Merge pull request #148 from cancervariants/issue-140

Issue 140
cancervariants · Sep 1, 2021 · fc25658 · fc25658
2 parents 97b0cbf + 9e7436b
commit fc25658
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diff --git a/Pipfile b/Pipfile
@@ -35,3 +35,4 @@ httptools = "*"
 gene-normalizer = ">=0.1.17"
 pyliftover = "*"
 boto3 = "*"
+"ga4gh.vrsatile.pydantic" = "*"
diff --git a/README.md b/README.md
@@ -101,11 +101,7 @@ pytest tests/
 
 ### Starting the Variation Normalization Service Locally
 `gene-normalizer`s dynamodb must be running and run the following:
-```
-docker-compose -f docker-compose.yml up
-```
 
-From the _root_ directory of the repository:
 ```
 uvicorn variation.main:app --reload
 ```

diff --git a/docker-compose.yml b/docker-compose.yml
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -16,9 +16,8 @@ appdirs==1.4.4
 appnope==0.1.2; sys_platform == 'darwin'
 argcomplete==1.12.3
 argh==0.26.2
-argon2-cffi==20.1.0
+argon2-cffi==21.1.0; python_version >= '3.5'
 asgiref==3.4.1; python_version >= '3.6'
-async-generator==1.10; python_version >= '3.5'
 attrs==21.2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 babel==2.9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 backcall==0.2.0
@@ -27,14 +26,14 @@ backports.entry-points-selectable==1.1.0; python_version >= '2.7'
 beautifulsoup4==4.9.3
 biocommons.seqrepo==0.6.4
 bioutils==0.5.5; python_version >= '3.6'
-bleach==4.0.0; python_version >= '3.6'
-boto3==1.18.20
-botocore==1.21.20; python_version >= '3.6'
+bleach==4.1.0; python_version >= '3.6'
+boto3==1.18.31
+botocore==1.21.31; python_version >= '3.6'
 bs4==0.0.1
 canonicaljson==1.4.0; python_version ~= '3.5'
 certifi==2021.5.30
 cffi==1.14.6
-cfgv==3.3.0; python_full_version >= '3.6.1'
+cfgv==3.3.1; python_full_version >= '3.6.1'
 charset-normalizer==2.0.4; python_version >= '3'
 civicpy==1.1.3; python_version >= '3.5'
 click==8.0.1; python_version >= '3.6'
@@ -54,12 +53,13 @@ docopt==0.6.2
 docutils==0.17.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 entrypoints==0.3; python_version >= '2.7'
 fake-useragent==0.1.11
-fastapi==0.68.0
+fastapi==0.68.1
 filelock==3.0.12
 flake8-docstrings==1.6.0
 flake8==3.9.2
-frozendict==2.0.5; python_version >= '3.6'
+frozendict==2.0.6; python_version >= '3.6'
 ga4gh.vrs[extras]==0.7.0rc3
+ga4gh.vrsatile.pydantic==0.0.1
 gene-normalizer==0.1.17
 gffutils==0.10.1
 h11==0.12.0; python_version >= '3.6'
@@ -68,29 +68,29 @@ httptools==0.3.0
 humanfriendly==9.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 identify==2.2.13; python_full_version >= '3.6.1'
 idna==3.2; python_version >= '3'
-importlib-metadata==4.6.3; python_version >= '3.6'
+importlib-metadata==4.8.1; python_version >= '3.6'
 inflection==0.5.1; python_version >= '3.5'
 iniconfig==1.1.1
-ipykernel==6.1.0
+ipykernel==6.3.0
 ipython-genutils==0.2.0
-ipython==7.26.0; python_version >= '3.7'
+ipython==7.27.0; python_version >= '3.7'
 ipywidgets==7.6.3
 jedi==0.18.0; python_version >= '3.6'
 jinja2==3.0.1; python_version >= '3.6'
 jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 json5==0.9.6
 jsonschema==3.2.0
-jupyter-client==6.1.12; python_version >= '3.5'
+jupyter-client==7.0.2; python_full_version >= '3.6.1'
 jupyter-console==6.4.0; python_version >= '3.6'
 jupyter-core==4.7.1; python_version >= '3.6'
 jupyter-server==1.10.2; python_version >= '3.6'
 jupyter==1.0.0
 jupyterlab-pygments==0.1.2
-jupyterlab-server==2.7.0; python_version >= '3.6'
