From 4658d32698ec9b72869bf71cffdc7bc49bcf4072 Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Wed, 19 Apr 2023 13:11:19 -0700 Subject: [PATCH 1/5] Add support for limiting the solr schema to a "top class" --- Pipfile | 23 - linkml_solr/cli.py | 23 +- linkml_solr/query.py | 9 +- linkml_solr/solrschemagen.py | 6 + poetry.lock | 1705 +++++++++++++++++----------------- pyproject.toml | 8 +- 6 files changed, 907 insertions(+), 867 deletions(-) delete mode 100644 Pipfile diff --git a/Pipfile b/Pipfile deleted file mode 100644 index 346e6ed..0000000 --- a/Pipfile +++ /dev/null @@ -1,23 +0,0 @@ -[[source]] -url = "https://pypi.org/simple" -verify_ssl = true -name = "pypi" - -[packages] -linkml = "*" -linkml-runtime = ">=1.1.24" -linkml-dataops = "*" -pyparsing = "~=2.4" -sparqlwrapper = "*" -pysolr = "*" -requests = "*" -flatten-dict = "*" -linkml-solr = {editable = true, path = "."} -json-flattener = ">= 0.1.7" - -[dev-packages] -tox = "*" -linkml-solr = {editable = true, path = "."} - -[pipenv] -allow_prereleases = true diff --git a/linkml_solr/cli.py b/linkml_solr/cli.py index 3fa2842..afd3ba2 100644 --- a/linkml_solr/cli.py +++ b/linkml_solr/cli.py @@ -4,6 +4,7 @@ import logging import subprocess +from linkml_runtime.dumpers import YAMLDumper from linkml_runtime.linkml_model import SchemaDefinition from linkml_runtime.loaders import yaml_loader from linkml_solr import SolrQueryEngine, SolrEndpoint, DEFAULT_CORE, DEFAULT_SOLR_URL @@ -163,7 +164,19 @@ def add_cores(cores, schema, container, url, port): default=DEFAULT_SOLR_URL, show_default=True, help='solr url.') -def create_schema(schema, url, core): +@click.option('--debug', + default=False, + is_flag=True, + help='Print generated schema to stdout rather before loading into Solr.') +@click.option('--dry-run', + default=False, + is_flag=True, + help='Generate schema but do not load into Solr.') +@click.option('--top-class', '-t', + default=None, + show_default=True, + help='Solr document in this core is one instance of this class') +def create_schema(schema, url, core, debug, dry_run, top_class): """ Creates a solr schema from a LinkML schema """ @@ -171,8 +184,12 @@ def create_schema(schema, url, core): from linkml.generators.yamlgen import YAMLGenerator schema_obj = YAMLGenerator(schema).schema qe = SolrQueryEngine(schema=schema_obj, - endpoint=SolrEndpoint(url=f'{url}/{core}')) - qe.load_schema() + endpoint=SolrEndpoint(url=f'{url}/{core}'), + top_class=top_class) + + gen = qe.load_schema(dry_run=dry_run) + if debug: + print(gen.serialize()) if __name__ == '__main__': diff --git a/linkml_solr/query.py b/linkml_solr/query.py index 7281e3d..7f26563 100644 --- a/linkml_solr/query.py +++ b/linkml_solr/query.py @@ -36,6 +36,7 @@ class SolrQueryEngine(QueryEngine): mapper: LinkMLMapper = None discriminator_field: SlotDefinitionName = None python_classes: List[Type[YAMLRoot]] = None + top_class: str = None def __post_init__(self): # TODO: use schemaview @@ -256,7 +257,7 @@ def _get_fieldtypes(self, strict=True): obj = self._response_json(response, strict=strict) return [f['name'] for f in obj.get('fieldTypes', [])] - def load_schema(self): + def load_schema(self, dry_run: bool = False) -> SolrSchemaGenerator: """ Adds a schema to SOLR corresponding to a LinkML schema """ @@ -275,10 +276,10 @@ def load_schema(self): 'name': 'date', 'class': 'solr.TrieDateField', }}, path='schema') - gen = SolrSchemaGenerator(self.schema) + gen = SolrSchemaGenerator(self.schema, top_class=self.top_class) gen.serialize() post_obj = gen.post_request for f in post_obj['add-field']: - if f['name'] not in existing_fields: + if f['name'] not in existing_fields and not dry_run: self._solr_request({'add-field': f}, path='schema') - + return gen diff --git a/linkml_solr/solrschemagen.py b/linkml_solr/solrschemagen.py index 9da0eb6..49ffe6b 100644 --- a/linkml_solr/solrschemagen.py +++ b/linkml_solr/solrschemagen.py @@ -79,6 +79,8 @@ def get_transaction(self, class_name: Union[str, ClassDefinitionName] = None) -> sv = self.schemaview field_dict = {} for cn, c in sv.all_classes().items(): + if self.topCls is not None and str(cn) != str(self.topCls): + continue if class_name is None or str(cn) == str(class_name): for s in sv.class_induced_slots(cn): field = self.get_field(s) @@ -109,6 +111,10 @@ def get_field(self, slot: SlotDefinition) -> Field: @shared_arguments(SolrSchemaGenerator) +@click.option('--top-class', '-t', + default=None, + show_default=True, + help='Solr document in this core is one instance of this class') @click.command() def cli(yamlfile, **kwargs): """ Generate SOLR Schema representation of a LinkML model """ diff --git a/poetry.lock b/poetry.lock index 3869a87..4fa9b60 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,5 @@ +# This file is automatically @generated by Poetry and should not be changed by hand. + [[package]] name = "alabaster" version = "0.7.12" @@ -5,6 +7,10 @@ description = "A configurable sidebar-enabled Sphinx theme" category = "main" optional = false python-versions = "*" +files = [ + {file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"}, + {file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"}, +] [[package]] name = "antlr4-python3-runtime" @@ -13,14 +19,25 @@ description = "ANTLR 4.9.3 runtime for Python 3.7" category = "main" optional = false python-versions = "*" +files = [ + {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, +] [[package]] -name = "argparse" -version = "1.4.0" -description = "Python command-line parsing library" +name = "arrow" +version = "1.2.3" +description = "Better dates & times for Python" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.6" +files = [ + {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, + {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, +] + +[package.dependencies] +python-dateutil = ">=2.7.0" +typing-extensions = {version = "*", markers = "python_version < \"3.8\""} [[package]] name = "attrs" @@ -29,12 +46,16 @@ description = "Classes Without Boilerplate" category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +files = [ + {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"}, + {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"}, +] [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] -docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] +dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "sphinx", "sphinx-notfound-page", "zope.interface"] +docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] +tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "zope.interface"] +tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six"] [[package]] name = "babel" @@ -43,10 +64,26 @@ description = "Internationalization utilities" category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "Babel-2.10.1-py3-none-any.whl", hash = "sha256:3f349e85ad3154559ac4930c3918247d319f21910d5ce4b25d439ed8693b98d2"}, + {file = "Babel-2.10.1.tar.gz", hash = "sha256:98aeaca086133efb3e1e2aad0396987490c8425929ddbcfe0550184fdc54cd13"}, +] [package.dependencies] pytz = ">=2015.7" +[[package]] +name = "cached-property" +version = "1.5.2" +description = "A decorator for caching properties in classes." +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "cached-property-1.5.2.tar.gz", hash = "sha256:9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130"}, + {file = "cached_property-1.5.2-py2.py3-none-any.whl", hash = "sha256:df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0"}, +] + [[package]] name = "certifi" version = "2021.10.8" @@ -54,6 +91,10 @@ description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false python-versions = "*" +files = [ + {file = "certifi-2021.10.8-py2.py3-none-any.whl", hash = "sha256:d62a0163eb4c2344ac042ab2bdf75399a71a2d8c7d47eac2e2ee91b9d6339569"}, + {file = "certifi-2021.10.8.tar.gz", hash = "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"}, +] [[package]] name = "cfgraph" @@ -62,6 +103,9 @@ description = "rdflib collections flattening graph" category = "main" optional = false python-versions = "*" +files = [ + {file = "CFGraph-0.2.1.tar.gz", hash = "sha256:b57fe7044a10b8ff65aa3a8a8ddc7d4cd77bf511b42e57289cd52cbc29f8fe74"}, +] [package.dependencies] rdflib = ">=0.4.2" @@ -73,6 +117,10 @@ description = "Universal encoding detector for Python 2 and 3" category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +files = [ + {file = "chardet-4.0.0-py2.py3-none-any.whl", hash = "sha256:f864054d66fd9118f2e67044ac8981a54775ec5b67aed0441892edb553d21da5"}, + 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Open, modern and activ category = "main" optional = false python-versions = ">=3.5.0" +files = [ + {file = "charset-normalizer-2.0.12.tar.gz", hash = "sha256:2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597"}, + {file = "charset_normalizer-2.0.12-py3-none-any.whl", hash = "sha256:6881edbebdb17b39b4eaaa821b438bf6eddffb4468cf344f09f89def34a8b1df"}, +] [package.extras] -unicode_backport = ["unicodedata2"] +unicode-backport = ["unicodedata2"] [[package]] name = "click" @@ -92,6 +144,10 @@ description = "Composable command line interface toolkit" category = "main" optional = false python-versions = ">=3.7" +files = [ + {file = "click-8.1.2-py3-none-any.whl", hash = "sha256:24e1a4a9ec5bf6299411369b208c1df2188d9eb8d916302fe6bf03faed227f1e"}, + {file = "click-8.1.2.tar.gz", hash = "sha256:479707fe14d9ec9a0757618b7a100a0ae4c4e236fac5b7f80ca68028141a1a72"}, +] [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} @@ -104,6 +160,10 @@ 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"pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] + +[metadata] +lock-version = "2.0" +python-versions = "^3.7.6" +content-hash = "531bfaba71e70f465ed2be406fdf63a83941aca80aa8c058c767dd1e70960574" diff --git a/pyproject.toml b/pyproject.toml index 1886f35..1778bd3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,15 +1,15 @@ [tool.poetry] name = "linkml-solr" -version = "0.1.3" +version = "0.1.4" description = "" -authors = ["Chris Mungall "] +authors = ["Chris Mungall ", "Kevin Schaper Date: Wed, 19 Apr 2023 13:18:00 -0700 Subject: [PATCH 2/5] Update linkml --- poetry.lock | 183 ++++++++++++++++++++++++++++++++++++++++--------- pyproject.toml | 2 +- 2 files changed, 151 insertions(+), 34 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4fa9b60..213255d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. [[package]] name = "alabaster" @@ -139,14 +139,14 @@ unicode-backport = ["unicodedata2"] [[package]] name = "click" -version = "8.1.2" +version = "8.1.3" description = "Composable command line interface toolkit" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "click-8.1.2-py3-none-any.whl", hash = "sha256:24e1a4a9ec5bf6299411369b208c1df2188d9eb8d916302fe6bf03faed227f1e"}, - {file = "click-8.1.2.tar.gz", hash = "sha256:479707fe14d9ec9a0757618b7a100a0ae4c4e236fac5b7f80ca68028141a1a72"}, + {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"}, + {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"}, ] [package.dependencies] @@ -165,6 +165,31 @@ files = [ {file = "colorama-0.4.4.tar.gz", hash = "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b"}, ] +[[package]] +name = "curies" +version = "0.4.5" +description = "Idiomatic conversion between URIs and compact URIs (CURIEs)." +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "curies-0.4.5-py3-none-any.whl", hash = "sha256:73281f6616ec47c8d46d842def7a2021416c9ac10f580f9116125abf4bd2f943"}, + {file = "curies-0.4.5.tar.gz", hash = "sha256:c01626183b520db1b4af6a1fd41ee6d02462fea4ce54d8c5a528e5782268589c"}, +] + +[package.dependencies] +pytrie = "*" +requests = "*" + +[package.extras] +bioregistry = ["bioregistry (>=0.5.136)"] +docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-theme"] +fastapi = ["fastapi", "httpx"] +flask = ["flask"] +pandas = ["pandas"] +rdflib = ["rdflib"] +tests = ["coverage", "pytest"] + [[package]] name = "decorator" version = "5.1.1" @@ -231,6 +256,21 @@ files = [ {file = "et_xmlfile-1.1.0.tar.gz", hash = "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c"}, ] +[[package]] +name = "exceptiongroup" +version = "1.1.1" +description = "Backport of PEP 654 (exception groups)" +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "exceptiongroup-1.1.1-py3-none-any.whl", hash = "sha256:232c37c63e4f682982c8b6459f33a8981039e5fb8756b2074364e5055c498c9e"}, + {file = "exceptiongroup-1.1.1.tar.gz", hash = "sha256:d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785"}, +] + +[package.extras] +test = ["pytest (>=6)"] + [[package]] name = "filelock" version = "3.6.0" @@ -423,6 +463,18 @@ zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"] testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +[[package]] +name = "iniconfig" +version = "2.0.0" +description = "brain-dead simple config-ini parsing" +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"}, + {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, +] + [[package]] name = "isodate" version = "0.6.1" @@ -595,14 +647,14 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "linkml" -version = "1.4.2" +version = "1.5.0" description = "Linked Open Data Modeling Language" category = "main" optional = false python-versions = ">=3.7.6,<4.0.0" files = [ - {file = "linkml-1.4.2-py3-none-any.whl", hash = "sha256:4fd809a56b34b3489ae9180bc83f74a66dcac26fd00eebf294b10a8ad2527086"}, - {file = "linkml-1.4.2.tar.gz", hash = "sha256:f4eefa657c13ddb279402db9f7660acafdf2d021c17ae2fa3c36b274832dfe21"}, + {file = "linkml-1.5.0-py3-none-any.whl", hash = "sha256:8f8d23f7f7bd6a10a5130d28ea576f7ceccd14e123ad4c0365bb53bc58664ba0"}, + {file = "linkml-1.5.0.tar.gz", hash = "sha256:120fac9dd5a27d3dabc5e45fdeaf0b2fe187fe5f59bf7bc0806ebb5a884e6942"}, ] [package.dependencies] @@ -615,7 +667,7 @@ jinja2 = ">=3.1.0" jsonasobj2 = ">=1.0.3,<2.0.0" jsonschema = {version = ">=4.0.0", extras = ["format"]} linkml-dataops = "*" -linkml-runtime = ">=1,<2" +linkml-runtime = ">=1.5.0" myst-parser = "*" openpyxl = "*" parse = "*" @@ -659,24 +711,26 @@ linkml-runtime = ">=1.1.6" [[package]] name = "linkml-runtime" -version = "1.2.7" +version = "1.5.1" description = "Runtime environment for LinkML, the Linked open data modeling language" category = "main" optional = false -python-versions = ">=3.7.1,<4.0.0" +python-versions = ">=3.7.6,<4.0.0" files = [ - {file = "linkml_runtime-1.2.7-py3-none-any.whl", hash = "sha256:ba02d958af88ebc3eff8b521adb61b89049ced91523d637543dffe1493ae9900"}, - {file = "linkml_runtime-1.2.7.tar.gz", hash = "sha256:8fa7d89a370217759a4e1c883c9da17e3dbb4144e55cfc5a4bd3d69b66b66d3e"}, + {file = "linkml_runtime-1.5.1-py3-none-any.whl", hash = "sha256:1ae23259500d7fde465313547d8be33049fc071857e6c546b5212b23a9bf0016"}, + {file = "linkml_runtime-1.5.1.tar.gz", hash = "sha256:fd5cdd6403ae5e087e1e5e4023542a6da6e6df4538e9b516c30d6315f8be61dc"}, ] [package.dependencies] click = "*" +curies = ">=0.4.0,<0.5.0" deprecated = "*" hbreader = "*" json-flattener = ">=0.1.9" jsonasobj2 = ">=1.0.4,<2.0.0" jsonschema = ">=3.2.0" -prefixcommons = "*" +prefixcommons = ">=0.1.12" +prefixmaps = ">=0.1.4" pyyaml = "*" rdflib = ">=6.0.0" requests = "*" @@ -906,22 +960,21 @@ files = [ [[package]] name = "prefixcommons" -version = "0.1.9" -description = "Library for working prefixcommons.org CURIEs" +version = "0.1.12" +description = "A python API for working with ID prefixes" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.7,<4.0" files = [ - {file = "prefixcommons-0.1.9-py3-none-any.whl", hash = "sha256:2ff99e9f2c27f41e6beb831742ca88ddae129b2de6dcc81b0b27f0de69cb2e8a"}, - {file = "prefixcommons-0.1.9.tar.gz", hash = "sha256:a4a6decd6c1a2497b2b10193fa4ed69ed91cea20deb3a9781815b6bf3f3e1003"}, + {file = "prefixcommons-0.1.12-py3-none-any.whl", hash = "sha256:16dbc0a1f775e003c724f19a694fcfa3174608f5c8b0e893d494cf8098ac7f8b"}, + {file = "prefixcommons-0.1.12.tar.gz", hash = "sha256:22c4e2d37b63487b3ab48f0495b70f14564cb346a15220f23919eb0c1851f69f"}, ] [package.dependencies] -pyyaml = "*" -requests = "*" - -[package.extras] -test = ["pytest"] +click = ">=8.1.3,<9.0.0" +pytest-logging = ">=2015.11.4,<2016.0.0" +PyYAML = ">=6.0,<7.0" +requests = ">=2.28.1,<3.0.0" [[package]] name = "prefixmaps" @@ -1137,6 +1190,44 @@ requests = ">=2.9.1" [package.extras] solrcloud = ["kazoo (>=2.5.0)"] +[[package]] +name = "pytest" +version = "7.3.1" +description = "pytest: simple powerful testing with Python" +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "pytest-7.3.1-py3-none-any.whl", hash = "sha256:3799fa815351fea3a5e96ac7e503a96fa51cc9942c3753cda7651b93c1cfa362"}, + {file = "pytest-7.3.1.tar.gz", hash = "sha256:434afafd78b1d78ed0addf160ad2b77a30d35d4bdf8af234fe621919d9ed15e3"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "sys_platform == \"win32\""} +exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} +importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} +iniconfig = "*" +packaging = "*" +pluggy = ">=0.12,<2.0" +tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} + +[package.extras] +testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"] + +[[package]] +name = "pytest-logging" +version = "2015.11.4" +description = "Configures logging and allows tweaking the log level with a py.test flag" +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "pytest-logging-2015.11.4.tar.gz", hash = "sha256:cec5c85ecf18aab7b2ead5498a31b9f758680ef5a902b9054ab3f2bdbb77c896"}, +] + +[package.dependencies] +pytest = ">=2.8.1" + [[package]] name = "python-dateutil" version = "2.8.2" @@ -1152,6 +1243,20 @@ files = [ [package.dependencies] six = ">=1.5" +[[package]] +name = "pytrie" +version = "0.4.0" +description = "A pure Python implementation of the trie data structure." +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "PyTrie-0.4.0.tar.gz", hash = "sha256:8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379"}, +] + +[package.dependencies] +sortedcontainers = "*" + [[package]] name = "pytz" version = "2022.1" @@ -1270,25 +1375,25 @@ rdflib-jsonld = "0.6.1" [[package]] name = "requests" -version = "2.27.1" +version = "2.28.2" description = "Python HTTP for Humans." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">=3.7, <4" files = [ - {file = "requests-2.27.1-py2.py3-none-any.whl", hash = "sha256:f22fa1e554c9ddfd16e6e41ac79759e17be9e492b3587efa038054674760e72d"}, - {file = "requests-2.27.1.tar.gz", hash = "sha256:68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61"}, + {file = "requests-2.28.2-py3-none-any.whl", hash = "sha256:64299f4909223da747622c030b781c0d7811e359c37124b4bd368fb8c6518baa"}, + {file = "requests-2.28.2.tar.gz", hash = "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf"}, ] [package.dependencies] certifi = ">=2017.4.17" -charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""} -idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""} +charset-normalizer = ">=2,<4" +idna = ">=2.5,<4" urllib3 = ">=1.21.1,<1.27" [package.extras] -socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] -use-chardet-on-py3 = ["chardet (>=3.0.2,<5)"] +socks = ["PySocks (>=1.5.6,!