From 3f91af1afe1e1604ef5f19e54ad8691e98351bb8 Mon Sep 17 00:00:00 2001
From: Alexander Berger <alexander.berger@jax.org>
Date: Mon, 16 Sep 2024 07:27:32 -0400
Subject: [PATCH 1/5] Update annotator get_ncbo_link function to use requests

---
 poetry.lock      | 582 +++++++++++++++++++++++++++--------------------
 pyproject.toml   |   2 +-
 src/annotator.py |  29 +--
 3 files changed, 350 insertions(+), 263 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index ebd97e55..b54d1197 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
 
 [[package]]
 name = "amqp"
@@ -52,13 +52,13 @@ files = [
 
 [[package]]
 name = "authlib"
-version = "1.3.1"
+version = "1.3.2"
 description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "Authlib-1.3.1-py2.py3-none-any.whl", hash = "sha256:d35800b973099bbadc49b42b256ecb80041ad56b7fe1216a362c7943c088f377"},
-    {file = "authlib-1.3.1.tar.gz", hash = "sha256:7ae843f03c06c5c0debd63c9db91f9fda64fa62a42a77419fa15fbb7e7a58917"},
+    {file = "Authlib-1.3.2-py2.py3-none-any.whl", hash = "sha256:ede026a95e9f5cdc2d4364a52103f5405e75aa156357e831ef2bfd0bc5094dfc"},
+    {file = "authlib-1.3.2.tar.gz", hash = "sha256:4b16130117f9eb82aa6eec97f6dd4673c3f960ac0283ccdae2897ee4bc030ba2"},
 ]
 
 [package.dependencies]
@@ -155,74 +155,89 @@ zstd = ["zstandard"]
 
 [[package]]
 name = "certifi"
-version = "2024.7.4"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
-    {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
+    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
 [[package]]
 name = "cffi"
-version = "1.16.0"
+version = "1.17.1"
 description = "Foreign Function Interface for Python calling C code."
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
@@ -281,38 +296,38 @@ testing = ["pytest (>=3.5,!=3.7.3)", "pytest-black-multipy", "pytest-checkdocs (
 
 [[package]]
 name = "cryptography"
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 optional = false
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 [package.dependencies]
@@ -325,7 +340,7 @@ nox = ["nox"]
 pep8test = ["check-sdist", "click", "mypy", "ruff"]
 sdist = ["build"]
 ssh = ["bcrypt (>=3.1.5)"]
-test = ["certifi", "cryptography-vectors (==43.0.0)", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
+test = ["certifi", "cryptography-vectors (==43.0.1)", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
 test-randomorder = ["pytest-randomly"]
 
 [[package]]
@@ -424,22 +439,26 @@ files = [
 
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+version = "8.5.0"
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 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
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+cover = ["pytest-cov"]
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 perf = ["ipython"]
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+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+type = ["pytest-mypy"]
 
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 name = "intermine"
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 [package.extras]
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 [[package]]
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 [[package]]
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 [package.dependencies]
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 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [metadata]
 lock-version = "2.0"
diff --git a/pyproject.toml b/pyproject.toml
index c2b8f2d5..b5ff5189 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-legacy"
-version = "1.4.2"
+version = "1.4.3"
 description = ""
 authors = ["Alexander Berger <alexander.berger@jax.org>"]
 readme = "README.md"
diff --git a/src/annotator.py b/src/annotator.py
index 14b8a8ec..8f08beb6 100644
--- a/src/annotator.py
+++ b/src/annotator.py
@@ -13,6 +13,7 @@
 # END Upload Fix
 
 import geneweaverdb
+from time import sleep
 
 
 NCBO_URL = 'http://data.bioontology.org'
@@ -140,7 +141,7 @@ def fetch_ncbo_annotations(text, ncboids):
 
 def get_ncbo_link(link):
     """
-    Since NCBO enjoys testing the sanity of it's users, (almost) every member
+    Since NCBO enjoys testing the sanity of its users, (almost) every member
     of an object returned by the NCBO API is in the form of a link which then
     requires further API calls to retrieve the data.
     This function calls any API returned link and (hopefully) returns the
@@ -149,29 +150,29 @@ def get_ncbo_link(link):
     :arg str: JSON-LD link
     :ret dict: json object representing whatever data we retrieved
     """
-
-    opener = urllib.request.build_opener()
-    opener.addheaders = [('Authorization', 'apikey token=' + API_KEY)]
+    headers = {
+        'Authorization': f'apikey token={API_KEY}'
+    }
 
     for _ in range(3):
         try:
-            res = opener.open(link)
-            res = res.read()
-
-        except urllib.error.HTTPError as e:
+            response = requests.get(link, headers=headers)
+            response.raise_for_status()
+            return response.json()
+        except requests.HTTPError as e:
             print('Failed to retrieve annotation data from an NCBO link:')
             print(e)
+            sleep(1)
+            continue
+        except Exception as e:
+            print('Unknown error fetching annotations:')
+            print(e)
+            sleep(1)
             continue
-
-        ## Success
-        break
-
     else:
         print('Failed to retrieve data from an NCBO URL')
         return None
 
