From ff376aba088a2fa891c671ad97d3c9e9f1180939 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Tue, 3 Dec 2024 13:43:07 -0500
Subject: [PATCH 01/21] Update packages

---
 servers/cromwell/requirements.txt | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/servers/cromwell/requirements.txt b/servers/cromwell/requirements.txt
index 08f6f6ff..3fa78d35 100644
--- a/servers/cromwell/requirements.txt
+++ b/servers/cromwell/requirements.txt
@@ -1,18 +1,18 @@
-certifi==2022.12.7
+certifi==2024.7.4
 chardet==3.0.4
 click==8.1.3
 clickclick==1.2.2
-connexion==2.14.1
+connexion==3.1.0
 Flask==2.2.5
 gevent==23.9
-greenlet==2.0.2
+greenlet==3.1.1
 gunicorn==22.0.0
-idna==2.7
+idna==2.8
 inflection==0.3.1
 itsdangerous==2.1.2
 Jinja2==3.1.2
 ../jm_utils
-jsonschema==2.6.0
+jsonschema==4.17.3
 MarkupSafe==2.1.1
 pathlib==1.0.1
 python-dateutil==2.6.0
@@ -30,4 +30,4 @@ six==1.11.0
 swagger-spec-validator==2.7.6
 typing==3.6.1
 urllib3==1.26.5
-Werkzeug==2.2.3
+Werkzeug==3.0.6

From 324e6c909f6f54b2e3f7acc25a9a3a585d7a71d2 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 4 Dec 2024 11:38:26 -0500
Subject: [PATCH 02/21] Don't upgrade greenlet

---
 servers/cromwell/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/servers/cromwell/requirements.txt b/servers/cromwell/requirements.txt
index 3fa78d35..68429ebe 100644
--- a/servers/cromwell/requirements.txt
+++ b/servers/cromwell/requirements.txt
@@ -5,7 +5,7 @@ clickclick==1.2.2
 connexion==3.1.0
 Flask==2.2.5
 gevent==23.9
-greenlet==3.1.1
+greenlet==2.0.2
 gunicorn==22.0.0
 idna==2.8
 inflection==0.3.1

From ac64b483a2c651e65b2151ee18b27a523a59df5c Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 4 Dec 2024 16:13:56 -0500
Subject: [PATCH 03/21] Remove special pyyaml handling

---
 servers/cromwell/Dockerfile       | 7 -------
 servers/cromwell/Dockerfile.dev   | 7 -------
 servers/cromwell/requirements.txt | 8 --------
 3 files changed, 22 deletions(-)

diff --git a/servers/cromwell/Dockerfile b/servers/cromwell/Dockerfile
index 5e93df0f..09d7dd9c 100644
--- a/servers/cromwell/Dockerfile
+++ b/servers/cromwell/Dockerfile
@@ -13,13 +13,6 @@ WORKDIR /app
 COPY --from=0 /job-manager/servers/jm_utils /app/jm_utils
 COPY --from=0 /job-manager/servers/cromwell/jobs /app/jobs
 COPY ./servers/cromwell/ /app/jobs
-# Below is a link explaining where the individual PyYAML install command comes from
-# https://github.com/yaml/pyyaml/issues/736#issuecomment-1653209769
-# In short, due to Cython 3 being released, PyYAML needs to have it's Cython dependency contrained, otherwise it will fail to install due to deprecated features
-# However installation of PyYAML uses a "wheel", which is basically a pre-compiled version of the package
-# This is problematic for requirements.txt as it cannot specify a wheel, only a source package
-# So we need to install PyYAML separately with the constraint defined in constraints.txt
-RUN cd jobs && PIP_CONSTRAINT=constraints.txt pip install PyYAML==5.4.1
 RUN cd jobs && pip install -r requirements.txt
 # We installed jm_utils so don't need local copy anymore, which breaks imports
 RUN rm -rf jm_utils
diff --git a/servers/cromwell/Dockerfile.dev b/servers/cromwell/Dockerfile.dev
index 42a19f8d..34f1d273 100644
--- a/servers/cromwell/Dockerfile.dev
+++ b/servers/cromwell/Dockerfile.dev
@@ -8,13 +8,6 @@ ADD servers/jm_utils /app/jm_utils
 ADD servers/cromwell/jobs /app/jobs
 COPY servers/cromwell/requirements.txt /app/jobs
 COPY servers/cromwell/constraints.txt /app/jobs
-# Below is a link explaining where the individual PyYAML install command comes from
-# https://github.com/yaml/pyyaml/issues/736#issuecomment-1653209769
-# In short, due to Cython 3 being released, PyYAML needs to have it's Cython dependency contrained, otherwise it will fail to install due to deprecated features
-# However installation of PyYAML uses a "wheel", which is basically a pre-compiled version of the package
-# This is problematic for requirements.txt as it cannot specify a wheel, only a source package
-# So we need to install PyYAML separately with the constraint defined in constraints.txt
-RUN cd jobs && PIP_CONSTRAINT=constraints.txt pip install PyYAML==5.4.1
 RUN cd jobs && pip install -r requirements.txt
 # We installed jm_utils so don't need local copy anymore, which breaks imports
 RUN rm -rf jm_utils
diff --git a/servers/cromwell/requirements.txt b/servers/cromwell/requirements.txt
index 68429ebe..4cda6651 100644
--- a/servers/cromwell/requirements.txt
+++ b/servers/cromwell/requirements.txt
@@ -17,14 +17,6 @@ MarkupSafe==2.1.1
 pathlib==1.0.1
 python-dateutil==2.6.0
 pytz==2022.4
-# Below is a link explaining why the PyYAML package is commented out
-# https://github.com/yaml/pyyaml/issues/736#issuecomment-1653209769
-# In short, due to Cython 3 being released, PyYAML needs to have it's Cython dependency contrained, otherwise it'll fail to install due to deprecated features
-# However installation of PyYAML uses a "wheel", which is basically a pre-compiled version of the package
-# This is problematic for requirements.txt as it cannot specify a wheel, only a source package
-# So we need to install PyYAML separately with the constraint defined in constraints.txt via pip install as opposed to here
-# You can see the above implemented in the Dockerfiles
-# PyYAML==5.4
 requests==2.28.1
 six==1.11.0
 swagger-spec-validator==2.7.6

From e5bc10ee85827fffc89dcaccdbd0657cb489c56a Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 4 Dec 2024 16:14:18 -0500
Subject: [PATCH 04/21] Updates for new connexion version

---
 servers/cromwell/jobs/__main__.py | 4 ++--
 servers/cromwell/jobs/encoder.py  | 6 +++---
 servers/cromwell/requirements.txt | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/servers/cromwell/jobs/__main__.py b/servers/cromwell/jobs/__main__.py
index c69c92c0..91de735a 100644
--- a/servers/cromwell/jobs/__main__.py
+++ b/servers/cromwell/jobs/__main__.py
@@ -54,8 +54,8 @@
     # Allow unknown args if we aren't the main program, these include flags to
     # gunicorn.
     args, _ = parser.parse_known_args()
-options = {"swagger_ui": False}
-app = connexion.App(__name__, specification_dir='./swagger/', options=options)
+options = connexion.options.SwaggerUIOptions(swagger_ui = False)
+app = connexion.App(__name__, specification_dir='./swagger/', swagger_ui_options=options)
 DEFAULT_CROMWELL_CREDENTIALS = {'cromwell_user': '', 'cromwell_password': ''}
 
