feat!: Apply VRS 1.3 Changes (#409)

- Copy Number Changes
  - Absolute Copy Number --> Copy Number Count
  - Relative Copy Number --> Copy Number Change
  - vac --> cn
  - vrc --> cx
  - abs_cnv -> cn_var
  - rel_cnv -> cx_var
- EFO Changes
    - complete loss --> efo:0030069
    - partial loss --> efo:0030067
    - copy neutral --> efo:0030064
    - low-level gain --> efo:0030071
    - high-level gain —> efo:0030072
  - Default Characteristics (this follows what is in staging)
    - partial loss --> efo:0030067
    - low-level gain --> efo:0030071
- license-file --> license_file in setup.cfg
- Update ga4gh.vrs, ga4gh.vrsatile.pydantic, gene-normalizer, and cool-seq-tool versions for VRS 1.3
- The classifier tests were failing, so I removed the `ConfidenceRating` prefix in `confidence` in the classifier fixtures

Author: korikuzma

Pipfile

@@ -23,9 +23,9 @@ psycopg2-binary = "*"
 fastapi = "*"
 uvicorn = "*"
 pydantic = "*"
-"ga4gh.vrs" = {version = "~=0.8.1.dev0", extras = ["extras"]}
-gene-normalizer = "~=0.1.32"
+"ga4gh.vrs" = {version = "~=0.8.1", extras = ["extras"]}
+gene-normalizer = "~=0.1.35"
 pyliftover = "*"
 boto3 = "*"
-"ga4gh.vrsatile.pydantic" = "~=0.0.11"
-cool-seq-tool = ">=0.1.11"
+"ga4gh.vrsatile.pydantic" = "~=0.0.12"
+cool-seq-tool = ">=0.1.13"

docs/hgvs_dup_del_mode.md

@@ -1,17 +1,17 @@
 # HGVS Dup Del Mode
 
 This mode helps us interpret deletions and duplications that are represented as HGVS expressions.\
-The mode can be set to `default`, `absolute_cnv`, `relative_cnv`, `repeated_seq_expr`, or `literal_seq_expr`.
+The mode can be set to `default`, `copy_number_count`, `copy_number_change`, `repeated_seq_expr`, or `literal_seq_expr`.
 
 
 ## Default Characteristics
 
 - if baseline_copies is not set and endpoints are ambiguous:
-    - relative_cnv
-    - if relative_copy_class not provided:
-        - relative_copy_class = `partial loss` if del, `low-level gain` if dup
+    - copy_number_change
+    - if copy_change not provided:
+        - copy_change = `efo:0030067` (loss) if del, `efo:0030070` (gain) if dup
 - elif baseline_copies is provided:
-    - absolute_cnv
+    - copy_number_count
     - copies are baseline_copies + 1 for dup, baseline_copies - 1 for del
 - elif len del or dup > 100bp: (use outermost coordinates)
     - repeated_seq_expr with a derived_seq_expr subject (Allele)

