Implementation of sssom-schema as a package (#264)

* changes w.r.t changing source of truth

* dependency added for `sssom-schema` for tox

* data update

* replaced `match_type` => `mapping_justification`

* provided by `sssom-schema`

* linted

* updated test file

* correct json

* new test file

* new test data as per sssom-schema

* edited as per sssom-schema changes

* formatting

* multivalued_slots is now dynamically deduced

* linted

* flake8 ed

* formatted

* constants moved to one place and refactored

* linted

* linted

* fixed errors

* wrong import

* smarter way of getting multivalued slots

* typo fixed semapv instea  of ssemapv

* deleted

* unnecessary at this point.

* typo

* replace with https://w3id.org/sssom/

* addedprefix map
#  semapv: "https://w3id.org/semapv/"

* linted

* update checkout and setup python versions

* whitelist sssom-schema

* rolled back whitelisting

* dropped 3.7 testing

* rolled back to 3.7

* test

* added self install

* removed unnecessary dependency

* commented

* undid last few commits

* grade unnecessary

* test

* anchored veresion

* testing

* removed version

* undo deps

* refactored

* refactored

* refactored

* removed datamodel and yaml

* test

* fixed in sssom-schema

* explicilty install sssom-schema

* added enum for mapping_justifications

* remove explcit install of sssom-schema

* removed sci-kit learn

* Update cli.py

* switched link back to master branch

Co-authored-by: Nico Matentzoglu <[email protected]>

Author: hrshdhgd

Diff for: .github/workflows/qc.yml

@@ -9,23 +9,23 @@ on:
 
 jobs:
   build:
-
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         python-version: ["3.7", "3.9", "3.10"]
         os: [ ubuntu-latest, windows-latest ]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         pip install --upgrade pip
-        pip install --upgrade tox
+        pip install tox
     - name: Check manifest
       run: tox -e manifest
     - name: Lint with flake8

Diff for: MANIFEST.in

@@ -23,4 +23,4 @@ global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
 exclude odk.bat environment.sh cli.md Makefile tox.ini
 
 # Specific files to include
-include LICENSE sssom/sssom.yaml
+include LICENSE

Diff for: Makefile

@@ -44,8 +44,6 @@ sssom/external_context.py: schema/sssom.external.context.jsonld
 sssom/internal_context.py: schema/sssom.context.jsonld
 	echo "\"\"\"This module contains an autogenerated copy of the internal SSSOM context.\"\"\"" > $@
 	echo "" >> $@
-	echo "# This is autogenerated and super hacky." >> $@
-	echo "multivalued_slots = [\"match_type\", \"creator_id\", \"creator_label\", \"author_id\", \"author_label\", \"reviewer_id\", \"reviewer_label\", \"license\", \"mapping_set_source\", \"subject_match_field\", \"object_match_field\", \"match_string\", \"subject_preprocessing\", \"object_preprocessing\",\"see_also\",]"  >> $@
 	echo "sssom_context = \"\"\""  >> $@
 	cat $< >> $@
 	echo "\"\"\""  >> $@

Diff for: schema/cliquesummary.yaml

@@ -1,14 +1,14 @@
-id: http://w3id.org/sssom/schema/cliquesummary/
+id: https://w3id.org/sssom/schema/cliquesummary/
 name: sssom-cliquesummary
 description: Data dictionary for clique summaries
 imports:
 - biolinkml:types
 prefixes:
   biolinkml: https://w3id.org/biolink/biolinkml/
-  sssom: http://w3id.org/sssom/
-  sssom.cs: http://w3id.org/sssom/cliquesummary
+  sssom: https://w3id.org/sssom/
+  sssom.cs: https://w3id.org/sssom/cliquesummary
 see_also:
-- http://w3id.org/sssom/SSSOM.md
+- https://w3id.org/sssom/SSSOM.md
 default_curi_maps:
 - semweb_context
 - obo_context

Diff for: schema/sssom.context.jsonld

@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from sssom.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2022-02-14T15:33:37\n    Schema: sssom\n    metamodel version: 1.7.0\n    model version: None\n    \n    id: http://w3id.org/sssom/schema/\n    description: Datamodel for Simple Standard for Sharing Ontology Mappings (SSSOM)\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from sssom.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2022-02-14T15:33:37\n    Schema: sssom\n    metamodel version: 1.7.0\n    model version: None\n    \n    id: https://w3id.org/sssom/schema/\n    description: Datamodel for Simple Standard for Sharing Ontology Mappings (SSSOM)\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "Orphanet": {
          "@id": "http://www.orpha.net/ORDO/Orphanet_",
@@ -20,8 +20,8 @@
       "prov": "http://www.w3.org/ns/prov#",
       "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
       "skos": "http://www.w3.org/2004/02/skos/core#",
-      "sssom": "http://w3id.org/sssom/",
-      "@vocab": "http://w3id.org/sssom/",
+      "sssom": "https://w3id.org/sssom/",
+      "@vocab": "https://w3id.org/sssom/",
       "author_id": {
          "@type": "rdfs:Resource",
          "@id": "pav:authoredBy"
@@ -82,7 +82,7 @@
             "meaning": "@id"
          }
       },
-      "match_type": {
+      "mapping_justification": {
          "@context": {
             "@vocab": "@null",
             "text": "skos:notation",

Diff for: schema/sssom.schema.json

@@ -76,7 +76,7 @@
                "$ref": "#/$defs/MatchTermTypeEnum",
                "description": "Specifies what type of terms are being matched (class, property, or individual)."
             },
-            "match_type": {
+            "mapping_justification": {
                "description": "The kind of match that led to the mapping, e.g. Logical or Lexical.",
                "items": {
                   "$ref": "#/$defs/MatchTypeEnum"
@@ -201,7 +201,7 @@
             "subject_id",
             "predicate_id",
             "object_id",
-            "match_type"
+            "mapping_justification"
          ],
          "title": "Mapping",
          "type": "object"
@@ -395,7 +395,7 @@
          "type": "string"
       }
    },
-   "$id": "http://w3id.org/sssom/schema/",
+   "$id": "https://w3id.org/sssom/schema/",
    "$schema": "http://json-schema.org/draft-07/schema#",
    "additionalProperties": true,
    "metamodel_version": "1.7.0",