=1.5.7)"] +use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "rfc3339-validator" @@ -1432,6 +1537,18 @@ files = [ {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"}, ] +[[package]] +name = "sortedcontainers" +version = "2.4.0" +description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "sortedcontainers-2.4.0-py2.py3-none-any.whl", hash = "sha256:a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0"}, + {file = "sortedcontainers-2.4.0.tar.gz", hash = "sha256:25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88"}, +] + [[package]] name = "sparqlslurper" version = "0.5.1" @@ -1684,7 +1801,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} +greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and platform_machine == \"aarch64\" or python_version >= \"3\" and platform_machine == \"ppc64le\" or python_version >= \"3\" and platform_machine == \"x86_64\" or python_version >= \"3\" and platform_machine == \"amd64\" or python_version >= \"3\" and platform_machine == \"AMD64\" or python_version >= \"3\" and platform_machine == \"win32\" or python_version >= \"3\" and platform_machine == \"WIN32\""} importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} [package.extras] @@ -1956,4 +2073,4 @@ testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>= [metadata] lock-version = "2.0" python-versions = "^3.7.6" -content-hash = "531bfaba71e70f465ed2be406fdf63a83941aca80aa8c058c767dd1e70960574" +content-hash = "bc4af5ea2a5c276c40aef6ac1612d93990c933ae4e2eee7ca20133341b7ac731" diff --git a/pyproject.toml b/pyproject.toml index 1778bd3..d1c7a69 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ lsolr = "linkml_solr.cli:main" [tool.poetry.dependencies] python = "^3.7.6" -linkml = "^1.4.2" +linkml = "^1.5.0" linkml-runtime = "^1.2.7" pysolr = "^3.9.0" linkml-dataops = "^0.1.0" From 4b898c7c7a46af06d05cde51ed276d21f9c52f3c Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Wed, 19 Apr 2023 13:28:22 -0700 Subject: [PATCH 3/5] Fix python version in action --- .github/workflows/main.yaml | 2 +- .github/workflows/pr-test.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 0045b9d..a9650a1 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -10,7 +10,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.7.4, 3.8, 3.9] + python-version: [3.7.6, 3.8, 3.9] steps: - uses: actions/checkout@v2 diff --git a/.github/workflows/pr-test.yaml b/.github/workflows/pr-test.yaml index 254f858..752ea25 100644 --- a/.github/workflows/pr-test.yaml +++ b/.github/workflows/pr-test.yaml @@ -10,7 +10,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [ 3.7.5, 3.8, 3.9 ] + python-version: [ 3.7.6, 3.8, 3.9 ] steps: - uses: actions/checkout@v2 - name: Set up Python ${{ matrix.python-version }} From f0450b422bc846b3298dc128ef15f28b3c53993f Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Wed, 25 Oct 2023 10:04:21 -0700 Subject: [PATCH 4/5] Update PR test version: py3.7 off of the bottom and add 3.10 --- .github/workflows/pr-test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pr-test.yaml b/.github/workflows/pr-test.yaml index 752ea25..1a6831a 100644 --- a/.github/workflows/pr-test.yaml +++ b/.github/workflows/pr-test.yaml @@ -10,7 +10,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [ 3.7.6, 3.8, 3.9 ] + python-version: [ 3.8, 3.9, 3.10 ] steps: - uses: actions/checkout@v2 - name: Set up Python ${{ matrix.python-version }} From 747ec7772752ee596638c94e54269b65804cb0a9 Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Wed, 25 Oct 2023 10:07:28 -0700 Subject: [PATCH 5/5] see how 3.8, 3.9 works, then figure out why 3.10 is bringing in 3.1 in the gh action --- .github/workflows/pr-test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pr-test.yaml b/.github/workflows/pr-test.yaml index 1a6831a..31262fb 100644 --- a/.github/workflows/pr-test.yaml +++ b/.github/workflows/pr-test.yaml @@ -10,7 +10,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [ 3.8, 3.9, 3.10 ] + python-version: [ 3.8, 3.9] steps: - uses: actions/checkout@v2 - name: Set up Python ${{ matrix.python-version }}