requirements-dev.txt

@@ -7,63 +7,63 @@ argon2-cffi==21.3.0 ; python_version >= '3.6'
 argon2-cffi-bindings==21.2.0 ; python_version >= '3.6'
 asttokens==2.2.1
 asyncpg==0.27.0 ; python_full_version >= '3.7.0'
-attrs==22.2.0 ; python_version >= '3.6'
+attrs==23.1.0 ; python_version >= '3.7'
 backcall==0.2.0
-beautifulsoup4==4.12.0 ; python_full_version >= '3.6.0'
+beautifulsoup4==4.12.2 ; python_full_version >= '3.6.0'
 biocommons.seqrepo==0.6.5
 bioutils==0.5.7 ; python_version >= '3.6'
 bleach==6.0.0 ; python_version >= '3.7'
-boto3==1.26.105
-botocore==1.29.105 ; python_version >= '3.7'
+boto3==1.26.123
+botocore==1.29.123 ; python_version >= '3.7'
 bs4==0.0.1
 canonicaljson==2.0.0 ; python_version >= '3.7'
 certifi==2022.12.7 ; python_version >= '3.6'
 cffi==1.15.1
 cfgv==3.3.1 ; python_full_version >= '3.6.1'
 charset-normalizer==3.1.0 ; python_full_version >= '3.7.0'
-click==8.1.3 ; python_version >= '3.7'
+click==8.1.3
 coloredlogs==15.0.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 comm==0.1.3 ; python_version >= '3.6'
 configparser==5.3.0 ; python_version >= '3.7'
-cool-seq-tool==0.1.10
-coverage[toml]==7.2.2 ; python_version >= '3.7'
+cool-seq-tool==0.1.13
+coverage[toml]==7.2.5 ; python_version >= '3.7'
 cssselect==1.2.0 ; python_version >= '3.7'
-debugpy==1.6.6 ; python_version >= '3.7'
+cython==0.29.34 ; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'
+debugpy==1.6.7 ; python_version >= '3.7'
 decorator==5.1.1 ; python_version >= '3.5'
 defusedxml==0.7.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 distlib==0.3.6
-exceptiongroup==1.1.1 ; python_version < '3.11'
 executing==1.2.0
 fake-useragent==1.1.3
-fastapi==0.95.0
+fastapi==0.95.1
 fastjsonschema==2.16.3
-filelock==3.10.7 ; python_version >= '3.7'
+filelock==3.12.0 ; python_version >= '3.7'
 flake8==6.0.0
 flake8-annotations==3.0.0
 flake8-docstrings==1.7.0
 flake8-import-order==0.18.2
 flake8-quotes==3.3.2
-ga4gh.vrs[extras]==0.8.1.dev0
-ga4gh.vrsatile.pydantic==0.0.11
-gene-normalizer==0.1.32
+ga4gh.vrs[extras]==0.8.1
+ga4gh.vrsatile.pydantic==0.0.12
+gene-normalizer==0.1.35
 h11==0.14.0 ; python_version >= '3.7'
 hgvs==1.5.4 ; python_version >= '3.6'
 humanfriendly==10.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-identify==2.5.22 ; python_version >= '3.7'
+identify==2.5.23 ; python_version >= '3.7'
 idna==3.4 ; python_version >= '3.5'
-importlib-metadata==6.1.0 ; python_version >= '3.7'
+importlib-metadata==6.6.0 ; python_version >= '3.7'
 inflection==0.5.1 ; python_version >= '3.5'
 iniconfig==2.0.0 ; python_version >= '3.7'
 ipykernel==6.22.0
-ipython==8.12.0 ; python_version >= '3.8'
+ipython==8.13.1 ; python_version >= '3.9'
 ipython-genutils==0.2.0
 ipywidgets==8.0.6 ; python_version >= '3.7'
 jedi==0.18.2 ; python_version >= '3.6'
 jinja2==3.1.2 ; python_version >= '3.7'
 jmespath==1.0.1 ; python_version >= '3.7'
 jsonschema==3.2.0
 jupyter==1.0.0
-jupyter-client==8.1.0 ; python_version >= '3.8'
+jupyter-client==8.2.0 ; python_version >= '3.8'
 jupyter-console==6.6.3 ; python_version >= '3.7'
 jupyter-core==5.3.0 ; python_version >= '3.8'
 jupyter-events==0.6.3 ; python_version >= '3.7'
@@ -77,29 +77,29 @@ markupsafe==2.1.2 ; python_version >= '3.7'
 matplotlib-inline==0.1.6 ; python_version >= '3.5'
 mccabe==0.7.0 ; python_version >= '3.6'
 mistune==2.0.5
-nbclassic==0.5.4 ; python_version >= '3.7'
-nbclient==0.7.3 ; python_full_version >= '3.7.0'
-nbconvert==7.3.0 ; python_version >= '3.7'
+nbclassic==0.5.6 ; python_version >= '3.7'
+nbclient==0.7.4 ; python_full_version >= '3.7.0'
+nbconvert==7.3.1 ; python_version >= '3.7'
 nbformat==5.8.0 ; python_version >= '3.7'