+jupyterlab-server==2.7.2; python_version >= '3.6'
 jupyterlab-widgets==1.0.0; python_version >= '3.6'
-jupyterlab==3.1.6
-keyring==23.0.1; python_version >= '3.6'
-kiwisolver==1.3.1; python_version >= '3.6'
+jupyterlab==3.1.9
+keyring==23.1.0; python_version >= '3.6'
+kiwisolver==1.3.2; python_version >= '3.7'
 lxml==4.6.3
 markdown==3.3.4; python_version >= '3.6'
 markupsafe==2.0.1; python_version >= '3.6'
@@ -99,17 +99,17 @@ matplotlib==3.4.3
 mccabe==0.6.1
 mistune==0.8.4
 nbclassic==0.3.1; python_version >= '3.6'
-nbclient==0.5.3; python_full_version >= '3.6.1'
+nbclient==0.5.4; python_full_version >= '3.6.1'
 nbconvert==6.1.0; python_version >= '3.7'
 nbformat==5.1.3; python_version >= '3.5'
 nest-asyncio==1.5.1; python_version >= '3.5'
 networkx==2.6.2; python_version >= '3.7'
 nodeenv==1.6.0
 notebook==6.4.3; python_version >= '3.6'
-numpy==1.21.1; python_version >= '3.7'
+numpy==1.21.2; python_version < '3.11' and python_version >= '3.7'
 obonet==0.3.0; python_version >= '3.5'
 packaging==21.0; python_version >= '3.6'
-pandas==1.3.1; python_full_version >= '3.7.1'
+pandas==1.3.2; python_full_version >= '3.7.1'
 pandocfilters==1.4.3
 parse==1.19.0
 parsley==1.3
@@ -120,23 +120,23 @@ pillow==8.3.1; python_version >= '3.6'
 pkginfo==1.7.1
 platformdirs==2.2.0; python_version >= '3.6'
 pluggy==0.13.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pre-commit==2.14.0
+pre-commit==2.14.1
 prometheus-client==0.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-prompt-toolkit==3.0.19; python_full_version >= '3.6.1'
+prompt-toolkit==3.0.20; python_full_version >= '3.6.2'
 psycopg2-binary==2.9.1; python_version >= '3.6'
 ptyprocess==0.7.0
 py==1.10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pycodestyle==2.7.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pycparser==2.20; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pydantic==1.8.2
 pydocstyle==6.1.1; python_version >= '3.6'
-pyee==8.1.0
-pyfaidx==0.6.1
+pyee==8.2.2
+pyfaidx==0.6.2
 pyflakes==2.3.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pygments==2.9.0; python_version >= '3.5'
+pygments==2.10.0; python_version >= '3.5'
 pyliftover==0.4
 pyparsing==2.4.7; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pyppeteer==0.2.5; python_version < '4' and python_full_version >= '3.6.1'
+pyppeteer==0.2.6; python_full_version >= '3.6.1' and python_full_version < '4.0.0'
 pyquery==1.4.3
 pyrsistent==0.18.0; python_version >= '3.6'
 pysam==0.16.0.1
@@ -148,7 +148,7 @@ pytz==2021.1
 pyyaml==5.4.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 pyzmq==22.2.1; python_version >= '3.6'
 qtconsole==5.1.1; python_version >= '3.6'
-qtpy==1.9.0
+qtpy==1.10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 readme-renderer==29.0
 requests-html==0.10.0; python_version >= '3.6'
 requests-toolbelt==0.9.1
@@ -157,32 +157,32 @@ requests==2.26.0
 rfc3986==1.5.0
 s3transfer==0.5.0; python_version >= '3.6'
 send2trash==1.8.0
-simplejson==3.17.3; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
+simplejson==3.17.5; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
 six==1.16.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 sniffio==1.2.0; python_version >= '3.5'
 snowballstemmer==2.1.0
 soupsieve==2.2.1; python_version >= '3'
 sqlparse==0.4.1; python_version >= '3.5'
 starlette==0.14.2; python_version >= '3.6'
 tabulate==0.8.9
-terminado==0.11.0; python_version >= '3.6'
+terminado==0.11.1; python_version >= '3.6'