 # Load credentials for cromwell
diff --git a/servers/cromwell/jobs/encoder.py b/servers/cromwell/jobs/encoder.py
index 21ebcdbc..3bdd0594 100644
--- a/servers/cromwell/jobs/encoder.py
+++ b/servers/cromwell/jobs/encoder.py
@@ -1,9 +1,9 @@
 from six import iteritems
 from jobs.models.base_model_ import Model
-from connexion.apps.flask_app import FlaskJSONEncoder
+from connexion.jsonifier import JSONEncoder as ConnexionJSONEncoder
 
 
-class JSONEncoder(FlaskJSONEncoder):
+class JSONEncoder(ConnexionJSONEncoder):
     include_nulls = False
 
     def default(self, o):
@@ -16,4 +16,4 @@ def default(self, o):
                 attr = o.attribute_map[attr]
                 dikt[attr] = value
             return dikt
-        return FlaskJSONEncoder.default(self, o)
+        return ConnexionJSONEncoder.default(self, o)
diff --git a/servers/cromwell/requirements.txt b/servers/cromwell/requirements.txt
index 4cda6651..8e9cadf1 100644
--- a/servers/cromwell/requirements.txt
+++ b/servers/cromwell/requirements.txt
@@ -2,7 +2,7 @@ certifi==2024.7.4
 chardet==3.0.4
 click==8.1.3
 clickclick==1.2.2
-connexion==3.1.0
+connexion[flask]==3.1.0
 Flask==2.2.5
 gevent==23.9
 greenlet==2.0.2

From 30ac65d4a4a1a05e3dadbbb7e3378ad818b162f7 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 6 Dec 2024 09:58:57 -0500
Subject: [PATCH 05/21] Additional updates

---
 servers/cromwell/requirements.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/servers/cromwell/requirements.txt b/servers/cromwell/requirements.txt
index 8e9cadf1..0f6f70cf 100644
--- a/servers/cromwell/requirements.txt
+++ b/servers/cromwell/requirements.txt
@@ -3,13 +3,13 @@ chardet==3.0.4
 click==8.1.3
 clickclick==1.2.2
 connexion[flask]==3.1.0
-Flask==2.2.5
+Flask==3.0.3
 gevent==23.9
 greenlet==2.0.2
 gunicorn==22.0.0
 idna==2.8
 inflection==0.3.1
-itsdangerous==2.1.2
+itsdangerous==2.2
 Jinja2==3.1.2
 ../jm_utils
 jsonschema==4.17.3

From 080dfc42845cbb5c2893337f7cdf73626715dbcf Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Thu, 12 Dec 2024 16:52:00 -0500
Subject: [PATCH 06/21] Run with uvicorn for connexion 3

---
 servers/cromwell/Dockerfile.dev   | 2 +-
 servers/cromwell/requirements.txt | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/servers/cromwell/Dockerfile.dev b/servers/cromwell/Dockerfile.dev
index 34f1d273..5c1e13fe 100644
--- a/servers/cromwell/Dockerfile.dev
+++ b/servers/cromwell/Dockerfile.dev
@@ -14,4 +14,4 @@ RUN rm -rf jm_utils
 
 # Missing required arguments -b PORT, -e ... which must be provided by the
 # docker image user.
-ENTRYPOINT ["/bin/bash", "/scripts/await_md5_match.sh", "/app/jobs/models/.jobs.yaml.md5", "--", "gunicorn", "jobs:run()"]
+ENTRYPOINT ["/bin/bash", "/scripts/await_md5_match.sh", "/app/jobs/models/.jobs.yaml.md5", "--", "gunicorn", "-k uvicorn.workers.UvicornWorker", "jobs:run()"]
diff --git a/servers/cromwell/requirements.txt b/servers/cromwell/requirements.txt
index 0f6f70cf..d2600cf7 100644
--- a/servers/cromwell/requirements.txt
+++ b/servers/cromwell/requirements.txt
@@ -23,3 +23,4 @@ swagger-spec-validator==2.7.6
 typing==3.6.1
 urllib3==1.26.5
 Werkzeug==3.0.6
+uvicorn==0.32.1

From 8219ab3f43e09d0cf9bb6192ee557b0c01e19a10 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Thu, 12 Dec 2024 16:53:59 -0500
Subject: [PATCH 07/21] Play nice with Connexion 3

---
 servers/cromwell/jobs/__main__.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/servers/cromwell/jobs/__main__.py b/servers/cromwell/jobs/__main__.py
index 91de735a..832bcc1f 100644
--- a/servers/cromwell/jobs/__main__.py
+++ b/servers/cromwell/jobs/__main__.py
@@ -7,6 +7,7 @@
 from distutils.util import strtobool
 
 import connexion
+from connexion.jsonifier import Jsonifier
 import requests
 from requests.auth import HTTPBasicAuth
 
@@ -54,8 +55,12 @@
     # Allow unknown args if we aren't the main program, these include flags to
     # gunicorn.
     args, _ = parser.parse_known_args()
+
 options = connexion.options.SwaggerUIOptions(swagger_ui = False)
-app = connexion.App(__name__, specification_dir='./swagger/', swagger_ui_options=options)
+app = connexion.App(__name__, 
+                    specification_dir='./swagger/', 
+                    swagger_ui_options=options, 
+                    jsonifier=Jsonifier(cls=JSONEncoder))
 DEFAULT_CROMWELL_CREDENTIALS = {'cromwell_user': '', 'cromwell_password': ''}
 
 # Load credentials for cromwell
@@ -109,8 +114,9 @@ def loadCapabilities(capabilities_path):
 app.app.config['sam_url'] = args.sam_url
 app.app.config['use_caas'] = args.use_caas and args.use_caas.lower() == 'true'
 app.app.config['include_subworkflows'] = args.include_subworkflows
-app.app.json_encoder = JSONEncoder
-app.add_api('swagger.yaml', base_path=args.path_prefix)
+app.add_api('swagger.yaml', 
+            base_path=args.path_prefix, 
+            jsonifier=Jsonifier(cls=JSONEncoder))
 
 
 def run():
@@ -132,4 +138,4 @@ def run():
             logger.critical(err)
             logger.critical('Failed to connect to Cromwell: {}'.format(
                 args.cromwell_url))
-    return app.app
+    return app

From 841d2295a4bde4e817d5d29d1f940052d5c68052 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Thu, 12 Dec 2024 16:55:39 -0500
Subject: [PATCH 08/21] Add univorn for non-dev