 nest-asyncio==1.5.6 ; python_version >= '3.5'
 nodeenv==1.7.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6'
-notebook==6.5.3 ; python_version >= '3.7'
-notebook-shim==0.2.2 ; python_version >= '3.7'
-numpy==1.24.2 ; python_version >= '3.8'
-packaging==23.0 ; python_version >= '3.7'
-pandas==2.0.0 ; python_version >= '3.8'
+notebook==6.5.4 ; python_version >= '3.7'
+notebook-shim==0.2.3 ; python_version >= '3.7'
+numpy==1.24.3 ; python_version >= '3.8'
+packaging==23.1 ; python_version >= '3.7'
+pandas==2.0.1 ; python_version >= '3.8'
 pandocfilters==1.5.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 parse==1.19.0
 parsley==1.3
 parso==0.8.3 ; python_version >= '3.6'
 pexpect==4.8.0 ; sys_platform != 'win32'
 pickleshare==0.7.5
-platformdirs==3.2.0 ; python_version >= '3.7'
+platformdirs==3.5.0 ; python_version >= '3.7'
 pluggy==1.0.0 ; python_version >= '3.6'
 pre-commit==3.2.2
 prometheus-client==0.16.0 ; python_version >= '3.6'
 prompt-toolkit==3.0.38 ; python_full_version >= '3.7.0'
-psutil==5.9.4 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+psutil==5.9.5 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 psycopg2==2.9.6 ; python_version >= '3.6'
 psycopg2-binary==2.9.6
 ptyprocess==0.7.0
@@ -110,13 +110,13 @@ pydantic==1.10.7
 pydocstyle==6.3.0 ; python_version >= '3.6'
 pyee==8.2.2
 pyflakes==3.0.1 ; python_version >= '3.6'
-pygments==2.14.0 ; python_version >= '3.6'
+pygments==2.15.1 ; python_version >= '3.7'
 pyliftover==0.4
 pyppeteer==1.0.2 ; python_version >= '3.7' and python_version < '4.0'
 pyquery==2.0.0
 pyrsistent==0.19.3 ; python_version >= '3.7'
-pysam==0.20.0
-pytest==7.2.2
+pysam==0.21.0 ; python_version >= '3.6'
+pytest==7.3.1
 pytest-asyncio==0.21.0
 pytest-cov==4.0.0
 python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
@@ -127,33 +127,32 @@ pyyaml==6.0 ; python_version >= '3.6'
 pyzmq==25.0.2 ; python_version >= '3.6'
 qtconsole==5.4.2 ; python_version >= '3.7'
 qtpy==2.3.1 ; python_version >= '3.7'
-requests==2.28.2 ; python_version >= '3.7' and python_version < '4'
+requests==2.29.0 ; python_version >= '3.7'
 requests-html==0.10.0 ; python_full_version >= '3.6.0'
 rfc3339-validator==0.1.4 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 rfc3986-validator==0.1.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 s3transfer==0.6.0 ; python_version >= '3.7'
-send2trash==1.8.0
-setuptools==67.6.1 ; python_version >= '3.7'
+send2trash==1.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+setuptools==67.7.2 ; python_version >= '3.7'
 six==1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
 sniffio==1.3.0 ; python_version >= '3.7'
 snowballstemmer==2.2.0
-soupsieve==2.4 ; python_version >= '3.7'
-sqlparse==0.4.3 ; python_version >= '3.5'
+soupsieve==2.4.1 ; python_version >= '3.7'
+sqlparse==0.4.4 ; python_version >= '3.5'
 stack-data==0.6.2
 starlette==0.26.1 ; python_version >= '3.7'
 tabulate==0.9.0 ; python_version >= '3.7'
 terminado==0.17.1 ; python_version >= '3.7'
 tinycss2==1.2.1 ; python_version >= '3.7'
-tomli==2.0.1 ; python_version < '3.11'
-tornado==6.2 ; python_version >= '3.7'
+tornado==6.3.1 ; python_version >= '3.8'
 tqdm==4.65.0 ; python_version >= '3.7'
 traitlets==5.9.0 ; python_version >= '3.7'
 typing-extensions==4.5.0 ; python_version >= '3.7'
 tzdata==2023.3 ; python_version >= '2'
 urllib3==1.26.15 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-uvicorn==0.21.1
+uvicorn==0.22.0
 -e .
-virtualenv==20.21.0 ; python_version >= '3.7'
+virtualenv==20.23.0 ; python_version >= '3.7'
 w3lib==2.1.1 ; python_version >= '3.7'
 wcwidth==0.2.6
 webencodings==0.5.1