 testpath==0.5.0; python_version >= '3.5'
 toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 tornado==6.1; python_version >= '3.5'
-tqdm==4.62.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+tqdm==4.62.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 traitlets==5.0.5; python_version >= '3.7'
 twine==3.4.2
-typing-extensions==3.10.0.0
-urllib3==1.26.6; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'
-uvicorn==0.14.0
+typing-extensions==3.10.0.1
+urllib3==1.26.6; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_full_version < '4.0.0'
+uvicorn==0.15.0
 uvloop==0.16.0
 vcfpy==0.13.3
 virtualenv==20.7.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 w3lib==1.22.0
 wcwidth==0.2.5
 webencodings==0.5.1
 websocket-client==1.2.1; python_version >= '3.6'
-websockets==8.1
+websockets==9.1
 widgetsnbextension==3.5.1
 yoyo-migrations==7.3.2
 zipp==3.5.0; python_version >= '3.6'
diff --git a/requirements.txt b/requirements.txt
@@ -17,8 +17,8 @@ backports-datetime-fromisoformat==1.0.0
 beautifulsoup4==4.9.3
 biocommons.seqrepo==0.6.4
 bioutils==0.5.5; python_version >= '3.6'
-boto3==1.18.20
-botocore==1.21.20; python_version >= '3.6'
+boto3==1.18.31
+botocore==1.21.31; python_version >= '3.6'
 bs4==0.0.1
 canonicaljson==1.4.0; python_version ~= '3.5'
 certifi==2021.5.30
@@ -31,45 +31,47 @@ cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3
 decorator==5.0.9; python_version >= '3.5'
 deprecation==2.1.0
 fake-useragent==0.1.11
-fastapi==0.68.0
-frozendict==2.0.5; python_version >= '3.6'
+fastapi==0.68.1
+frozendict==2.0.6; python_version >= '3.6'
 ga4gh.vrs[extras]==0.7.0rc3
+ga4gh.vrsatile.pydantic==0.0.1
 gene-normalizer==0.1.17
 gffutils==0.10.1
 h11==0.12.0; python_version >= '3.6'
 hgvs==1.5.1
 httptools==0.3.0
 humanfriendly==9.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 idna==3.2; python_version >= '3'
+importlib-metadata==4.8.1; python_version >= '3.6'
 inflection==0.5.1; python_version >= '3.5'
 ipython-genutils==0.2.0
-ipython==7.26.0; python_version >= '3.7'
+ipython==7.27.0; python_version >= '3.7'
 jedi==0.18.0; python_version >= '3.6'
 jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 jsonschema==3.2.0
 lxml==4.6.3
 markdown==3.3.4; python_version >= '3.6'
 matplotlib-inline==0.1.2; python_version >= '3.5'
 networkx==2.6.2; python_version >= '3.7'
-numpy==1.21.1; python_version >= '3.7'
+numpy==1.21.2; python_version < '3.11' and python_version >= '3.7'
 obonet==0.3.0; python_version >= '3.5'
 packaging==21.0; python_version >= '3.6'
-pandas==1.3.1; python_full_version >= '3.7.1'
+pandas==1.3.2; python_full_version >= '3.7.1'
 parse==1.19.0
 parsley==1.3
 parso==0.8.2; python_version >= '3.6'
 pexpect==4.8.0; sys_platform != 'win32'
 pickleshare==0.7.5
-prompt-toolkit==3.0.19; python_full_version >= '3.6.1'
+prompt-toolkit==3.0.20; python_full_version >= '3.6.2'
 psycopg2-binary==2.9.1; python_version >= '3.6'
 ptyprocess==0.7.0
 pydantic==1.8.2
-pyee==8.1.0
-pyfaidx==0.6.1
-pygments==2.9.0; python_version >= '3.5'
+pyee==8.2.2
+pyfaidx==0.6.2
+pygments==2.10.0; python_version >= '3.5'
 pyliftover==0.4
 pyparsing==2.4.7; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pyppeteer==0.2.5; python_version < '4' and python_full_version >= '3.6.1'
+pyppeteer==0.2.6; python_full_version >= '3.6.1' and python_full_version < '4.0.0'
 pyquery==1.4.3
 pyrsistent==0.18.0; python_version >= '3.6'
 pysam==0.16.0.1
