From bc97b5ba48212fff0e51f7b884aef915b4f66922 Mon Sep 17 00:00:00 2001 From: cmungall Date: Tue, 24 May 2022 15:57:10 -0700 Subject: [PATCH 1/3] Make ontology fed to relation-graph safe for graph walking. See https://github.com/balhoff/relation-graph/issues/130 --- src/semsql/builder/build.Makefile | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/semsql/builder/build.Makefile b/src/semsql/builder/build.Makefile index 1c2284e..bf6cfd3 100644 --- a/src/semsql/builder/build.Makefile +++ b/src/semsql/builder/build.Makefile @@ -38,6 +38,9 @@ $(TEMPLATE): $(THIS_DIR)/sql_schema/semsql.sql mv $@.tmp $@ .PRECIOUS: $(TEMPLATE) +%-min.owl: %.owl + robot remove -i $< --axioms "equivalent disjoint annotation" -o $@ + # -- MAIN TARGET -- # A db is constructed from # (1) triples loaded using rdftab @@ -61,7 +64,7 @@ $(TEMPLATE): $(THIS_DIR)/sql_schema/semsql.sql # will be simplified in future. See: # - https://github.com/balhoff/relation-graph/issues/123 # - https://github.com/balhoff/relation-graph/issues/25 -%-$(RGSUFFIX).tsv: %.owl +%-$(RGSUFFIX).tsv: %-min.owl $(RG) --disable-owl-nothing true \ --ontology-file $<\ --output-file $@.ttl.tmp \ From bd2674f8e0dc0565b6ec4caaedb556475d4dce6b Mon Sep 17 00:00:00 2001 From: cmungall Date: Tue, 24 May 2022 15:59:00 -0700 Subject: [PATCH 2/3] adding view2table --- src/semsql/builder/cli.py | 37 +++++++++++++++++++++++++++++++ src/semsql/sqlutils/view2table.py | 29 ++++++++++-------------- src/semsql/sqlutils/viewgen.py | 3 +-- 3 files changed, 50 insertions(+), 19 deletions(-) diff --git a/src/semsql/builder/cli.py b/src/semsql/builder/cli.py index 587abec..962794b 100644 --- a/src/semsql/builder/cli.py +++ b/src/semsql/builder/cli.py @@ -3,6 +3,9 @@ import click import logging import semsql.builder.builder as builder +from linkml_runtime import SchemaView +from linkml_runtime.utils.formatutils import underscore +from semsql.sqlutils.viewgen import get_viewdef from sqlalchemy import text @@ -68,6 +71,40 @@ def query(input, query): print(row) +@main.command() +@click.argument('inputs', nargs=-1) +@click.option('--index/--no-index', default=True, help='Create indexes on each column') +@click.option('--name', '-n', help='Name of class/view to materialize. If blank, will perform for ALL') +def view2table(inputs, name: str, index: bool): + """ + Generates a command that turns a view into a table + + See https://github.com/cmungall/semantic-sql/issues/9 + + Example usage: + ``` + semsql view2table src/linkml/rdf.yaml -n rdfs_label_statement | sqlite3 db/pato.db + ``` + """ + for input in inputs: + with open(input, 'r') as stream: + sv = SchemaView(input) + schema = sv.schema + for cn, c in sv.all_classes().items(): + tn = underscore(cn) + if name is None or str(cn) == name or tn == name: + view = get_viewdef(c) + if view is not None: + print(f'DROP VIEW {tn};') + print(f'CREATE TABLE {tn} AS {view};') + if index: + for sn in sv.class_slots(cn): + colname = underscore(sn) + print(f'CREATE INDEX {tn}_{colname} ON {tn}({colname});') + else: + logging.error(f'No view for {cn}') + + if __name__ == '__main__': main() diff --git a/src/semsql/sqlutils/view2table.py b/src/semsql/sqlutils/view2table.py index 1f33362..cfd3c82 100644 --- a/src/semsql/sqlutils/view2table.py +++ b/src/semsql/sqlutils/view2table.py @@ -1,19 +1,13 @@ import click from typing import List + +from linkml_runtime import SchemaView from linkml_runtime.linkml_model import SchemaDefinition, ClassDefinitionName, SlotDefinitionName -from linkml.utils.formatutils import underscore -from linkml.utils.schemaloader import SchemaLoader -from semsql import get_viewdef - -def all_slots(schema: SchemaDefinition, cn: ClassDefinitionName) -> List[SlotDefinitionName]: - c = schema.classes[cn] - slots = list(c.slots) - if c.is_a: - slots += all_slots(schema, c.is_a) - if c.mixins: - for m in c.mixins: - slots += all_slots(schema, m) - return slots +from linkml_runtime.utils.formatutils import underscore +from semsql.sqlutils.viewgen import get_viewdef + + + @click.command() @click.argument('inputs', nargs=-1) @@ -32,16 +26,17 @@ def cli(inputs, name: str, index: bool): """ for input in inputs: with open(input, 'r') as stream: - schema = SchemaLoader(input).schema - for cn, c in schema.classes.items(): + sv = SchemaView(input) + schema = sv.schema + for cn, c in sv.all_classes().items(): tn = underscore(cn) if name is None or str(cn) == name or tn == name: - view = get_viewdef(schema, c) + view = get_viewdef(c) if view is not None: print(f'DROP VIEW {tn};') print(f'CREATE TABLE {tn} AS {view};') if index: - for sn in all_slots(schema, cn): + for sn in sv.class_slots(cn): colname = underscore(sn) print(f'CREATE