diff --git a/requirements-unlocked.txt b/requirements-unlocked.txt new file mode 100644 index 00000000..fab79a51 --- /dev/null +++ b/requirements-unlocked.txt @@ -0,0 +1,38 @@ +pyparsing +click +linkml-runtime +networkx +numpy +pandas +pandasql +pyyaml +rdflib +recommonmark +scikit_learn +scipy +setuptools +sparqlwrapper +validators +# joeflack4 2022/02/24: I commented these specific versions out for now because of these errors: +# ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. +# sparqlslurper 0.4.1 requires rdflib~=5.0, but you have rdflib 6.1.1 which is incompatible. +# pyshexc 0.8.3 requires rdflib~=5.0, but you have rdflib 6.1.1 which is incompatible. +# pyshex 0.7.20 requires rdflib~=5.0, but you have rdflib 6.1.1 which is incompatible. +# linkml 1.0.2 requires rdflib~=5.0, but you have rdflib 6.1.1 which is incompatible. +# linkml-model 1.0.0 requires rdflib~=5.0, but you have rdflib 6.1.1 which is incompatible. +# pyparsing==2.4.7 +# click +# linkml-runtime>=1.1.12 +# networkx +# numpy +# pandas +# pandasql +# pyyaml +# rdflib>=6 +# recommonmark>=0.7 +# scikit_learn +# scipy +# setuptools +# sparqlwrapper +# validators +# validators>=0.0 \ No newline at end of file diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..342539fc --- /dev/null +++ b/requirements.txt @@ -0,0 +1,96 @@ +alabaster==0.7.12 +antlr4-python3-runtime==4.9.2 +appdirs==1.4.4 +attrs==21.2.0 +Babel==2.9.1 +cachetools==4.2.2 +certifi==2021.5.30 +CFGraph==0.2.1 +chardet==4.0.0 +charset-normalizer==2.0.3 +click==7.1.2 +commonmark==0.9.1 +decorator==4.4.2 +Deprecated==1.2.12 +distlib==0.3.2 +docutils==0.17.1 +filelock==3.0.12 +frozendict==2.0.3 +graphviz==0.17 +greenlet==1.1.0 +hbreader==0.9.1 +idna==3.2 +imagesize==1.2.0 +iniconfig==1.1.1 +isodate==0.6.0 +Jinja2==3.0.1 +joblib==1.0.1 +json-flattener==0.1.7 +jsonasobj==1.2.1 +jsonasobj2==1.0.4 +jsonschema==3.2.0 +linkml==1.0.2 +linkml-model==1.0.0 +linkml-runtime==1.1.24 +lxml==4.6.3 +MarkupSafe==2.0.1 +networkx==2.5.1 +numpy==1.21.1 +packaging==21.0 +pandas==1.1.5 +pandasql==0.7.3 +parse==1.19.0 +pbr==5.6.0 +pluggy==0.13.1 +prefixcommons==0.1.9 +prologterms==0.0.6 +py==1.10.0 +Pygments==2.9.0 +PyJSG==0.11.6 +PyLD==2.0.3 +PyLDmod==2.0.5 +pyparsing==2.4.7 +pyrsistent==0.18.0 +PyShEx==0.7.20 +PyShExC==0.8.3 +pytest==6.2.4 +python-dateutil==2.8.2 +pytz==2021.1 +PyYAML==5.4.1 +rdflib==6.1.1 +rdflib-jsonld==0.6.1 +rdflib-pyld-compat==0.1.0 +rdflib-pyldmod-compat==0.1.2 +rdflib-shim==1.0.3 +recommonmark==0.7.1 +requests==2.26.0 +scikit-learn==0.24.2 +scipy==1.7.0 +ShExJSG==0.7.1 +six==1.16.0 +snowballstemmer==2.1.0 +sparqlslurper==0.4.1 +SPARQLWrapper==1.8.5 +Sphinx==2.4.4 +sphinx-click==2.3.1 +sphinx-rtd-theme==0.4.3 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==1.4.21 +stevedore==3.3.0 +testfixtures==6.18.0 +threadpoolctl==2.2.0 +toml==0.10.2 +tox==3.23.1 +urllib3==1.26.6 +validators==0.18.2 +virtualenv==20.4.7 +virtualenv-clone==0.5.4 +virtualenvwrapper==4.8.4 +watchdog==2.1.3 +wrapt==1.12.1 +zipp==3.5.0 diff --git a/sssom/cli.py b/sssom/cli.py index a1e0a20b..b4b003e0 100644 --- a/sssom/cli.py +++ b/sssom/cli.py @@ -24,12 +24,12 @@ from rdflib import Graph from scipy.stats import chi2_contingency -from .cliques import split_into_cliques, summarize_cliques -from .io import convert_file, parse_file, split_file, validate_file -from .parsers import read_sssom_table -from .rdf_util import rewire_graph -from .sparql_util import EndpointConfig, query_mappings -from .util import ( +from sssom.cliques import split_into_cliques, summarize_cliques +from sssom.io import convert_file, parse_file, split_file, validate_file +from sssom.parsers import read_sssom_table +from sssom.rdf_util import rewire_graph +from sssom.sparql_util import EndpointConfig, query_mappings +from sssom.util import ( SSSOM_EXPORT_FORMATS, SSSOM_READ_FORMATS, MappingSetDataFrame, @@ -41,7 +41,7 @@ remove_unmatched, to_mapping_set_dataframe, ) -from .writers import write_table +from sssom.writers import write_table # Click input options common across commands input_argument = click.argument("input", required=True, type=click.Path()) diff --git a/sssom/util.py b/sssom/util.py index 6782ba13..2e81bf40 100644 --- a/sssom/util.py +++ b/sssom/util.py @@ -43,12 +43,13 @@ PREFIX_MAP_KEY = "curie_map" SSSOM_READ_FORMATS = [ - "tsv", - "rdf", + "json", "owl", + "rdf", + "tsv", "alignment-api-xml", "obographs-json", - "json", + "snomed-icd10cm-map-tsv" ] SSSOM_EXPORT_FORMATS = ["tsv", "rdf", "owl", "json"]