-    return json.loads(res)
-
 
 def parse_ncbo_annotations(annots):
     """

From 4759761b84e1ae1caab99dfbac5ca417e6435ce4 Mon Sep 17 00:00:00 2001
From: Alexander Berger <alexander.berger@jax.org>
Date: Mon, 16 Sep 2024 09:08:16 -0400
Subject: [PATCH 2/5] Adding better logging information

---
 src/annotator.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/annotator.py b/src/annotator.py
index 8f08beb6..bc3c5d5c 100644
--- a/src/annotator.py
+++ b/src/annotator.py
@@ -133,7 +133,7 @@ def fetch_ncbo_annotations(text, ncboids):
     ## for-else construct: if the loop doesn't break (in our case this
     ## indicates success) then this statement is executed
     else:
-        print('Failed to retrieve annotation data after three attempts')
+        print('Failed to retrieve NCBO annotation data after three attempts')
         return []
 
     return json.loads(res)
@@ -262,7 +262,7 @@ def fetch_monarch_annotations(text):
     ## for-else construct: if the loop doesn't break (in our case this
     ## indicates success) then this statement is executed
     else:
-        print('Failed to retrieve annotation data after three attempts')
+        print('Failed to retrieve Monarch annotation data after three attempts')
         return []
 
     return json.loads(res)

From c21b124decfa9e251c88fd2548b70483cf60256a Mon Sep 17 00:00:00 2001
From: Alexander Berger <alexander.berger@jax.org>
Date: Mon, 16 Sep 2024 09:46:50 -0400
Subject: [PATCH 3/5] Even better logging

---
 src/annotator.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/annotator.py b/src/annotator.py
index bc3c5d5c..e902b513 100644
--- a/src/annotator.py
+++ b/src/annotator.py
@@ -154,19 +154,21 @@ def get_ncbo_link(link):
         'Authorization': f'apikey token={API_KEY}'
     }
 
+    response = None
     for _ in range(3):
         try:
             response = requests.get(link, headers=headers)
             response.raise_for_status()
             return response.json()
         except requests.HTTPError as e:
-            print('Failed to retrieve annotation data from an NCBO link:')
-            print(e)
+            print(f'HTTPError on attempt {attempt + 1}: {e}')
+            if response is not None:
+                print(f'Response content: {response.content}')  # Log the response content
             sleep(1)
             continue
         except Exception as e:
-            print('Unknown error fetching annotations:')
-            print(e)
+            print(f'Unknown error on attempt {attempt + 1}: {e}')
+            print(traceback.format_exc())  # Print the full traceback for debugging
             sleep(1)
             continue
     else:

From 8dd9109d97b672afc9419f2a1575b96e512d90c1 Mon Sep 17 00:00:00 2001
From: Alexander Berger <alexander.berger@jax.org>
Date: Mon, 16 Sep 2024 13:22:14 -0400
Subject: [PATCH 4/5] Increase worker timeout

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

diff --git a/Dockerfile b/Dockerfile
index 9f2398d0..400e6250 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -36,4 +36,4 @@ RUN poetry install --only-root
 
 WORKDIR /app/src
 
-CMD ["poetry", "run", "gunicorn", "--limit-request-line", "8190", "--bind", "0.0.0.0:8000", "application:app"]
+CMD ["poetry", "run", "gunicorn", "--timeout", "300", "--limit-request-line", "8190", "--bind", "0.0.0.0:8000", "application:app"]

From b84012a315b61b6aa85f55f6f3c0b731516631a1 Mon Sep 17 00:00:00 2001
From: Alexander Berger <alexander.berger@jax.org>
Date: Mon, 16 Sep 2024 14:48:42 -0400
Subject: [PATCH 5/5] Add missing attempt var in for loop

---
 src/annotator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/annotator.py b/src/annotator.py
index e902b513..97cd10af 100644
--- a/src/annotator.py
+++ b/src/annotator.py
@@ -155,7 +155,7 @@ def get_ncbo_link(link):
     }
 
     response = None
-    for _ in range(3):
+    for attempt in range(3):
         try:
             response = requests.get(link, headers=headers)
             response.raise_for_status()