INDEX {tn}_{colname} ON {tn}({colname});') diff --git a/src/semsql/sqlutils/viewgen.py b/src/semsql/sqlutils/viewgen.py index 493c571..75cea01 100644 --- a/src/semsql/sqlutils/viewgen.py +++ b/src/semsql/sqlutils/viewgen.py @@ -1,12 +1,11 @@ import click -from typing import List from linkml_runtime.linkml_model import SchemaDefinition, ClassDefinition from linkml.utils.schemaloader import load_raw_schema, SchemaLoader from linkml_runtime.utils.formatutils import underscore VIEW_CODE = 'sqlview>>' -def get_viewdef(schema: SchemaDefinition, c: ClassDefinition) -> str: +def get_viewdef(c: ClassDefinition) -> str: """ Return all VIEW definitions for a class :param schema: From beb29848d129f7202fed5e15b6fd83d5df6530c8 Mon Sep 17 00:00:00 2001 From: cmungall Date: Tue, 24 May 2022 16:00:01 -0700 Subject: [PATCH 3/3] bump --- poetry.lock | 250 +++++++++++++++++++++++++++---------------------- pyproject.toml | 2 +- 2 files changed, 138 insertions(+), 114 deletions(-) diff --git a/poetry.lock b/poetry.lock index c23d126..988820e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -49,11 +49,11 @@ pytz = ">=2015.7" [[package]] name = "certifi" -version = "2021.10.8" +version = "2022.5.18.1" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false -python-versions = "*" +python-versions = ">=3.6" [[package]] name = "cfgraph" @@ -144,7 +144,7 @@ python-versions = ">=3.6" [[package]] name = "ghp-import" -version = "2.0.2" +version = "2.1.0" description = "Copy your docs directly to the gh-pages branch." category = "dev" optional = false @@ -206,7 +206,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "4.11.3" +version = "4.11.4" description = "Read metadata from Python packages" category = "main" optional = false @@ -220,6 +220,21 @@ docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] perf = ["ipython"] testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] +[[package]] +name = "importlib-resources" +version = "5.7.1" +description = "Read resources from Python packages" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} + +[package.extras] +docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] + [[package]] name = "isodate" version = "0.6.1" @@ -313,7 +328,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "jsonschema" -version = "4.4.0" +version = "4.5.1" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false @@ -321,6 +336,7 @@ python-versions = ">=3.7" [package.dependencies] attrs = ">=17.4.0" +importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""} pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2" [package.extras] @@ -329,7 +345,7 @@ format_nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "linkml" -version = "1.2.10" +version = "1.2.11" description = "Linked Open Data Modeling Language" category = "main" optional = false @@ -346,7 +362,7 @@ jinja2 = "*" jsonasobj2 = ">=1.0.3,<2.0" jsonschema = ">=3.0.1" linkml-dataops = "*" -linkml-runtime = ">=1.2.4,<1.3.0" +linkml-runtime = ">=1.2.12,<1.3.0" myst-parser = "*" openpyxl = "*" pandas = "*" @@ -383,7 +399,7 @@ linkml-runtime = ">=1.1.6" [[package]] name = "linkml-runtime" -version = "1.2.9" +version = "1.2.15" description = "Runtime environment for LinkML, the Linked open data modeling language" category = "main" optional = false @@ -403,7 +419,7 @@ requests = "*" [[package]] name = "markdown" -version = "3.3.6" +version = "3.3.7" description = "Python implementation of Markdown." category = "dev" optional = false @@ -524,7 +540,7 @@ testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest [[package]] name = "numpy" -version = "1.22.3" +version = "1.22.4" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -532,7 +548,7 @@ python-versions = ">=3.8" [[package]] name = "openpyxl" -version = "3.0.9" +version = "3.0.10" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" category = "main" optional = false @@ -606,8 +622,8 @@ test = ["pytest"] [[package]] name = "pydantic" -version = "1.9.0" -description = "Data validation and settings management using python 3.6 type hinting" +version = "1.9.1" +description = "Data validation and settings management using python type hints" category = "main" optional = false python-versions = ">=3.6.1" @@ -641,7 +657,7 @@ jsonasobj = ">=1.2.1" [[package]] name = "pyparsing" -version = "3.0.8" +version = "3.0.9" description = "pyparsing module - Classes and methods to define and execute parsing grammars" category = "main" optional = false @@ -1081,7 +1097,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "watchdog" -version = "2.1.7" +version = "2.1.8" description = "Filesystem events monitoring" category = "main" 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