Merge pull request #3452 from broadinstitute/dev

Dev
broadinstitute · Jun 23, 2023 · c200fdc · c200fdc
2 parents f860a2c + 60d0185
commit c200fdc
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 ## dev
 
+## 6/23/23
+* Add a 'rank' field to the RnaSeqSpliceOutlier model (REQUIRES DB MIGRATION)
+* Remove hail python dependency
+
 ## 6/2/23
 * Update Clinvar filtering and display
 

diff --git a/requirements.in b/requirements.in
@@ -10,7 +10,6 @@ social-auth-core                  # the Python social authentication package. Re
 elasticsearch==7.9.1              # elasticsearch client
 elasticsearch-dsl==7.2.1          # elasticsearch query utilities
 gunicorn                          # web server
-hail<0.3                          # provides convenient apis for working with files in google cloud storage
 jmespath
 openpyxl                          # library for reading/writing Excel files
 pillow                            # required dependency of Djagno ImageField-type database records

diff --git a/requirements.txt b/requirements.txt
@@ -1,79 +1,29 @@
 #
-# This file is autogenerated by pip-compile with Python 3.9
-# by the following command:
+# This file is autogenerated by pip-compile with python 3.9
+# To update, run:
 #
 #    pip-compile requirements.in
 #
-aiohttp==3.8.4
-    # via
-    #   aiohttp-session
-    #   hail
-aiohttp-session==2.12.0
-    # via hail
-aiosignal==1.3.1
-    # via aiohttp
 asgiref==3.6.0
     # via django
 async-timeout==4.0.2
-    # via
-    #   aiohttp
-    #   redis
-asyncinit==0.2.4
-    # via hail
-attrs==22.2.0
-    # via aiohttp
-avro==1.11.1
-    # via hail
-azure-core==1.26.3
-    # via
-    #   azure-identity
-    #   azure-storage-blob
-    #   msrest
-azure-identity==1.12.0
-    # via hail
-azure-storage-blob==12.14.1
-    # via hail
-bokeh==1.4.0
-    # via hail
-boto3==1.26.76
-    # via hail
-botocore==1.29.76
-    # via
-    #   boto3
-    #   hail
-    #   s3transfer
+    # via redis
 cachetools==5.3.0
     # via google-auth
 certifi==2022.12.7
     # via
     #   elasticsearch
-    #   msrest
     #   requests
 cffi==1.15.1
     # via cryptography
 charset-normalizer==3.0.1
-    # via
-    #   aiohttp
-    #   requests
-commonmark==0.9.1
-    # via rich
+    # via requests
 cryptography==39.0.1
-    # via
-    #   azure-identity
-    #   azure-storage-blob
-    #   msal
-    #   pyjwt
-    #   social-auth-core
-decorator==4.4.2
-    # via hail
+    # via social-auth-core
 defusedxml==0.7.1
     # via
     #   python3-openid
     #   social-auth-core
-deprecated==1.2.13
-    # via hail
-dill==0.3.6
-    # via hail
 django==3.2.19
     # via
     #   -r requirements.in
@@ -103,11 +53,6 @@ elasticsearch-dsl==7.2.1
     # via -r requirements.in
 et-xmlfile==1.1.0
     # via openpyxl
-frozenlist==1.3.3
-    # via
-    #   aiohttp
-    #   aiosignal
-    #   hail
 google-api-core==2.11.0
     # via
     #   google-cloud-core
@@ -117,13 +62,10 @@ google-auth==2.14.1
     #   google-api-core
     #   google-cloud-core
     #   google-cloud-storage
-    #   hail
 google-cloud-core==2.3.2
     # via google-cloud-storage
 google-cloud-storage==2.7.0
-    # via
-    #   django-storages
-    #   hail
+    # via django-storages
 google-crc32c==1.5.0
     # via google-resumable-media
 google-resumable-media==2.4.1
@@ -132,82 +74,24 @@ googleapis-common-protos==1.58.0
     # via google-api-core
 gunicorn==20.1.0
     # via -r requirements.in
-hail==0.2.109
-    # via -r requirements.in
-humanize==1.1.0
-    # via hail
-hurry-filesize==0.9
-    # via hail
 idna==3.4
-    # via
-    #   requests
-    #   yarl
-isodate==0.6.1
-    # via msrest
-janus==1.0.0
-    # via hail
-jinja2==3.0.3
-    # via
-    #   bokeh
-    #   hail
+    # via requests
 jmespath==1.0.1
-    # via
-    #   -r requirements.in
-    #   boto3
-    #   botocore
-markupsafe==2.1.2
-    # via jinja2
-msal==1.21.0
-    # via
-    #   azure-identity
-    #   msal-extensions
-msal-extensions==1.0.0
-    # via azure-identity
-msrest==0.7.1
-    # via azure-storage-blob
-multidict==6.0.4
-    # via
-    #   aiohttp
-    #   yarl
-nest-asyncio==1.5.6
-    # via hail
-numpy==1.24.2
-    # via
-    #   bokeh
-    #   hail
-    #   pandas
-    #   scipy
+    # via -r requirements.in
 oauthlib==3.2.2
     # via
     #   requests-oauthlib
     #   social-auth-core
 openpyxl==3.1.1
     # via -r requirements.in
-orjson==3.8.6
-    # via hail
-packaging==23.0
-    # via bokeh
-pandas==1.5.3
-    # via hail
-parsimonious==0.8.1
-    # via hail
 pillow==9.4.0
-    # via
-    #   -r requirements.in
-    #   bokeh
-plotly==5.10.0
-    # via hail
-portalocker==2.7.0
-    # via msal-extensions
+    # via -r requirements.in
 protobuf==3.20.2
     # via
     #   google-api-core
     #   googleapis-common-protos
-    #   hail
 psycopg2==2.9.5
     # via -r requirements.in
-py4j==0.10.9
-    # via pyspark
 pyasn1==0.4.8
     # via
     #   pyasn1-modules
@@ -216,72 +100,38 @@ pyasn1-modules==0.2.8
     # via google-auth
 pycparser==2.21
     # via cffi
-pygments==2.14.0
-    # via rich
-pyjwt[crypto]==2.6.0
-    # via
-    #   hail
-    #   msal
-    #   social-auth-core
+pyjwt==2.6.0
+    # via social-auth-core
 pyliftover==0.4
     # via -r requirements.in
-pyspark==3.1.3
-    # via hail
 python-dateutil==2.8.2
-    # via
-    #   bokeh
-    #   botocore
-    #   elasticsearch-dsl
-    #   pandas
-python-json-logger==2.0.7
-    # via hail
+    # via elasticsearch-dsl
 python3-openid==3.2.0
     # via social-auth-core
 pytz==2022.7.1
-    # via
-    #   django
-    #   pandas
-pyyaml==6.0
-    # via bokeh
+    # via django
 redis==4.5.4
     # via -r requirements.in
 requests==2.31.0
     # via
     #   -r requirements.in
-    #   azure-core
     #   django-anymail
     #   google-api-core
     #   google-cloud-storage
-    #   hail
-    #   msal
-    #   msrest
     #   requests-oauthlib
     #   requests-toolbelt
     #   slacker
     #   social-auth-core
 requests-oauthlib==1.3.1
-    # via
-    #   msrest
-    #   social-auth-core
+    # via social-auth-core
 requests-toolbelt==0.10.1
     # via -r requirements.in
-rich==12.6.0
-    # via hail
 rsa==4.9
     # via google-auth
-s3transfer==0.6.0
-    # via boto3
-scipy==1.9.3
-    # via hail
 six==1.16.0
     # via
-    #   azure-core
-    #   azure-identity
-    #   bokeh
     #   elasticsearch-dsl
     #   google-auth
-    #   isodate
-    #   parsimonious
     #   python-dateutil
 slacker==0.14.0
     # via -r requirements.in
@@ -293,35 +143,16 @@ social-auth-core==4.3.0
     # via
     #   -r requirements.in
     #   social-auth-app-django
-sortedcontainers==2.4.0
-    # via hail
 sqlparse==0.4.4
     # via django
-tabulate==0.9.0
-    # via hail
-tenacity==8.2.1
-    # via plotly
-tornado==6.3.2
-    # via bokeh
 tqdm==4.64.1
     # via -r requirements.in
-typing-extensions==4.5.0
-    # via
-    #   azure-core
-    #   janus
 urllib3==1.26.14
     # via
-    #   botocore
     #   elasticsearch
     #   requests
-uvloop==0.17.0
-    # via hail
 whitenoise==6.3.0
     # via -r requirements.in
-wrapt==1.14.1
-    # via deprecated
-yarl==1.8.2
-    # via aiohttp
 