requirements.txt

@@ -5,44 +5,45 @@ appdirs==1.4.4
 appnope==0.1.3 ; sys_platform == 'darwin'
 asttokens==2.2.1
 asyncpg==0.27.0 ; python_full_version >= '3.7.0'
-attrs==22.2.0 ; python_version >= '3.6'
+attrs==23.1.0 ; python_version >= '3.7'
 backcall==0.2.0
-beautifulsoup4==4.12.0 ; python_full_version >= '3.6.0'
+beautifulsoup4==4.12.2 ; python_full_version >= '3.6.0'
 biocommons.seqrepo==0.6.5
 bioutils==0.5.7 ; python_version >= '3.6'
-boto3==1.26.105
-botocore==1.29.105 ; python_version >= '3.7'
+boto3==1.26.123
+botocore==1.29.123 ; python_version >= '3.7'
 bs4==0.0.1
 canonicaljson==2.0.0 ; python_version >= '3.7'
 certifi==2022.12.7 ; python_version >= '3.6'
 charset-normalizer==3.1.0 ; python_full_version >= '3.7.0'
-click==8.1.3 ; python_version >= '3.7'
+click==8.1.3
 coloredlogs==15.0.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 configparser==5.3.0 ; python_version >= '3.7'
-cool-seq-tool==0.1.10
+cool-seq-tool==0.1.13
 cssselect==1.2.0 ; python_version >= '3.7'
+cython==0.29.34 ; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'
 decorator==5.1.1 ; python_version >= '3.5'
 executing==1.2.0
 fake-useragent==1.1.3
-fastapi==0.95.0
-ga4gh.vrs[extras]==0.8.1.dev0
-ga4gh.vrsatile.pydantic==0.0.11
-gene-normalizer==0.1.32
+fastapi==0.95.1
+ga4gh.vrs[extras]==0.8.1
+ga4gh.vrsatile.pydantic==0.0.12
+gene-normalizer==0.1.35
 h11==0.14.0 ; python_version >= '3.7'
 hgvs==1.5.4 ; python_version >= '3.6'
 humanfriendly==10.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 idna==3.4 ; python_version >= '3.5'
-importlib-metadata==6.1.0 ; python_version >= '3.7'
+importlib-metadata==6.6.0 ; python_version >= '3.7'
 inflection==0.5.1 ; python_version >= '3.5'
-ipython==8.12.0 ; python_version >= '3.8'
+ipython==8.13.1 ; python_version >= '3.9'
 jedi==0.18.2 ; python_version >= '3.6'
 jmespath==1.0.1 ; python_version >= '3.7'
 jsonschema==3.2.0
 lxml==4.9.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 markdown==3.4.3 ; python_version >= '3.7'
 matplotlib-inline==0.1.6 ; python_version >= '3.5'
-numpy==1.24.2 ; python_version >= '3.8'
-pandas==2.0.0 ; python_version >= '3.8'
+numpy==1.24.3 ; python_version >= '3.8'
+pandas==2.0.1 ; python_version >= '3.8'
 parse==1.19.0
 parsley==1.3
 parso==0.8.3 ; python_version >= '3.6'
@@ -55,24 +56,24 @@ ptyprocess==0.7.0
 pure-eval==0.2.2
 pydantic==1.10.7
 pyee==8.2.2
-pygments==2.14.0 ; python_version >= '3.6'
+pygments==2.15.1 ; python_version >= '3.7'
 pyliftover==0.4
 pyppeteer==1.0.2 ; python_version >= '3.7' and python_version < '4.0'
 pyquery==2.0.0
 pyrsistent==0.19.3 ; python_version >= '3.7'
-pysam==0.20.0
+pysam==0.21.0 ; python_version >= '3.6'
 python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
 python-jsonschema-objects==0.4.1
 pytz==2023.3
 pyyaml==6.0 ; python_version >= '3.6'
-requests==2.28.2 ; python_version >= '3.7' and python_version < '4'
+requests==2.29.0 ; python_version >= '3.7'
 requests-html==0.10.0 ; python_full_version >= '3.6.0'
 s3transfer==0.6.0 ; python_version >= '3.7'
-setuptools==67.6.1 ; python_version >= '3.7'
+setuptools==67.7.2 ; python_version >= '3.7'
 six==1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
 sniffio==1.3.0 ; python_version >= '3.7'
-soupsieve==2.4 ; python_version >= '3.7'
-sqlparse==0.4.3 ; python_version >= '3.5'
+soupsieve==2.4.1 ; python_version >= '3.7'
+sqlparse==0.4.4 ; python_version >= '3.5'
 stack-data==0.6.2
 starlette==0.26.1 ; python_version >= '3.7'
 tabulate==0.9.0 ; python_version >= '3.7'
@@ -81,7 +82,7 @@ traitlets==5.9.0 ; python_version >= '3.7'
 typing-extensions==4.5.0 ; python_version >= '3.7'
 tzdata==2023.3 ; python_version >= '2'
 urllib3==1.26.15 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-uvicorn==0.21.1
+uvicorn==0.22.0
 w3lib==2.1.1 ; python_version >= '3.7'
 wcwidth==0.2.6
 websockets==10.4 ; python_version >= '3.7'