---
 servers/cromwell/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/servers/cromwell/Dockerfile b/servers/cromwell/Dockerfile
index 09d7dd9c..5f549e6f 100644
--- a/servers/cromwell/Dockerfile
+++ b/servers/cromwell/Dockerfile
@@ -19,4 +19,4 @@ RUN rm -rf jm_utils
 
 # Missing required arguments -b PORT, -e ... which must be provided by the
 # docker image user.
-ENTRYPOINT ["gunicorn", "jobs:run()"]
+ENTRYPOINT ["gunicorn", "-k uvicorn.workers.UvicornWorker", "jobs:run()"]

From 051c1552a0694c09737dc1d901a43958820b58ce Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 13 Dec 2024 09:41:40 -0500
Subject: [PATCH 09/21] Make linter happy

---
 servers/cromwell/jobs/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/servers/cromwell/jobs/__main__.py b/servers/cromwell/jobs/__main__.py
index 832bcc1f..1058ba07 100644
--- a/servers/cromwell/jobs/__main__.py
+++ b/servers/cromwell/jobs/__main__.py
@@ -56,7 +56,7 @@
     # gunicorn.
     args, _ = parser.parse_known_args()
 
-options = connexion.options.SwaggerUIOptions(swagger_ui = False)
+options = connexion.options.SwaggerUIOptions(swagger_ui=False)
 app = connexion.App(__name__, 
                     specification_dir='./swagger/', 
                     swagger_ui_options=options, 

From 1945595b7076eee4e41c430086fefb788dc8511d Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 13 Dec 2024 09:52:04 -0500
Subject: [PATCH 10/21] Make linter happier

---
 servers/cromwell/jobs/__main__.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/servers/cromwell/jobs/__main__.py b/servers/cromwell/jobs/__main__.py
index 1058ba07..933b6feb 100644
--- a/servers/cromwell/jobs/__main__.py
+++ b/servers/cromwell/jobs/__main__.py
@@ -57,9 +57,9 @@
     args, _ = parser.parse_known_args()
 
 options = connexion.options.SwaggerUIOptions(swagger_ui=False)
-app = connexion.App(__name__, 
-                    specification_dir='./swagger/', 
-                    swagger_ui_options=options, 
+app = connexion.App(__name__,
+                    specification_dir='./swagger/',
+                    swagger_ui_options=options,
                     jsonifier=Jsonifier(cls=JSONEncoder))
 DEFAULT_CROMWELL_CREDENTIALS = {'cromwell_user': '', 'cromwell_password': ''}
 
@@ -114,8 +114,8 @@ def loadCapabilities(capabilities_path):
 app.app.config['sam_url'] = args.sam_url
 app.app.config['use_caas'] = args.use_caas and args.use_caas.lower() == 'true'
 app.app.config['include_subworkflows'] = args.include_subworkflows
-app.add_api('swagger.yaml', 
-            base_path=args.path_prefix, 
+app.add_api('swagger.yaml',
+            base_path=args.path_prefix,
             jsonifier=Jsonifier(cls=JSONEncoder))
 
 

From 77636a9310ff5bea626459dbc7210cf4eba12d4a Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 13 Dec 2024 10:20:48 -0500
Subject: [PATCH 11/21] Update test app creation

---
 servers/cromwell/jobs/test/__init__.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/servers/cromwell/jobs/test/__init__.py b/servers/cromwell/jobs/test/__init__.py
index 2e5d87f1..954b5408 100644
--- a/servers/cromwell/jobs/test/__init__.py
+++ b/servers/cromwell/jobs/test/__init__.py
@@ -1,6 +1,7 @@
 import logging
 
 import connexion
+from connexion.jsonifier import Jsonifier
 from flask_testing import TestCase
 
 from ..encoder import JSONEncoder
@@ -10,7 +11,11 @@ class BaseTestCase(TestCase):
 
     def create_app(self):
         logging.getLogger('connexion.operation').setLevel('ERROR')
-        app = connexion.App(__name__, specification_dir='../swagger/')
-        app.app.json_encoder = JSONEncoder
-        app.add_api('swagger.yaml')
-        return app.app
+        options = connexion.options.SwaggerUIOptions(swagger_ui=False)
+        app = connexion.App(__name__,
+                            specification_dir='../swagger/',
+                            swagger_ui_options=options,
+                            jsonifier=Jsonifier(cls=JSONEncoder))
+        app.add_api('swagger.yaml',
+                    jsonifier=Jsonifier(cls=JSONEncoder))
+        return app

From 72abe85b6cf6a80939ec01d9435dbd7296896c4b Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 13 Dec 2024 10:20:53 -0500
Subject: [PATCH 12/21] Doc fix

---
 servers/cromwell/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/servers/cromwell/README.md b/servers/cromwell/README.md
index 59589c49..c8a8612f 100644
--- a/servers/cromwell/README.md
+++ b/servers/cromwell/README.md
@@ -369,5 +369,5 @@ To run unit and integration tests on the python-flask app, install
 [`tox`](https://github.com/tox-dev/tox).
 ```
 cd servers/cromwell
-tox -- -s
+tox -- -s .
 ```

From 3066cf284d96665e8b0d8eaf907ecde6fea9af25 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 13 Dec 2024 16:11:25 -0500
Subject: [PATCH 13/21] Don't unnecessarily confuse us with stack traces

---
 servers/cromwell/jobs/__main__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/servers/cromwell/jobs/__main__.py b/servers/cromwell/jobs/__main__.py
index 933b6feb..6800ffdd 100644
--- a/servers/cromwell/jobs/__main__.py
+++ b/servers/cromwell/jobs/__main__.py
@@ -100,11 +100,11 @@ def loadCapabilities(capabilities_path):
             capabilities_config)
         return app.app.config['capabilities']
     except IOError as io_err:
-        logger.exception(
+        logger.error(
             'Failed to load capabilities config, using default display fields. %s',
             io_err)
     except TypeError as type_err:
-        logger.exception(
+        logger.error(
             'Failed to load capabilities config, using default display fields. %s',
             type_err)
 

From e29d61b4f5df985001f10e1ccd1f3ab4b9f0a3f9 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 13 Dec 2024 16:12:37 -0500
Subject: [PATCH 14/21] Update tests to not use flask_testing

---
 servers/cromwell/jobs/test/__init__.py        |  26 ++--
 servers/cromwell/jobs/test/test_auth_utils.py |  33 +++--
 .../cromwell/jobs/test/test_job_statuses.py   |   6 +-
 .../jobs/test/test_jobs_controller.py         | 116 ++++++++----------
 .../cromwell/jobs/test/test_task_statuses.py  |   5 +-
 servers/cromwell/test-requirements.txt        |   1 -
 6 files changed, 83 insertions(+), 104 deletions(-)

diff --git a/servers/cromwell/jobs/test/__init__.py b/servers/cromwell/jobs/test/__init__.py
index 954b5408..e441bc85 100644
--- a/servers/cromwell/jobs/test/__init__.py
+++ b/servers/cromwell/jobs/test/__init__.py
@@ -1,21 +1,21 @@
 import logging
 
 import connexion
+from flask import json
 from connexion.jsonifier import Jsonifier
-from flask_testing import TestCase
 
 from ..encoder import JSONEncoder
 
+def create_app():
+    logging.getLogger('connexion.operation').setLevel('ERROR')
+    options = connexion.options.SwaggerUIOptions(swagger_ui=False)
+    app = connexion.App(__name__,
+                        specification_dir='../swagger/',
+                        swagger_ui_options=options,
+                        jsonifier=Jsonifier(cls=JSONEncoder))
+    app.add_api('swagger.yaml',
+                jsonifier=Jsonifier(cls=JSONEncoder))
+    return app
 
