = "main" optional = false -python-versions = ">=3.6" - -[package.dependencies] -hbreader = "*" +python-versions = "*" +files = [ + {file = "jsonasobj-1.3.1-py3-none-any.whl", hash = "sha256:b9e329dc1ceaae7cf5d5b214684a0b100e0dad0be6d5bbabac281ec35ddeca65"}, + {file = "jsonasobj-1.3.1.tar.gz", hash = "sha256:d52e0544a54a08f6ea3f77fa3387271e3648655e0eace2f21e825c26370e44a2"}, +] [[package]] name = "jsonasobj2" @@ -991,6 +1752,10 @@ description = "JSON as python objects - version 2" category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "jsonasobj2-1.0.4-py3-none-any.whl", hash = "sha256:12e86f86324d54fcf60632db94ea74488d5314e3da554c994fe1e2c6f29acb79"}, + {file = "jsonasobj2-1.0.4.tar.gz", hash = "sha256:f50b1668ef478004aa487b2d2d094c304e5cb6b79337809f4a1f2975cc7fbb4e"}, +] [package.dependencies] 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-ipykernel = [] -ipython = [] -ipython-genutils = [] -ipywidgets = [] -isodate = [] -isoduration = [] -jedi = [] -jinja2 = [] -json-flattener = [] -jsonasobj = [] -jsonasobj2 = [] -jsonpatch = [] -jsonpath-ng = [] -jsonpointer = [] -jsonschema = [] -jupyter = [] -jupyter-client = [] -jupyter-console = [] -jupyter-core = [] -jupyter-server = [] -jupyterlab-pygments = [] -jupyterlab-widgets = [] -kgcl-rdflib = [] -kgcl-schema = [] -lark = [] -linkml = [] -linkml-dataops = [] -linkml-runtime = [] -lxml = [] -markdown = [] -markdown-it-py = [] -markupsafe = [] -matplotlib-inline = [] -mdit-py-plugins = [] -mdurl = [] -mergedeep = [] -mistune = [] -mkdocs = [] -more-click = [] -multidict = [] -mypy-extensions = [] -myst-parser = [] -nbclassic = [] -nbclient = [] -nbconvert = [] -nbformat = [] -nest-asyncio = [] -networkx = [] -notebook = [] -notebook-shim = [] -num2words = [] -numpy = [] -nxontology = [] -oaklib = [] -oauthlib = [] -ols-client = [] -ontodev-cogs = [] -ontoportal-client = [] -openpyxl = [] -packaging = [] -pandas = [] -pandasql = [] -pandera = [] -pandocfilters = [] -parse = [] -parso = [] -pexpect = [] -pickleshare = [] -platformdirs = [] -pluggy = [] -ply = [] -prefixcommons = [] -prefixmaps = [] -prometheus-client = [] -prompt-toolkit = [] -pronto = [] -protobuf = [] -psutil = [] -psycopg2-binary = [] -ptyprocess = [] -pure-eval = [] -py = [] -pyarrow = [] -pyasn1 = [] -pyasn1-modules = [] -pycparser = [] -pydantic = [] -pygments = [] -pyjsg = [] -pyparsing = [] -pyrsistent = [] -pyshex = [] -pyshexc = [] -pystow = [] -pytest = [] -pytest-logging = [] -python-dateutil = [] -pytrie = [] -pytz = [] -pywin32 = [] -pywinpty = [] -pyyaml = [] -pyyaml-env-tag = [] -pyzmq = [] -qtconsole = [] -qtpy = [] -quantulum3 = [] -ratelimit = [] -rdflib = [] -rdflib-jsonld = [] -rdflib-shim = [] -requests = [] -requests-oauthlib = [] -rfc3339-validator = [] -rfc3987 = [] -rsa = [] -"ruamel.yaml" = [] -"ruamel.yaml.clib" = [] -schemasheets = [] -scipy = [] -semsql = [] -send2trash = [] -shexjsg = [] -six = [] -sniffio = [] -snowballstemmer = [] -sortedcontainers = [] -soupsieve = [] -sparqlslurper = [] -sparqlwrapper = [] -sphinx = [] -sphinx-click = [] -sphinx-pdj-theme = [] -sphinx-rtd-theme = [] -sphinxcontrib-applehelp = [] -sphinxcontrib-devhelp = [] -sphinxcontrib-htmlhelp = [] -sphinxcontrib-jsmath = [] -sphinxcontrib-mermaid = [] -sphinxcontrib-qthelp = [] -sphinxcontrib-serializinghtml = [] -sqlalchemy = [] -sqlalchemy-utils = [] -sssom = [] -sssom-schema = [] -stack-data = [] -strsimpy = [] -tabulate = [] -termcolor = [] -terminado = [] -tinycss2 = [] -tomli = [] -tomlkit = [] -tornado = [] -tox = [] -tqdm = [] -traitlets = [] -typing-extensions = [] -typing-inspect = [] -uri-template = [] -uritemplate = [] -urllib3 = [] -validators = [] -virtualenv = [] -watchdog = [] -wcwidth = [] -webcolors = [] -webencodings = [] -websocket-client = [] -widgetsnbextension = [] -wrapt = [] -xmltodict = [] -yarl = [] -zipp = [] +content-hash = "f0d199db033932f20a37cce0255a6115dcd3f0eac484a41dafb578dcf185d076" diff --git a/pyproject.toml b/pyproject.toml index 917a15d..4358a4f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ packages = [ [tool.poetry.dependencies] python = "^3.9" -linkml = "^1.3.5" +linkml = ">=1.5.4" mkdocs = "^1.2.3" pandas = "^1.3.5" python-dateutil = "^2.8.2" diff --git a/schema_automator/cli.py b/schema_automator/cli.py index fbce81f..ccd5bc3 100644 --- a/schema_automator/cli.py +++ b/schema_automator/cli.py @@ -13,7 +13,7 @@ from linkml_runtime.linkml_model import SchemaDefinition from oaklib.selector import get_resource_from_shorthand, get_implementation_from_shorthand -from schema_automator import JsonLdAnnotator +from schema_automator import JsonLdAnnotator, FrictionlessImportEngine from schema_automator.annotators.schema_annotator import SchemaAnnotator from schema_automator.generalizers.csv_data_generalizer import CsvDataGeneralizer from schema_automator.generalizers.generalizer import DEFAULT_CLASS_NAME, DEFAULT_SCHEMA_NAME @@ -44,6 +44,9 @@ default=DEFAULT_SCHEMA_NAME, show_default=True, help='Schema name') +schema_id_option = click.option( + '--schema-id', + help='Schema id') annotator_option = click.option( '--annotator', '-A', @@ -52,6 +55,18 @@ "--use-attributes/--no-use-attributes", help="If true, use attributes over slots/slot_usage" ) +column_separator_option = click.option('--column-separator', '-s', default='\t', help='separator') + +# generalizer options + +downcase_header_option = click.option('--downcase-header/--no-downcase-header', default=False, help='if true make headers lowercase') +snakecase_header_option = click.option('--snakecase-header/--no-snakecase-header', default=False, help='if true make headers snakecase') +infer_foreign_keys_option = click.option('--infer-foreign-keys/--no-infer-foreign-keys', default=False, help='infer ranges/foreign keys') +enum_columns_option = click.option('--enum-columns', '-E', multiple=True, help='column(s) that is forced to be an enum') +enum_mask_columns_option = click.option('--enum-mask-columns', multiple=True, help='column(s) that are excluded from being enums') +max_enum_size_option = click.option('--max-enum-size', default=50, help='do not create an enum if more than max distinct members') +enum_threshold_option = click.option('--enum-threshold', default=0.1, help='if the number of distinct values / rows is less than this, do not make an enum') + @click.group() @click.option("-v", "--verbose", @@ -89,13 +104,12 @@ def main(verbose: int, quiet: bool): @schema_name_option @annotator_option @click.option('--class-name', '-c', default=DEFAULT_CLASS_NAME, help='Core class name in schema') -@click.option('--column-separator', '-s', default='\t', help='separator') -@click.option('--downcase-header/--no-downcase-header', default=False, help='if true make headers lowercase') -@click.option('--enum-columns', '-E', multiple=True, help='column that is forced to be an enum') -@click.option('--enum-threshold', type=click.FLOAT, help='set high to be more inclusive') -@click.option('--max-enum-size', - type=click.INT, - help='set high to be more inclusive') +@column_separator_option +@downcase_header_option +@snakecase_header_option +@enum_columns_option +@enum_threshold_option +@max_enum_size_option @click.option('--data-dictionary-row-count', type=click.INT, help='rows that provide metadata about columns') @@ -128,13 +142,12 @@ def generalize_tsv(tsvfile, output, class_name, schema_name, pandera: bool, anno @click.argument('tsvfiles', nargs=-1) # input TSV (must have column headers @output_option @schema_name_option -@click.option('--column-separator', '-s', default='\t', help='separator') -@click.option('--downcase-header/--no-downcase-header', default=False, help='if true make headers lowercase') -@click.option('--infer-foreign-keys/--no-infer-foreign-keys', default=False, help='infer ranges/foreign keys') -@click.option('--enum-columns', '-E', multiple=True, help='column(s) that is forced to be an enum') -@click.option('--enum-mask-columns', multiple=True, help='column(s) that are excluded from being enums') -@click.option('--max-enum-size', default=50, help='do not create an enum if more than max distinct members') -@click.option('--enum-threshold', default=0.1, help='if the number of distinct values / rows is less than this, do not make an enum') +@column_separator_option +@downcase_header_option +@snakecase_header_option +@enum_columns_option +@enum_threshold_option +@max_enum_size_option @click.option('--robot/--no-robot', default=False, help='set if the TSV is a ROBOT template') def generalize_tsvs(tsvfiles, output, schema_name, **kwargs): """ @@ -157,6 +170,12 @@ def generalize_tsvs(tsvfiles, output, schema_name, **kwargs): @click.argument('url') # input TSV (must have column headers @output_option @schema_name_option +@column_separator_option +@downcase_header_option +@snakecase_header_option +@enum_columns_option +@enum_threshold_option +@max_enum_size_option @click.option('--class-name', '-c', default=DEFAULT_CLASS_NAME, help='Core class name in schema') @click.option('--pandera/--no-pandera', default=False, help='set to use panderas as inference engine') @click.option('--data-output', help='Path to file of downloaded data') @@ -179,8 +198,13 @@ def generalize_htmltable(url, output, class_name, schema_name, pandera: bool, dfs = pd.read_html(url) logging.info(f"{url} has {len(dfs)} tables") df = dfs[table_number] - importer = TableImportEngine(**kwargs) - schema = importer.import_from_dataframe(df) + if data_output: + df.to_csv(data_output, index=False, sep="\t") + if pandera: + ge = PandasDataGeneralizer(**kwargs) + else: + ge = CsvDataGeneralizer(**kwargs) + schema = ge.convert_from_dataframe(df, class_name=class_name, schema_name=schema_name) write_schema(schema, output) @@ -241,13 +265,15 @@ def import_htmltable(url, output, class_name, schema_name, columns, table_number: int, data_output, **kwargs): """ - Generalizes from a table parsed from a URL + Imports from a table parsed from a URL using SchemaSheets Uses pandas/beautiful soup """ dfs = pd.read_html(url) logging.info(f"{url} has {len(dfs)} tables") df = dfs[table_number] + if data_output: + df.to_csv(data_output, index=False, sep="\t") ie = TableImportEngine(columns=columns.split(","), **kwargs) schema = ie.import_from_dataframe(df) write_schema(schema, output) @@ -339,6 +365,26 @@ def import_json_schema(input, output, import_project: bool, schema_name, format, ie.import_project(input, output, name=schema_name, format=format) +@main.command() +@click.argument('input') +@output_option +@schema_name_option +@schema_id_option +def import_frictionless(input, output, schema_name, schema_id, **kwargs): + """ + Imports from Frictionless data package to LinkML + + See :ref:`importers` for more on the importer framework + + Example: + + schemauto import-frictionless cfde.package.json + """ + ie = FrictionlessImportEngine(**kwargs) + schema = ie.convert(input, name=schema_name, id=schema_id) + write_schema(schema, output) + + @main.command() @click.argument('owlfile') @output_option @@ -428,7 +474,7 @@ def generalize_rdf(rdffile, dir, output, **args): @output_option def annotate_schema(schema: str, input: str, output: str, **kwargs): """ - Annotate all elements of a schema + Annotate