setup.cfg

@@ -6,7 +6,7 @@ description = VICC normalization routine for variations
 long_description = file:README.md
 long_description_content_type = text/markdown
 home-page = https://github.com/cancervariants/variation-normalization
-license-file = LICENSE
+license_files = LICENSE
 license = MIT
 
 classifiers =
@@ -29,12 +29,12 @@ install_requires =
     fastapi
     uvicorn
     pydantic
-    ga4gh.vrs[extras] ~= 0.8.1.dev0
-    gene-normalizer ~= 0.1.32
+    ga4gh.vrs[extras] ~= 0.8.1
+    gene-normalizer ~= 0.1.35
     pyliftover
     boto3
-    ga4gh.vrsatile.pydantic ~= 0.0.11
-    cool-seq-tool >= 0.1.11
+    ga4gh.vrsatile.pydantic ~= 0.0.12
+    cool-seq-tool >= 0.1.13
 
 tests_require =
     pytest

tests/classifiers/classifier_base.py

@@ -1,7 +1,9 @@
 """A module for testing classifier classes."""
 import yaml
+from gene.database.dynamodb import DynamoDbDatabase
 from gene.query import QueryHandler as GeneQueryHandler
 
+from variation.schemas.classification_response_schema import ConfidenceRating
 from variation.tokenizers import Tokenize
 from variation.tokenizers import GeneSymbol
 from tests import PROJECT_ROOT
@@ -19,7 +21,7 @@ def setUp(self):
             {"should_match": [], "should_not_match": []}
         )
         self.classifier = self.classifier_instance()
-        self.tokenizer = Tokenize(GeneSymbol(GeneQueryHandler()))
+        self.tokenizer = Tokenize(GeneSymbol(GeneQueryHandler(DynamoDbDatabase())))
 
     def classifier_instance(self):
         """Check that the classifier_instance method is implemented."""
@@ -35,8 +37,8 @@ def test_matches(self):
             tokens = self.tokenizer.perform(x["query"], [])
             classification = self.classifier.match(tokens)
             self.assertIsNotNone(classification, msg=x)
-            self.assertEqual(x["confidence"],
-                             str(classification.confidence),
+            self.assertEqual(getattr(ConfidenceRating, x["confidence"]),
+                             classification.confidence,
                              msg=x)
 
     def test_not_matches(self):