-class BaseTestCase(TestCase):
-
-    def create_app(self):
-        logging.getLogger('connexion.operation').setLevel('ERROR')
-        options = connexion.options.SwaggerUIOptions(swagger_ui=False)
-        app = connexion.App(__name__,
-                            specification_dir='../swagger/',
-                            swagger_ui_options=options,
-                            jsonifier=Jsonifier(cls=JSONEncoder))
-        app.add_api('swagger.yaml',
-                    jsonifier=Jsonifier(cls=JSONEncoder))
-        return app
+def json_dumps(o):
+    return json.dumps(0, cls=JSONEncoder)
diff --git a/servers/cromwell/jobs/test/test_auth_utils.py b/servers/cromwell/jobs/test/test_auth_utils.py
index d45eb706..cb2b47b9 100644
--- a/servers/cromwell/jobs/test/test_auth_utils.py
+++ b/servers/cromwell/jobs/test/test_auth_utils.py
@@ -5,20 +5,27 @@
 from asyncio.log import logger
 
 import requests_mock
+import unittest
 
 from ..__main__ import loadCapabilities
 from ..models.capabilities_response import CapabilitiesResponse
-from . import BaseTestCase
 
+from . import create_app, json_dumps
 
-class TestAuthUtils(BaseTestCase):
+
+class TestAuthUtils(unittest.TestCase):
 
     def setUp(self):
+        self.app = create_app()
         self.base_url = 'https://test-cromwell.org'
+        self.client = self.app.test_client()
+
+    def assertStatus(self, response, expectedStatus):
+        self.assertEqual(response.status_code, expectedStatus)
 
     @requests_mock.mock()
     def test_token_auth_returns_200(self, mock_request):
-        self.app.config.update({
+        self.app.app.config.update({
             'cromwell_url': self.base_url,
             'cromwell_user': '',
             'cromwell_password': '',
@@ -34,16 +41,14 @@ def _request_callback(request, context):
         query_url = self.base_url + '/query'
         mock_request.post(query_url, json=_request_callback)
 
-        response = self.client.open('/jobs/query',
-                                    method='POST',
+        response = self.client.post('/jobs/query',
                                     headers={'Authentication': 'Bearer 12345'},
-                                    data={},
-                                    content_type='application/json')
+                                    json="{}")
         self.assertStatus(response, 200)
 
     @requests_mock.mock()
     def test_basic_auth_returns_200(self, mock_request):
-        self.app.config.update({
+        self.app.app.config.update({
             'cromwell_url': self.base_url,
             'cromwell_user': 'user',
             'cromwell_password': 'password',
@@ -58,24 +63,18 @@ def _request_callback(request, context):
         query_url = self.base_url + '/query'
         mock_request.post(query_url, json=_request_callback)
 
-        response = self.client.open('/jobs/query',
-                                    method='POST',
-                                    data={},
-                                    content_type='application/json')
+        response = self.client.post('/jobs/query', json="{}")
         self.assertStatus(response, 200)
 
     def test_no_auth_with_caas_returns_401(self):
-        self.app.config.update({
+        self.app.app.config.update({
             'cromwell_url': self.base_url,
             'cromwell_user': '',
             'cromwell_password': '',
             'use_caas': True,
             'capabilities': {}
         })
-        response = self.client.open('/jobs/query',
-                                    method='POST',
-                                    data={},
-                                    content_type='application/json')
+        response = self.client.post('/jobs/query', data="{}")
         self.assertStatus(response, 401)
 
 
diff --git a/servers/cromwell/jobs/test/test_job_statuses.py b/servers/cromwell/jobs/test/test_job_statuses.py
index babe123b..6e2adeed 100644
--- a/servers/cromwell/jobs/test/test_job_statuses.py
+++ b/servers/cromwell/jobs/test/test_job_statuses.py
@@ -2,12 +2,12 @@
 
 from __future__ import absolute_import
 
-from jobs.controllers.utils import job_statuses
+import unittest
 
-from . import BaseTestCase
+from jobs.controllers.utils import job_statuses
 
 
-class TestJobStatuses(BaseTestCase):
+class TestJobStatuses(unittest.TestCase):
 
     def test_cromwell_execution_status_converts_correctly(self):
         for key, status in job_statuses.ApiStatus.__dict__.items():
diff --git a/servers/cromwell/jobs/test/test_jobs_controller.py b/servers/cromwell/jobs/test/test_jobs_controller.py
index d9275f14..24f45399 100644
--- a/servers/cromwell/jobs/test/test_jobs_controller.py
+++ b/servers/cromwell/jobs/test/test_jobs_controller.py
@@ -6,6 +6,7 @@
 
 import dateutil.parser
 import requests_mock
+import unittest
 from dateutil.tz import *
 from flask import json
 from jobs.controllers import jobs_controller
@@ -15,22 +16,27 @@
 from jobs.models.update_job_labels_request import UpdateJobLabelsRequest
 from jobs.models.update_job_labels_response import UpdateJobLabelsResponse
 
-from . import BaseTestCase
+from . import create_app, json_dumps
 
 
-class TestJobsController(BaseTestCase):
+class TestJobsController(unittest.TestCase):
     """ JobsController integration test stubs """
     maxDiff = None
 
     def setUp(self):
+        self.app = create_app()
         self.base_url = 'https://test-cromwell.org'
-        self.app.config.update({
+        self.app.app.config.update({
             'cromwell_url': self.base_url,
             'cromwell_user': 'user',
             'cromwell_password': 'password',
             'use_caas': False,
             'capabilities': {}
         })
+        self.client = self.app.test_client()
+
+    def assertStatus(self, response, expectedStatus):
+        self.assertEqual(response.status_code, expectedStatus)
 
     @requests_mock.mock()
     def test_abort_job(self, mock_request):
@@ -47,8 +53,7 @@ def _request_callback(request, context):
         abort_url = self.base_url + '/{id}/abort'.format(id=workflow_id)
         mock_request.post(abort_url, json=_request_callback)
 
-        response = self.client.open('/jobs/{id}/abort'.format(id=workflow_id),
-                                    method='POST')
+        response = self.client.post('/jobs/{id}/abort'.format(id=workflow_id))
         self.assertStatus(response, 204)
 
     @requests_mock.mock()
@@ -69,8 +74,7 @@ def _request_callback(request, context):
         abort_url = self.base_url + '/{id}/abort'.format(id=workflow_id)
         mock_request.post(abort_url, json=_request_callback)
 