all elements of a schema. This uses OAK (https://incatools.github.io/ontology-access-kit), and you can provide any OAK backend that supports text annotation. @@ -471,6 +517,10 @@ def enrich_schema(schema: str, input: str, output: str, annotate: bool, **args): """ Enrich a schema using an ontology. + Here, "enrich" means copying over metadata from the ontology to the schema. + For example, if the schema has a class "Gene" that is mapped to a SO class for "gene", + then calling this command will copy the SO class definition to the schema class. + This will use OAK to add additional metadata using uris and mappings in the schema. For example, if your schema has a class with a mapping to a SO class, diff --git a/schema_automator/generalizers/csv_data_generalizer.py b/schema_automator/generalizers/csv_data_generalizer.py index b5e5376..cb8c6e8 100644 --- a/schema_automator/generalizers/csv_data_generalizer.py +++ b/schema_automator/generalizers/csv_data_generalizer.py @@ -15,6 +15,7 @@ from linkml_runtime import SchemaView from linkml_runtime.linkml_model import SchemaDefinition, ClassDefinition, TypeDefinition, SlotDefinition from linkml_runtime.linkml_model.meta import UniqueKey +from linkml_runtime.utils.formatutils import underscore from quantulum3 import parser as q_parser from dataclasses import dataclass, field @@ -93,6 +94,9 @@ class CsvDataGeneralizer(Generalizer): downcase_header: bool = False """If true, coerce column names to be lower case""" + snakecase_header: bool = False + """If true, coerce column names to be snake case""" + infer_foreign_keys: bool = False """For multi-CVS files, infer linkages between rows""" @@ -127,10 +131,14 @@ def infer_linkages(self, files: List[str], **kwargs) -> List[ForeignKey]: c = os.path.splitext(os.path.basename(file))[0] if self.downcase_header: c = c.lower() + if self.snakecase_header: + c = underscore(c) logging.info(f'READING {file} ') df = pd.read_csv(file, sep=self.column_separator, skipinitialspace=True).fillna("") if self.downcase_header: df = df.rename(columns=str.lower) + if self.snakecase_header: + df = df.rename(columns=underscore) exclude = [] for col in df.columns: vals = set(df[col].tolist()) @@ -242,6 +250,8 @@ def convert_multiple(self, files: List[str], **kwargs) -> SchemaDefinition: c = os.path.splitext(os.path.basename(file))[0] if self.downcase_header: c = c.lower() + if self.snakecase_header: + c = underscore(c) s = self.convert(file, class_name=c, **kwargs) if s is not None: schemas.append(s) @@ -267,6 +277,16 @@ def convert(self, file: str, **kwargs) -> SchemaDefinition: rr = csv.DictReader(tsv_file, fieldnames=header, delimiter=self.column_separator, skipinitialspace=False) return self.convert_dicts([r for r in rr], **kwargs) + def convert_from_dataframe(self, df: pd.DataFrame, **kwargs) -> SchemaDefinition: + """ + Converts a single dataframe to a single-class schema + + :param df: + :param kwargs: + :return: + """ + return self.convert_dicts(df.to_dict('records'), **kwargs) + def read_slot_tsv(self, file: str, **kwargs) -> Dict: with open(file, newline='') as tsv_file: rows_list = csv.reader(tsv_file, delimiter=self.column_separator) @@ -359,6 +379,8 @@ def convert_dicts(self, for row in rr: if self.downcase_header: row = {k.lower(): v for k, v in row.items()} + if self.snakecase_header: + row = {underscore(k): v for k, v in row.items()} n += 1 if n == 1 and self.robot: for k, v in row.items(): @@ -784,60 +806,5 @@ def add_missing_to_schema(schema: SchemaDefinition): description='Holds a measurement serialized as a string') -@click.group() -def main(): - pass - - -@main.command() -@click.argument('tsvfile') # input TSV (must have column headers -@click.option('--output', '-o', help='Output