 # The following packages are considered to be unsafe in a requirements file:
 # setuptools
diff --git a/seqr/fixtures/1kg_project.json b/seqr/fixtures/1kg_project.json
@@ -1375,6 +1375,7 @@
     "pk": 1,
     "fields": {
         "sample": 151,
+        "rank": 0,
         "gene_id": "ENSG00000106554",
         "p_value": 1.08E-56,
         "z_score": 12.34,
@@ -1394,6 +1395,7 @@
     "pk": 2,
     "fields": {
         "sample": 153,
+        "rank": 0,
         "gene_id": "ENSG00000268903",
         "p_value": 1.08E-56,
         "z_score": 12.34,
@@ -1487,6 +1489,32 @@
         "file_path": "/readviz/NA19675.cram"
     }
 },
+{
+    "model": "seqr.igvsample",
+    "pk": 146,
+    "fields": {
+        "guid": "S000146_na20870",
+        "created_date": "2017-02-05T06:42:55.397Z",
+        "created_by": null,
+        "last_modified_date": "2017-03-13T09:07:49.744Z",
+        "individual": 7,
+        "sample_type": "alignment",
+        "file_path": "gs://readviz/NA20870.cram"
+    }
+},
+{
+    "model": "seqr.igvsample",
+    "pk": 147,
+    "fields": {
+        "guid": "S000147_na20870",
+        "created_date": "2017-02-05T06:42:55.397Z",
+        "created_by": null,
+        "last_modified_date": "2017-03-13T09:07:49.744Z",
+        "individual": 7,
+        "sample_type": "gcnv",
+        "file_path": "gs://datasets-gcnv/NA20870.bed.gz"
+    }
+},
 {
     "model": "seqr.varianttagtype",
     "pk": 1,