-        response = self.client.open('/jobs/{id}/abort'.format(id=workflow_id),
-                                    method='POST')
+        response = self.client.post('/jobs/{id}/abort'.format(id=workflow_id))
         self.assertStatus(response, 404)
 
     @requests_mock.mock()
@@ -142,13 +146,11 @@ def _request_callback_get_job(request, context):
 
         payload = UpdateJobLabelsRequest(
             labels={"test_label": "test_label_value"})
-        response = self.client.open(
+        response = self.client.post(
             '/jobs/{id}/updateLabels'.format(id=workflow_id),
-            method='POST',
-            data=json.dumps(payload),
-            content_type='application/json')
+            json=json_dumps(payload))
         self.assertStatus(response, 200)
-        self.assertEquals(response.json,
+        self.assertEquals(response.json(),
                           {"labels": {
                               "test_label": "test_label_value"
                           }})
@@ -224,11 +226,9 @@ def _request_callback_get_job(request, context):
 
         payload = UpdateJobLabelsRequest(
             labels={"new_test_label": "new_test_label_value"})
-        response = self.client.open(
+        response = self.client.post(
             '/jobs/{id}/updateLabels'.format(id=workflow_id),
-            method='POST',
-            data=json.dumps(payload),
-            content_type='application/json')
+            json=json_dumps(payload))
 
         expected_result = UpdateJobLabelsResponse.from_dict({
             "labels": {
@@ -238,7 +238,7 @@ def _request_callback_get_job(request, context):
             }
         })
 
-        result = UpdateJobLabelsResponse.from_dict(response.json)
+        result = UpdateJobLabelsResponse.from_dict(response.json())
 
         self.assertStatus(response, 200)
         self.assertDictEqual(result.labels, expected_result.labels)
@@ -257,13 +257,11 @@ def _request_callback(request, context):
         mock_request.patch(update_label_url, json=_request_callback)
 
         payload = UpdateJobLabelsRequest(labels={"": "test_invalid_label"})
-        response = self.client.open(
+        response = self.client.post(
             '/jobs/{id}/updateLabels'.format(id=workflow_id),
-            method='POST',
-            data=json.dumps(payload),
-            content_type='application/json')
+            json=json_dumps(payload))
         self.assertStatus(response, 400)
-        self.assertEquals(json.loads(response.data)['detail'], error_message)
+        self.assertEquals(response.json()['detail'], error_message)
 
     @requests_mock.mock()
     def test_update_job_labels_internal_server_error(self, mock_request):
@@ -280,13 +278,11 @@ def _request_callback(request, context):
 
         payload = UpdateJobLabelsRequest(
             labels={"test_label": "test_label_value"})
-        response = self.client.open(
+        response = self.client.post(
             '/jobs/{id}/updateLabels'.format(id=workflow_id),
-            method='POST',
-            data=json.dumps(payload),
-            content_type='application/json')
+            json=json_dumps(payload))
         self.assertStatus(response, 500)
-        self.assertEquals(json.loads(response.data)['detail'], error_message)
+        self.assertEquals(response.json()['detail'], error_message)
 
     @requests_mock.mock()
     def test_update_job_labels_not_found(self, mock_request):
@@ -306,13 +302,11 @@ def _request_callback(request, context):
 
         payload = UpdateJobLabelsRequest(
             labels={"test_label": "test_label_value"})
-        response = self.client.open(
+        response = self.client.post(
             '/jobs/{id}/updateLabels'.format(id=workflow_id),
-            method='POST',
-            data=json.dumps(payload),
-            content_type='application/json')
+            json=json_dumps(payload))
         self.assertStatus(response, 404)
-        self.assertEquals(json.loads(response.data)['detail'], error_message)
+        self.assertEquals(response.json()['detail'], error_message)
 
     @requests_mock.mock()
     def test_update_job_labels_undefined_unsupported_media_type_exception(
@@ -329,13 +323,11 @@ def _request_callback(request, context):
         mock_request.patch(update_label_url, json=_request_callback)
 
         payload = UpdateJobLabelsRequest(labels={"test_label": None})
-        response = self.client.open(
+        response = self.client.post(
             '/jobs/{id}/updateLabels'.format(id=workflow_id),
-            headers={'Accept': 'application/json'},
-            method='POST',
-            data=json.dumps(payload))
+            json=json_dumps(payload))
         self.assertStatus(response, 415)
-        self.assertEquals(json.loads(response.data)['detail'], error_message)
+        self.assertEquals(response.json()['detail'], error_message)
 
     @requests_mock.mock()
     def test_get_job_returns_200(self, mock_request):
@@ -400,10 +392,9 @@ def _request_callback(request, context):
         cromwell_url = self.base_url + '/{id}/metadata'.format(id=workflow_id)
         mock_request.get(cromwell_url, json=_request_callback)
 
-        response = self.client.open('/jobs/{id}'.format(id=workflow_id),
-                                    method='GET')
+        response = self.client.get('/jobs/{id}'.format(id=workflow_id))
         self.assertStatus(response, 200)
-        response_data = json.loads(response.data)
+        response_data = response.json()
         expected_data = {
             'name': workflow_name,
             'id': workflow_id,
@@ -481,10 +472,9 @@ def _request_callback(request, context):
         cromwell_url = self.base_url + '/{id}/metadata'.format(id=workflow_id)
         mock_request.get(cromwell_url, json=_request_callback)
 
-        response = self.client.open('/jobs/{id}'.format(id=workflow_id),
-                                    method='GET')
+        response = self.client.get('/jobs/{id}'.format(id=workflow_id))
         self.assertStatus(response, 200)
-        response_data = json.loads(response.data)
+        response_data = response.json()
         expected_data = {
             'name': workflow_name,
             'id': workflow_id,
@@ -595,10 +585,9 @@ def _request_callback(request, context):
         cromwell_url = self.base_url + '/{id}/metadata'.format(id=workflow_id)
         mock_request.get(cromwell_url, json=_request_callback)
 
-        response = self.client.open('/jobs/{id}'.format(id=workflow_id),
-                                    method='GET')
+        response = self.client.get('/jobs/{id}'.format(id=workflow_id))
         self.assertStatus(response, 200)
-        response_data = json.loads(response.data)
+        response_data = response.json()
         expected_data = {
             'name': workflow_name,
             'id': workflow_id,
@@ -740,11 +729,10 @@ def _request_callback(request, context):
         cromwell_url = self.base_url + '/{id}/metadata'.format(id=workflow_id)
         mock_request.get(cromwell_url, json=_request_callback)
 
-        response = self.client.open('/jobs/{id}/{task}/attempts'.format(
-            id=workflow_id, task='task'),
-                                    method='GET')
+        response = self.client.get('/jobs/{id}/{task}/attempts'.format(
+            id=workflow_id, task='task'))
         self.assertStatus(response, 200)
-        response_data = json.loads(response.data)
+        response_data = response.json()
         expected_data = {
             'attempts': [{
                 'attemptNumber': 1,
@@ -852,13 +840,12 @@ def _request_callback(request, context):
         cromwell_url = self.base_url + '/{id}/metadata'.format(id=workflow_id)
         mock_request.get(cromwell_url, json=_request_callback)
 