file') -@click.option('--class_name', '-c', default='example', help='Core class name in schema') -@click.option('--schema_name', '-n', default='example', help='Schema name') -@click.option('--separator', '-s', default='\t', help='separator') -@click.option('--downcase-header/--no-downcase-header', default=False, help='if true make headers lowercase') -@click.option('--enum-columns', '-E', multiple=True, help='column that is forced to be an enum') -@click.option('--robot/--no-robot', default=False, help='set if the TSV is a ROBOT template') -def tsv2model(tsvfile, output, separator, class_name, schema_name, **kwargs): - """ Infer a model from a TSV """ - ie = CsvDataGeneralizer(**kwargs) - schema = ie.convert(tsvfile, class_name=class_name, schema_name=schema_name) - write_schema(schema, output) - - -@main.command() -@click.argument('tsvfiles', nargs=-1) # input TSV (must have column headers -@click.option('--output', '-o', help='Output file') -@click.option('--schema_name', '-n', default='example', help='Schema name') -@click.option('--file_separator', '-s', default='\t', help='separator') -@click.option('--downcase-header/--no-downcase-header', default=False, help='if true make headers lowercase') -@click.option('--infer-foreign-keys/--no-infer-foreign-keys', default=False, help='infer ranges/foreign keys') -@click.option('--enum-columns', '-E', multiple=True, help='column(s) that is forced to be an enum') -@click.option('--enum-mask-columns', multiple=True, help='column(s) that are excluded from being enums') -@click.option('--max-enum-size', default=50, help='do not create an enum if more than max distinct members') -@click.option('--enum-threshold', default=0.1, help='if the number of distinct values / rows is less than this, do not make an enum') -@click.option('--robot/--no-robot', default=False, help='set if the TSV is a ROBOT template') -def tsvs2model(tsvfiles, output, schema_name, **kwargs): - """ Infer a model from multiple TSVs """ - ie = CsvDataGeneralizer(**kwargs) - schema = ie.convert_multiple(tsvfiles, schema_name=schema_name) - write_schema(schema, output) - - -@main.command() -@click.argument('yamlfile') -@click.option('--zooma-confidence', '-Z', help='zooma confidence') -@click.option('--results', '-r', help='mapping results file') -def enrich(yamlfile, results, **args): - """ Infer a model from a TSV """ - yamlobj = yaml.load(open(yamlfile)) - cache = {} - infer_enum_meanings(yamlobj, cache=cache) - if results is not None: - with open(results, "w") as io: - io.write(yaml.dump(cache)) - print(yaml.dump(yamlobj, default_flow_style=False, sort_keys=False)) - - if __name__ == '__main__': main() diff --git a/schema_automator/importers/frictionless_import_engine.py b/schema_automator/importers/frictionless_import_engine.py index 14a9d79..3c3e57e 100644 --- a/schema_automator/importers/frictionless_import_engine.py +++ b/schema_automator/importers/frictionless_import_engine.py @@ -46,7 +46,7 @@ class FrictionlessImportEngine(ImportEngine): """ - def convert(self, file: str, id: str,name: str, **kwargs) -> SchemaDefinition: + def convert(self, file: str, id: str=None, name: str=None, **kwargs) -> SchemaDefinition: """ Converts one or more JSON files into a Schema @@ -59,8 +59,6 @@ def convert(self, file: str, id: str,name: str, **kwargs) -> SchemaDefinition: schema = sb.schema if id: schema.id = id - if name: - sb.add_prefix(name, f"{id}/") if not name: name = package.name if name: @@ -128,7 +126,7 @@ def add_enum(self, sb: SchemaBuilder, field: fl.Field) -> EnumDefinition: if len(toks) == 2: [prefix, short] = toks pv = PermissibleValue(short, meaning=code) - sb.add_prefix(prefix, f"{sb.schema.id}/{prefix}/") + sb.add_prefix(prefix, f"{sb.schema.id}/{prefix}/", replace_if_present=True) e.permissible_values[pv.text] = pv