New Feature: SNOMED::ICD10CM Mapping Support

- Added feature to allow for conversion of these premade mappings provided by SNOMED into SSSOM format. (WIP)

General updates
- cli.py: Reorganized SSSOM_READ_FORMATS: Top half are plain data formats, and bottom half are special-case formats. Both halves of the list are alphabetically sorted.

Tentative updates
- Changed some relative imports to absolute imports, in order to speed up development and make debugging easier. It is possible that this could be a good permanent change too, though.

Dev updates
- requirements-unlocked.txt: Unversioned variation of requirements.txt
- requirements.txt: Included this because I don't know if setup.py is sufficient to install packages in a standalone dev environment. Also, it is shown to be expected in the documentation: https://mapping-commons.github.io/sssom-py/installation.html#installation-for-developers

Author: joeflack4

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

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

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())

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"]