-        response = self.client.open(
+        response = self.client.get(
             '/jobs/{id}/{task}/{index}/attempts'.format(id=workflow_id,
                                                         task='task',
-                                                        index=0),
-            method='GET')
+                                                        index=0))
         self.assertStatus(response, 200)
-        response_data = json.loads(response.data)
+        response_data = response.json()
         expected_data = {
             'attempts': [{
                 'attemptNumber': 1,
@@ -939,10 +926,9 @@ def _request_callback(request, context):
         cromwell_url = self.base_url + '/{id}/metadata'.format(id=workflow_id)
         mock_request.get(cromwell_url, json=_request_callback)
 
-        response = self.client.open('/jobs/{id}'.format(id=workflow_id),
-                                    method='GET')
+        response = self.client.get('/jobs/{id}'.format(id=workflow_id))
         self.assertStatus(response, 400)
-        self.assertEquals(json.loads(response.data)['detail'], error_message)
+        self.assertEquals(response.json()['detail'], error_message)
 
     @requests_mock.mock()
     def test_job_not_found(self, mock_request):
@@ -956,10 +942,9 @@ def _request_callback(request, context):
         cromwell_url = self.base_url + '/{id}/metadata'.format(id=workflow_id)
         mock_request.get(cromwell_url, json=_request_callback)
 
-        response = self.client.open('/jobs/{id}'.format(id=workflow_id),
-                                    method='GET')
+        response = self.client.get('/jobs/{id}'.format(id=workflow_id))
         self.assertStatus(response, 404)
-        self.assertEquals(json.loads(response.data)['detail'], error_message)
+        self.assertEquals(response.json()['detail'], error_message)
 
     @requests_mock.mock()
     def test_job_internal_server_error(self, mock_request):
@@ -973,10 +958,9 @@ def _request_callback(request, context):
         cromwell_url = self.base_url + '/{id}/metadata'.format(id=workflow_id)
         mock_request.get(cromwell_url, json=_request_callback)
 
-        response = self.client.open('/jobs/{id}'.format(id=workflow_id),
-                                    method='GET')
+        response = self.client.get('/jobs/{id}'.format(id=workflow_id))
         self.assertStatus(response, 500)
-        self.assertEquals(json.loads(response.data)['detail'], error_message)
+        self.assertEquals(response.json()['detail'], error_message)
 
     @requests_mock.mock()
     def test_query_jobs_returns_200(self, mock_request):
@@ -994,10 +978,8 @@ def _request_callback(request, context):
         mock_request.post(query_url, json=_request_callback)
 
         query = QueryJobsRequest()
-        response = self.client.open('/jobs/query',
-                                    method='POST',
-                                    data=json.dumps(query),
-                                    content_type='application/json')
+        response = self.client.post('/jobs/query',
+                                    json=json_dumps(query))
         self.assertStatus(response, 200)
 
     def test_empty_cromwell_query_params(self):
diff --git a/servers/cromwell/jobs/test/test_task_statuses.py b/servers/cromwell/jobs/test/test_task_statuses.py
index b5919aba..a63dda4d 100644
--- a/servers/cromwell/jobs/test/test_task_statuses.py
+++ b/servers/cromwell/jobs/test/test_task_statuses.py
@@ -3,15 +3,14 @@
 from __future__ import absolute_import
 
 import itertools
+import unittest
 
 from jobs.controllers import jobs_controller
 from jobs.controllers.utils import task_statuses
 from jobs.models.shard import Shard
 
-from . import BaseTestCase
 
-
-class TestTaskStatuses(BaseTestCase):
+class TestTaskStatuses(unittest.TestCase):
     # yapf: disable
     def test_cromwell_execution_to_api_maps_all_task_execution_statuses_correctly(self):
         self.assertEqual(task_statuses.cromwell_execution_to_api('NotStarted'), 'Submitted')
diff --git a/servers/cromwell/test-requirements.txt b/servers/cromwell/test-requirements.txt
index ff27c281..6be7455f 100644
--- a/servers/cromwell/test-requirements.txt
+++ b/servers/cromwell/test-requirements.txt
@@ -1,4 +1,3 @@
-flask_testing==0.8.1
 coverage>=4.0.3
 nose2>=0.12.0
 pluggy>=1.0.0

From 2b28efaff36f95f40e1241c5d51e74455d629523 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 13 Dec 2024 16:12:43 -0500
Subject: [PATCH 15/21] Fix test

---
 servers/cromwell/jobs/controllers/jobs_controller.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/servers/cromwell/jobs/controllers/jobs_controller.py b/servers/cromwell/jobs/controllers/jobs_controller.py
index a31e81d9..382235c7 100644
--- a/servers/cromwell/jobs/controllers/jobs_controller.py
+++ b/servers/cromwell/jobs/controllers/jobs_controller.py
@@ -30,7 +30,8 @@
 from jobs.models.update_job_labels_request import UpdateJobLabelsRequest
 from jobs.models.update_job_labels_response import UpdateJobLabelsResponse
 from werkzeug.exceptions import (BadRequest, Forbidden, InternalServerError,
-                                 NotFound, ServiceUnavailable, Unauthorized)
+                                 NotFound, ServiceUnavailable, Unauthorized,
+                                 UnsupportedMediaType)
 
 # This is needed to support different Python versions - this
 # package structure changed in Python 3.10.
@@ -559,6 +560,8 @@ def handle_error(response):
         raise BadRequest(_get_response_message(response))
     elif response.status_code == Forbidden.code:
         raise Forbidden(_get_response_message(response))
+    elif response.status_code == UnsupportedMediaType.code:
+        raise UnsupportedMediaType(_get_response_message(response))
     elif response.status_code == InternalServerError.code:
         raise InternalServerError(_get_response_message(response))
     elif response.status_code == NotFound.code:

From 8ab018acba2fb9090ea91ddf248ec132228b17e2 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 13 Dec 2024 16:13:49 -0500
Subject: [PATCH 16/21] Remove unused pip constraint

---
 servers/cromwell/constraints.txt | 1 -
 servers/cromwell/tox.ini         | 1 -
 2 files changed, 2 deletions(-)
 delete mode 100644 servers/cromwell/constraints.txt

diff --git a/servers/cromwell/constraints.txt b/servers/cromwell/constraints.txt
deleted file mode 100644
index f21f1571..00000000
--- a/servers/cromwell/constraints.txt
+++ /dev/null
@@ -1 +0,0 @@
-cython<3.0.0
\ No newline at end of file
diff --git a/servers/cromwell/tox.ini b/servers/cromwell/tox.ini
index 645784d3..fd606fa9 100644
--- a/servers/cromwell/tox.ini
+++ b/servers/cromwell/tox.ini
@@ -2,7 +2,6 @@
 envlist = py310
 