if e.name is sb.schema: raise NotImplementedError(f"Cannot yet merge enums") diff --git a/schema_automator/importers/rdfs_import_engine.py b/schema_automator/importers/rdfs_import_engine.py index e67da6d..c1ef959 100644 --- a/schema_automator/importers/rdfs_import_engine.py +++ b/schema_automator/importers/rdfs_import_engine.py @@ -104,13 +104,14 @@ def convert( if name is None: name = "example" sb = SchemaBuilder(name=name) + sb.add_defaults() schema = sb.schema for k, v in g.namespaces(): - sb.add_prefix(k, v) + sb.add_prefix(k, v, replace_if_present=True) if default_prefix is not None: schema.default_prefix = default_prefix if default_prefix not in schema.prefixes: - sb.add_prefix(default_prefix, model_uri) + sb.add_prefix(default_prefix, model_uri, replace_if_present=True) schema.id = schema.prefixes[default_prefix].prefix_reference cls_slots = defaultdict(list) props = [] @@ -155,7 +156,6 @@ def convert( c.slots = cls_slots.get(cn, []) c.class_uri = str(s.n3(g.namespace_manager)) sb.add_class(c) - sb.add_defaults() if identifier is not None: id_slot = SlotDefinition(identifier, identifier=True, range="uriorcurie") schema.slots[identifier] = id_slot diff --git a/schema_automator/importers/tabular_import_engine.py b/schema_automator/importers/tabular_import_engine.py index 9ab9e9f..4c6dfc9 100644 --- a/schema_automator/importers/tabular_import_engine.py +++ b/schema_automator/importers/tabular_import_engine.py @@ -40,6 +40,9 @@ def import_from_dataframe(self, df: pd.DataFrame): :return: """ tf = NamedTemporaryFile(delete=False) + if not self.columns: + raise ValueError("Must specify columns") + logging.info(f"Using columns: {self.columns}") ix = 1 line = pd.DataFrame(dict(zip(df.head(), self.columns)), index=[ix]) df = pd.concat([df.iloc[:ix-1], line, df.iloc[ix-1:]]).reset_index(drop=True) @@ -47,7 +50,6 @@ def import_from_dataframe(self, df: pd.DataFrame): df.insert(0, column="parent", value=[f">{self.element_type}"] + [self.parent] * (len(df) - 1)) - #print(df) df.to_csv(tf.name, sep='\t', index=False) #print(open(tf.name, 'r').read()) #element_map = dict(zip(df.head(), self.columns)) diff --git a/tests/resources/C2M2_datapackage.json b/tests/resources/C2M2_datapackage.json index bac869b..79db41c 100644 --- a/tests/resources/C2M2_datapackage.json +++ b/tests/resources/C2M2_datapackage.json @@ -88,6 +88,7 @@ "description": "A filename with no prepended PATH information", "type": "string", "constraints": { + "required": true, "pattern": "^[^\/\\:]+$" } }, @@ -258,7 +259,7 @@ "format": "any" }, { - "name": "assay_type", + "name": "sample_prep_method", "description": "An OBI CV term ID (from the 'planned process' branch of the vocabulary, excluding the 'assay' subtree) describing the preparation method that produced this biosample", "type": "string" }, @@ -286,9 +287,9 @@ } }, { - "fields": "assay_type", + "fields": "sample_prep_method", "reference": { - "resource": "assay_type", + "resource": "sample_prep_method", "fields": "id" } }, @@ -384,9 +385,7 @@ "cfde_subject_sex:0", "cfde_subject_sex:1", "cfde_subject_sex:2", - "cfde_subject_sex:3", - "cfde_subject_sex:4", - "cfde_subject_sex:5" + "cfde_subject_sex:3" ] }, { @@ -2483,7 +2482,9 @@ "cfde_subject_race:1", "cfde_subject_race:2", "cfde_subject_race:3", - "cfde_subject_race:4" + "cfde_subject_race:4", + "cfde_subject_race:5", + "cfde_subject_race:6" ] } ], @@ -2597,7 +2598,7 @@ "skipInitialSpace": true, "header": true }, - "description": "List of Ontology for Biomedical Investigations (OBI) CV terms used to describe types of experiment that generate C2M2 biosamples or results stored in C2M2 files", + "description": "List