@@ -80,20 +82,21 @@ pyyaml==5.4.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2,
 requests-html==0.10.0; python_version >= '3.6'
 requests==2.26.0
 s3transfer==0.5.0; python_version >= '3.6'
-simplejson==3.17.3; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
+simplejson==3.17.5; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
 six==1.16.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 soupsieve==2.2.1; python_version >= '3'
 sqlparse==0.4.1; python_version >= '3.5'
 starlette==0.14.2; python_version >= '3.6'
 tabulate==0.8.9
-tqdm==4.62.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+tqdm==4.62.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 traitlets==5.0.5; python_version >= '3.7'
-typing-extensions==3.10.0.0
-urllib3==1.26.6; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'
-uvicorn==0.14.0
+typing-extensions==3.10.0.1
+urllib3==1.26.6; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_full_version < '4.0.0'
+uvicorn==0.15.0
 uvloop==0.16.0
 vcfpy==0.13.3
 w3lib==1.22.0
 wcwidth==0.2.5
-websockets==8.1
+websockets==9.1
 yoyo-migrations==7.3.2
+zipp==3.5.0; python_version >= '3.6'
diff --git a/tests/classifiers/test_genomic_uncertain_deletion.py b/tests/classifiers/test_genomic_uncertain_deletion.py
@@ -0,0 +1,17 @@
+"""Module for testing Genomic Uncertain Deletion Classifier."""
+import unittest
+from variation.classifiers import GenomicUncertainDeletionClassifier
+from .classifier_base import ClassifierBase
+
+
+class TestGenomicUncertainDeletionClassifier(ClassifierBase,
+                                             unittest.TestCase):
+    """A class to test the Genomic Uncertain Deletion Classifier."""
+
+    def classifier_instance(self):
+        """Return Genomic Uncertain Deletion Classifier instance."""
+        return GenomicUncertainDeletionClassifier()
+
+    def fixture_name(self):
+        """Return Genomic Uncertain Deletion fixture name."""
+        return 'genomic_uncertain_deletion'
diff --git a/tests/fixtures/classifiers.yml b/tests/fixtures/classifiers.yml
@@ -274,4 +274,16 @@ genomic_insertion:
       confidence: ConfidenceRating.INTERSECTION
   should_not_match:
     - query: GENE 32867861_32867862insT
-    - query: accession:g.32867861_32867862insT
+    - query: accession:g.32867861_32867862insT
+
+genomic_uncertain_deletion:
+  should_match:
+    - query: NC_000023.11:g.(?_31120496)_(33339477_?)del
+      confidence: ConfidenceRating.EXACT
+    - query: NC_000023.11:g.(?_155980375)_(156013167_?)del
+      confidence: ConfidenceRating.EXACT
+    - query: NC_000023.11:g.(?_155980375)_(156013167_?)del foo
+      confidence: ConfidenceRating.INTERSECTION
+  should_not_match:
+    - query: GENE (?_155980375)_(156013167_?)del
+    - query: accession:g.(?_155980375)_(156013167_?)del
diff --git a/tests/fixtures/tokenizers.yml b/tests/fixtures/tokenizers.yml
@@ -347,4 +347,15 @@ genomic_insertion:
     - token: g.123_124insAGCX
     - token: c.169_170insAla
     - token: g.32867861_32867862delinsT
-    - token: 123_124insAGCX
+    - token: 123_124insAGCX
+
+genomic_uncertain_deletion:
+  should_match:
+    - token: g.(?_31120496)_(33339477_?)del
+    - token: g.(?_155980375)_(156013167_?)del
+  should_not_match:
+    - token: c.(?_169)_(170_?)del
+    - token: g.(31120496_?)_(?_33339477)del
+    - token: g.(?_31120496)_(33339477_?)delins
+    - token: (?_31120496)_(33339477_?)del
+    - token: g.(?_33339477)_(31120496_?)del