 [testenv]
-setenv=PIP_CONSTRAINT={toxinidir}/constraints.txt
 deps=-r{toxinidir}/requirements.txt
      -r{toxinidir}/test-requirements.txt
 

From 8efe7507022476b77b0e12f8fde3b122ef2f31b6 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 13 Dec 2024 16:17:14 -0500
Subject: [PATCH 17/21] Remove unused imports

---
 servers/cromwell/jobs/test/test_auth_utils.py      | 5 +----
 servers/cromwell/jobs/test/test_jobs_controller.py | 1 -
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/servers/cromwell/jobs/test/test_auth_utils.py b/servers/cromwell/jobs/test/test_auth_utils.py
index cb2b47b9..373879e2 100644
--- a/servers/cromwell/jobs/test/test_auth_utils.py
+++ b/servers/cromwell/jobs/test/test_auth_utils.py
@@ -7,10 +7,7 @@
 import requests_mock
 import unittest
 
-from ..__main__ import loadCapabilities
-from ..models.capabilities_response import CapabilitiesResponse
-
-from . import create_app, json_dumps
+from . import create_app
 
 
 class TestAuthUtils(unittest.TestCase):
diff --git a/servers/cromwell/jobs/test/test_jobs_controller.py b/servers/cromwell/jobs/test/test_jobs_controller.py
index 24f45399..a7d3c0cf 100644
--- a/servers/cromwell/jobs/test/test_jobs_controller.py
+++ b/servers/cromwell/jobs/test/test_jobs_controller.py
@@ -8,7 +8,6 @@
 import requests_mock
 import unittest
 from dateutil.tz import *
-from flask import json
 from jobs.controllers import jobs_controller
 from jobs.models.extended_fields import ExtendedFields
 from jobs.models.query_jobs_request import QueryJobsRequest

From 5b6c5d72f4a3be8ddbf54504ba24409fd49693be Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 13 Dec 2024 16:18:10 -0500
Subject: [PATCH 18/21] Linting

---
 servers/cromwell/jobs/test/__init__.py             | 5 +++--
 servers/cromwell/jobs/test/test_jobs_controller.py | 9 +++------
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/servers/cromwell/jobs/test/__init__.py b/servers/cromwell/jobs/test/__init__.py
index e441bc85..f8ea56e2 100644
--- a/servers/cromwell/jobs/test/__init__.py
+++ b/servers/cromwell/jobs/test/__init__.py
@@ -6,6 +6,7 @@
 
 from ..encoder import JSONEncoder
 
+
 def create_app():
     logging.getLogger('connexion.operation').setLevel('ERROR')
     options = connexion.options.SwaggerUIOptions(swagger_ui=False)
@@ -13,9 +14,9 @@ def create_app():
                         specification_dir='../swagger/',
                         swagger_ui_options=options,
                         jsonifier=Jsonifier(cls=JSONEncoder))
-    app.add_api('swagger.yaml',
-                jsonifier=Jsonifier(cls=JSONEncoder))
+    app.add_api('swagger.yaml', jsonifier=Jsonifier(cls=JSONEncoder))
     return app
 
+
 def json_dumps(o):
     return json.dumps(0, cls=JSONEncoder)
diff --git a/servers/cromwell/jobs/test/test_jobs_controller.py b/servers/cromwell/jobs/test/test_jobs_controller.py
index a7d3c0cf..b4f132d3 100644
--- a/servers/cromwell/jobs/test/test_jobs_controller.py
+++ b/servers/cromwell/jobs/test/test_jobs_controller.py
@@ -839,10 +839,8 @@ def _request_callback(request, context):
         cromwell_url = self.base_url + '/{id}/metadata'.format(id=workflow_id)
         mock_request.get(cromwell_url, json=_request_callback)
 
-        response = self.client.get(
-            '/jobs/{id}/{task}/{index}/attempts'.format(id=workflow_id,
-                                                        task='task',
-                                                        index=0))
+        response = self.client.get('/jobs/{id}/{task}/{index}/attempts'.format(
+            id=workflow_id, task='task', index=0))
         self.assertStatus(response, 200)
         response_data = response.json()
         expected_data = {
@@ -977,8 +975,7 @@ def _request_callback(request, context):
         mock_request.post(query_url, json=_request_callback)
 
         query = QueryJobsRequest()
-        response = self.client.post('/jobs/query',
-                                    json=json_dumps(query))
+        response = self.client.post('/jobs/query', json=json_dumps(query))
         self.assertStatus(response, 200)
 
     def test_empty_cromwell_query_params(self):

From 2936672c4b8993b709f0e0888373f6396c14768f Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 16 Dec 2024 10:11:38 -0500
Subject: [PATCH 19/21] Finish deleting constraints

---
 servers/cromwell/Dockerfile.dev | 1 -
 1 file changed, 1 deletion(-)

diff --git a/servers/cromwell/Dockerfile.dev b/servers/cromwell/Dockerfile.dev
index 5c1e13fe..65a68d46 100644
--- a/servers/cromwell/Dockerfile.dev
+++ b/servers/cromwell/Dockerfile.dev
@@ -7,7 +7,6 @@ WORKDIR /app
 ADD servers/jm_utils /app/jm_utils
 ADD servers/cromwell/jobs /app/jobs
 COPY servers/cromwell/requirements.txt /app/jobs
-COPY servers/cromwell/constraints.txt /app/jobs
 RUN cd jobs && pip install -r requirements.txt
 # We installed jm_utils so don't need local copy anymore, which breaks imports
 RUN rm -rf jm_utils

From 09ba5df39c749a35466cff9ab903c31d706b46c9 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Tue, 17 Dec 2024 10:21:17 -0500
Subject: [PATCH 20/21] Reorder API endpoints to make Starlette happy

---
 api/jobs.yaml | 160 +++++++++++++++++++++++++-------------------------
 1 file changed, 80 insertions(+), 80 deletions(-)

diff --git a/api/jobs.yaml b/api/jobs.yaml
index a1456b79..fc50607c 100644
--- a/api/jobs.yaml
+++ b/api/jobs.yaml
@@ -33,60 +33,56 @@ paths:
       tags:
         - Capabilities
 
-  '/jobs/{id}/abort':
-    post:
-      operationId: AbortJob
-      summary: Abort a job by ID
+  '/jobs/operationDetails':
+    get:
+      operationId: GetOperationDetails
+      summary: Call for operation details from the Google Pipelines API
       parameters:
-        - name: id
-          description: Job ID
+        - name: job
+          description: job ID
           required: true
+          in: query
           type: string
-          in: path
+        - name: operation
+          description: operation ID
+          type: string
+          in: query
       responses:
         '200':
           description: Success
-        '400':
-          $ref: '#/responses/BadRequest'
-        '401':
-          $ref: '#/responses/Unauthorized'
+          schema:
+            $ref: '#/definitions/JobOperationResponse'
         '404':
           $ref: '#/responses/NotFound'
-        '412':
-          $ref: '#/responses/JobTerminal'
         '500':
           $ref: '#/responses/ServerError'
       tags:
         - Jobs
 