of Ontology for Biomedical Investigations (OBI) CV terms used to describe types of experiment that generate results stored in C2M2 files", "schema": { "fields": [ { @@ -3264,6 +3265,53 @@ ] } }, + { + "profile": "tabular-data-resource", + "name": "sample_prep_method", + "title": "sample_prep_method", + "path": "sample_prep_method.tsv", + "dialect": { + "delimiter": "\t", + "doubleQuote": false, + "lineTerminator": "\n", + "skipInitialSpace": true, + "header": true + }, + "description": "List of Ontology for Biomedical Investigations (OBI) CV terms used to describe types of preparation methods that produce C2M2 biosamples", + "schema": { + "fields": [ + { + "name": "id", + "description": "An OBI CV term", + "type": "string", + "constraints": { + "required": true, + "unique": true + } + }, + { + "name": "name", + "description": "A short, human-readable, machine-read-friendly label for this OBI term", + "type": "string", + "constraints": { + "required": true + } + }, + { + "name": "description", + "description": "A human-readable description of this OBI term", + "type": "string" + }, + { + "name": "synonyms", + "description": "A list of synonyms for this term as identified by the OBI metadata", + "type": "array" + } + ], + "missingValues": [ "" ], + "primaryKey": "id" + } + }, { "profile": "tabular-data-resource", "name": "id_namespace", diff --git a/tests/test_importers/test_sql_importer.py b/tests/test_importers/test_sql_importer.py index 531505d..2cbe60d 100644 --- a/tests/test_importers/test_sql_importer.py +++ b/tests/test_importers/test_sql_importer.py @@ -35,9 +35,9 @@ def setUp(self) -> None: sb = SchemaBuilder() sb.add_class('Person', ['id', 'name', 'email', 'age', 'knows']) - sb.add_slot(SlotDefinition('id', identifier=True)) - sb.add_slot(SlotDefinition('age', range='integer')) - sb.add_slot(SlotDefinition('knows', range='Person', multivalued=True)) + sb.add_slot(SlotDefinition('id', identifier=True), replace_if_present=True) + sb.add_slot(SlotDefinition('age', range='integer'), replace_if_present=True) + sb.add_slot(SlotDefinition('knows', range='Person', multivalued=True), replace_if_present=True) sb.add_defaults() schema = sb.schema #print(yaml_dumper.dumps(schema)) @@ -67,7 +67,11 @@ def test_from_sql(self): for c in schemaview.all_classes().values(): self.assertIn(c.name, schemaview_rt.all_classes()) for s in schemaview.class_induced_slots(c.name): - self.assertIn(s.name, schemaview_rt.all_slots()) + if s.name == "knows": + # these slots are moved to join tables + self.assertNotIn(s.name, schemaview_rt.all_slots().keys()) + else: + self.assertIn(s.name, schemaview_rt.all_slots().keys()) person = schemaview_rt.get_class('Person') person_knows_join = schemaview_rt.get_class('Person_knows') id_slot = person.attributes['id'] @@ -75,7 +79,7 @@ def test_from_sql(self): self.assertTrue(id_slot.identifier) self.assertEqual('integer', age_slot.range) self.assertEqual('Person', person_knows_join.attributes['Person_id'].range) - self.assertEqual('Person', person_knows_join.attributes['knows'].range) + self.assertEqual('Person', person_knows_join.attributes['knows_id'].range) diff --git a/tests/test_importers/test_tabular_importer.py b/tests/test_importers/test_tabular_importer.py index 0368c77..84cf92b 100644 --- a/tests/test_importers/test_tabular_importer.py +++ b/tests/test_importers/test_tabular_importer.py @@ -3,7 +3,6 @@ import unittest import os from pathlib import Path -from sys import platform import pandas as pd @@ -21,7 +20,7 @@ class TestTableImporter(unittest.TestCase): def setUp(self) -> None: pass - def test_import(self): + def test_html_import(self): """ Test importing a table from HTML via BS """ @@ -37,3 +36,4 @@ def test_import(self): +