Merge pull request #205 from uc-cdis/chore/build_heal_tutorials

Chore/build heal tutorials
uc-cdis · Dec 9, 2024 · 46c3950 · 46c3950
2 parents 71699ba + 2af9852
commit 46c3950
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Showing 7 changed files with 120 additions and 4,479 deletions.
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -75,6 +75,10 @@
     {
       "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
     },
+    {
+      "path": "detect_secrets.filters.common.is_baseline_file",
+      "filename": ".secrets.baseline"
+    },
     {
       "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
       "min_level": 2
@@ -272,152 +276,6 @@
         "line_number": 491
       }
     ],
-    "HEAL-notebooks/combined_tutorials/JCOIN_Tracking_Opioid_Stigma.ipynb": [
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/JCOIN_Tracking_Opioid_Stigma.ipynb",
-        "hashed_secret": "86d47cca0d5b20b7a74b72d567d2e931deff0e23",
-        "is_verified": false,
-        "line_number": 780
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/JCOIN_Tracking_Opioid_Stigma.ipynb",
-        "hashed_secret": "709e3376853c66b228e0234f94f587e71c2a97f5",
-        "is_verified": false,
-        "line_number": 1017
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/JCOIN_Tracking_Opioid_Stigma.ipynb",
-        "hashed_secret": "07dcc182781305ee9c2866f9e1a22db8aca67586",
-        "is_verified": false,
-        "line_number": 1366
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/JCOIN_Tracking_Opioid_Stigma.ipynb",
-        "hashed_secret": "ca89696ece5a23d71d73273bbbc2d9bfabcd5ef3",
-        "is_verified": false,
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-      }
-    ],
-    "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb": [
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb",
-        "hashed_secret": "989ae1c0a697480fae00340ab24b3bd4a18903bd",
-        "is_verified": false,
-        "line_number": 238
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb",
-        "hashed_secret": "fbfd4c700bcca2280449452bc6d20e041f67db38",
-        "is_verified": false,
-        "line_number": 299
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb",
-        "hashed_secret": "fc3230fc9bc2b99200a584917ddb11a9d4ac13e8",
-        "is_verified": false,
-        "line_number": 371
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb",
-        "hashed_secret": "48adfb0d0e51de9f70a39bd93d50558189b41263",
-        "is_verified": false,
-        "line_number": 537
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb",
-        "hashed_secret": "ee65245c082a4c2625e7163a89e55c24b5641e24",
-        "is_verified": false,
-        "line_number": 599
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb",
-        "hashed_secret": "d444e79298bd95c96b57cc82c953e6ab7ede150f",
-        "is_verified": false,
-        "line_number": 680
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb",
-        "hashed_secret": "c7ca176ddf69dc4d06a5f3035c9922e2fa1b0837",
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-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb",
-        "hashed_secret": "7e6268d3d8f12d6bc39017524362b10f9982f383",
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-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb",
-        "hashed_secret": "d1a8bb8b7ae7bfdd73a0f546b1afe3cfd1e9340b",
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-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb",
-        "hashed_secret": "8758fca3db91ddf824e5abcfdbb205585f9dcd05",
-        "is_verified": false,
-        "line_number": 1976
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Overdose_Trajectories.ipynb",
-        "hashed_secret": "7f37d180d3e49a25c6bd8d063b8a588f6774bf96",
-        "is_verified": false,
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-      }
-    ],
-    "HEAL-notebooks/combined_tutorials/Opioid_Prevalence_And_Overdoses.ipynb": [
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Prevalence_And_Overdoses.ipynb",
-        "hashed_secret": "c5ab4a186feba6bb7a280416947f969246e1e0e3",
-        "is_verified": false,
-        "line_number": 700
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Prevalence_And_Overdoses.ipynb",
-        "hashed_secret": "b551bf0f74597abcdec403e738ce63df734cbed3",
-        "is_verified": false,
-        "line_number": 750
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-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Prevalence_And_Overdoses.ipynb",
-        "hashed_secret": "ad31a3d4b4805484b03f49e155e923299fc45086",
-        "is_verified": false,
-        "line_number": 793
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Prevalence_And_Overdoses.ipynb",
-        "hashed_secret": "3a0cbdad694cf12b49ce6322f8abcb09f4d6ee2b",
-        "is_verified": false,
-        "line_number": 884
-      },
-      {
-        "type": "Base64 High Entropy String",
-        "filename": "HEAL-notebooks/combined_tutorials/Opioid_Prevalence_And_Overdoses.ipynb",
-        "hashed_secret": "451109344dd8fd0f37c0a77afc764f745e6af6db",
-        "is_verified": false,
-        "line_number": 920
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-    ],
     "jupyter-jcoin/resources/JCOIN_Tracking_Opioid_Stigma.ipynb": [
       {
         "type": "Base64 High Entropy String",
@@ -527,5 +385,5 @@
       }
     ]
   },
-  "generated_at": "2024-10-30T19:05:43Z"
+  "generated_at": "2024-12-09T17:51:32Z"
 }
diff --git a/HEAL-notebooks/Dockerfile b/HEAL-notebooks/Dockerfile
@@ -5,6 +5,7 @@ ARG NOTEBOOK_DIR
 COPY $NOTEBOOK_DIR/ $HOME/
 
 RUN pip3 install healdata-utils
+RUN pip3 install gen3==4.25.1 # Pinning older gen3sdk for now while conflict is resolved
 RUN conda config --append channels conda-forge
 RUN conda install -c plotly plotly
 

diff --git a/HEAL-notebooks/combined_tutorials/BACPAC_Synthetic_Data_Analysis.ipynb b/HEAL-notebooks/combined_tutorials/BACPAC_Synthetic_Data_Analysis.ipynb
@@ -358,7 +358,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.20"
   }
  },
  "nbformat": 4,