-  '/jobs/{id}/updateLabels':
-    post:
-      operationId: UpdateJobLabels
-      summary: Update labels on a job.
+  '/jobs/tailFile':
+    get:
+      operationId: TailFileContents
+      summary: Get up to a certain amount (from the end) of content from the Google Storage API
       parameters:
-        - name: id
-          description: Job ID
+        - name: bucket
+          description: Google bucket ID
           required: true
+          in: query
           type: string
-          in: path
-        - name: body
+        - name: object
+          description: ID of the file stored in the Google bucket
           required: true
-          in: body
-          schema:
-            $ref: '#/definitions/UpdateJobLabelsRequest'
+          in: query
+          type: string
       responses:
         '200':
           description: Success
           schema:
-            $ref: '#/definitions/UpdateJobLabelsResponse'
-        '400':
-          $ref: '#/responses/BadRequest'
+            $ref: '#/definitions/FileContents'
         '404':
           $ref: '#/responses/NotFound'
         '500':
           $ref: '#/responses/ServerError'
-        '501':
-          description: Server does not implement this method.
       tags:
         - Jobs
 
@@ -117,10 +113,10 @@ paths:
       tags:
         - Jobs
 
-  '/jobs/{id}':
-    get:
-      operationId: GetJob
-      summary: Query for job and task-level metadata for a specified job
+  '/jobs/{id}/abort':
+    post:
+      operationId: AbortJob
+      summary: Abort a job by ID
       parameters:
         - name: id
           description: Job ID
@@ -130,75 +126,65 @@ paths:
       responses:
         '200':
           description: Success
-          schema:
-            $ref: '#/definitions/JobMetadataResponse'
         '400':
           $ref: '#/responses/BadRequest'
         '401':
           $ref: '#/responses/Unauthorized'
         '404':
           $ref: '#/responses/NotFound'
+        '412':
+          $ref: '#/responses/JobTerminal'
         '500':
           $ref: '#/responses/ServerError'
       tags:
         - Jobs
 
-  '/jobs/{id}/{task}/attempts':
-    get:
-      operationId: GetTaskAttempts
-      summary: Query for task-level metadata for a specified job
+  '/jobs/{id}/updateLabels':
+    post:
+      operationId: UpdateJobLabels
+      summary: Update labels on a job.
       parameters:
         - name: id
           description: Job ID
           required: true
           type: string
           in: path
-        - name: task
-          description: task name
+        - name: body
           required: true
-          type: string
-          in: path
+          in: body
+          schema:
+            $ref: '#/definitions/UpdateJobLabelsRequest'
       responses:
         '200':
           description: Success
           schema:
-            $ref: '#/definitions/JobAttemptsResponse'
+            $ref: '#/definitions/UpdateJobLabelsResponse'
         '400':
           $ref: '#/responses/BadRequest'
-        '401':
-          $ref: '#/responses/Unauthorized'
         '404':
           $ref: '#/responses/NotFound'
         '500':
           $ref: '#/responses/ServerError'
+        '501':
+          description: Server does not implement this method.
       tags:
         - Jobs
 
-  '/jobs/{id}/{task}/{index}/attempts':
+  '/jobs/{id}':
     get:
-      operationId: GetShardAttempts
-      summary: Query for shard-level metadata for a specified job
+      operationId: GetJob
+      summary: Query for job and task-level metadata for a specified job
       parameters:
         - name: id
           description: Job ID
           required: true
           type: string
           in: path
-        - name: task
-          description: task name
-          required: true
-          type: string
-          in: path
-        - name: index
-          description: shard index
-          required: true
-          type: string
-          in: path
       responses:
         '200':
           description: Success
           schema:
-            $ref: '#/definitions/JobAttemptsResponse'
+            $ref: '#/definitions/JobMetadataResponse'
         '400':
           $ref: '#/responses/BadRequest'
         '401':
@@ -210,25 +196,30 @@ paths:
       tags:
         - Jobs
 
-  '/jobs/operationDetails':
+  '/jobs/{id}/{task}/attempts':
     get:
-      operationId: GetOperationDetails
-      summary: Call for operation details from the Google Pipelines API
+      operationId: GetTaskAttempts
+      summary: Query for task-level metadata for a specified job
       parameters:
-        - name: job
-          description: job ID
+        - name: id
+          description: Job ID
           required: true
-          in: query
           type: string
-        - name: operation
-          description: operation ID
+          in: path
+        - name: task
+          description: task name
+          required: true
           type: string
-          in: query
+          in: path
       responses:
         '200':
           description: Success
           schema:
-            $ref: '#/definitions/JobOperationResponse'
+            $ref: '#/definitions/JobAttemptsResponse'
+        '400':
+          $ref: '#/responses/BadRequest'
+        '401':
+          $ref: '#/responses/Unauthorized'
         '404':
           $ref: '#/responses/NotFound'
         '500':
@@ -236,26 +227,35 @@ paths:
       tags:
         - Jobs
 
-  '/jobs/tailFile':
+  '/jobs/{id}/{task}/{index}/attempts':
     get:
-      operationId: TailFileContents
-      summary: Get up to a certain amount (from the end) of content from the Google Storage API
+      operationId: GetShardAttempts
+      summary: Query for shard-level metadata for a specified job
       parameters:
-        - name: bucket
-          description: Google bucket ID
+        - name: id
+          description: Job ID
           required: true
-          in: query
           type: string
-        - name: object
-          description: ID of the file stored in the Google bucket
+          in: path
+        - name: task
+          description: task name
+          required: true
+          type: string
+          in: path
+        - name: index
+          description: shard index
           required: true
-          in: query
           type: string
+          in: path
       responses:
         '200':
           description: Success
           schema:
-            $ref: '#/definitions/FileContents'
+            $ref: '#/definitions/JobAttemptsResponse'
+        '400':
+          $ref: '#/responses/BadRequest'
+        '401':
+          $ref: '#/responses/Unauthorized'
         '404':
           $ref: '#/responses/NotFound'
         '500':

From 2baaf08a2b6d132538d0d49fc8670ba07c8a4bba Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Thu, 2 Jan 2025 10:52:00 -0500
Subject: [PATCH 21/21] Add comment warning about API endpoint ordering

---
 api/jobs.yaml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/api/jobs.yaml b/api/jobs.yaml
index fc50607c..fe45e6eb 100644
--- a/api/jobs.yaml
+++ b/api/jobs.yaml
@@ -16,6 +16,13 @@ enum: &TIMEFRAME
   - DAYS_30
   - ALL_TIME
 
+# NOTE!!!
+# Due to the way the Connexion library handles this file, the order in which
+# endpoints are defined is important. More narrowly-defined URL paths must be
+# listed before wider ones. For example, it's important that /jobs/operationDetails
+# is earlier than /jobs/{id} in the below definition. When this is done incorrectly,
+# we get confusing errors about missing or incorrect parameters.
+
 paths:
   '/capabilities':
     get: