GDC MVS into NCI-GDC

.gitignore

@@ -1,3 +1,6 @@
 site/
 .DS_Store
-venv/
+.venv*/
+venv*/
+.vscode/
+docs/*/PDF/*.pdf

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+---
+repos:
+  - repo: git@github.com:Yelp/detect-secrets
+    rev: v1.5.0
+    hooks:
+      - id: detect-secrets
+        args: [--baseline, .secrets.baseline]
+  - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+    rev: 0.2.3
+    hooks:
+      - id: yamlfmt
+        args: [--mapping, '2', --sequence, '4', --offset, '2', --width, '80']
+  - repo: https://github.com/sirosen/texthooks
+    rev: 0.6.8
+    hooks:
+      - id: fix-smartquotes
+  - repo: https://github.com/jumanjihouse/pre-commit-hooks
+    rev: master
+    hooks:
+      - id: require-ascii

.secrets.baseline

@@ -0,0 +1,364 @@
+{
+  "version": "1.5.0",
+  "plugins_used": [
+    {
+      "name": "ArtifactoryDetector"
+    },
+    {
+      "name": "AWSKeyDetector"
+    },
+    {
+      "name": "AzureStorageKeyDetector"
+    },
+    {
+      "name": "Base64HighEntropyString",
+      "limit": 4.5
+    },
+    {
+      "name": "BasicAuthDetector"
+    },
+    {
+      "name": "CloudantDetector"
+    },
+    {
+      "name": "DiscordBotTokenDetector"
+    },
+    {
+      "name": "GitHubTokenDetector"
+    },
+    {
+      "name": "GitLabTokenDetector"
+    },
+    {
+      "name": "HexHighEntropyString",
+      "limit": 3
+    },
+    {
+      "name": "IbmCloudIamDetector"
+    },
+    {
+      "name": "IbmCosHmacDetector"
+    },
+    {
+      "name": "IPPublicDetector"
+    },
+    {
+      "name": "JwtTokenDetector"
+    },
+    {
+      "name": "KeywordDetector",
+      "keyword_exclude": ""
+    },
+    {
+      "name": "MailchimpDetector"
+    },
+    {
+      "name": "NpmDetector"
+    },
+    {
+      "name": "OpenAIDetector"
+    },
+    {
+      "name": "PrivateKeyDetector"
+    },
+    {
+      "name": "PypiTokenDetector"
+    },
+    {
+      "name": "SendGridDetector"
+    },
+    {
+      "name": "SlackDetector"
+    },
+    {
+      "name": "SoftlayerDetector"
+    },
+    {
+      "name": "SquareOAuthDetector"
+    },
+    {
+      "name": "StripeDetector"
+    },
+    {
+      "name": "TelegramBotTokenDetector"
+    },
+    {
+      "name": "TwilioKeyDetector"
+    }
+  ],
+  "filters_used": [
+    {
+      "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
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_indirect_reference"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_likely_id_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_lock_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_potential_uuid"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_sequential_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_swagger_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_templated_secret"
+    }
+  ],
+  "results": {
+    "Notebooks/Submission_June_2021/SAR.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "Notebooks/Submission_June_2021/SAR.json",
+        "hashed_secret": "1bb6d70d546645b59cdd9f56bad7f939ee55c67f",
+        "is_verified": false,
+        "line_number": 6,
+        "is_secret": false
+      }
+    ],
+    "docs/API/Users_Guide/Additional_Examples.md": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/API/Users_Guide/Additional_Examples.md",
+        "hashed_secret": "d9bbc424159a2c5ef89902e02caa2be6cff1817c",
+        "is_verified": false,
+        "line_number": 145,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/API/Users_Guide/Additional_Examples.md",
+        "hashed_secret": "34d2afab6dc6f76855d5f83cc2dbed2efd99ddfb",
+        "is_verified": false,
+        "line_number": 166,
+        "is_secret": false
+      }
+    ],
+    "docs/API/Users_Guide/Search_and_Retrieval.md": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/API/Users_Guide/Search_and_Retrieval.md",
+        "hashed_secret": "8b0471397a6dec83405ee2ae28edde87d02271a0",
+        "is_verified": false,
+        "line_number": 409,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/API/Users_Guide/Search_and_Retrieval.md",
+        "hashed_secret": "14f469780554b9dd75a3d03a267b3be725582499",
+        "is_verified": false,
+        "line_number": 432,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/API/Users_Guide/Search_and_Retrieval.md",
+        "hashed_secret": "6b505580b5bc4fab5bd4b2e0e10d621fea0614ee",
+        "is_verified": false,
+        "line_number": 468,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/API/Users_Guide/Search_and_Retrieval.md",
+        "hashed_secret": "98895ba87fa2e568b0f48b1afbddb9b45d8c8ec3",
+        "is_verified": false,
+        "line_number": 512,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/API/Users_Guide/Search_and_Retrieval.md",
+        "hashed_secret": "20b3183bf913ad4ef0d5ecd59c1de5437a7e8a04",
+        "is_verified": false,
+        "line_number": 556,
+        "is_secret": false
+      }
+    ],
+    "docs/API/Users_Guide/Submission.md": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/API/Users_Guide/Submission.md",
+        "hashed_secret": "93f5b94e262e685fee4a419438d60e82fafaf491",
+        "is_verified": false,
+        "line_number": 1205,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/API/Users_Guide/Submission.md",
+        "hashed_secret": "313355a8530a54c23567f7bbedd9f804bb269820",
+        "is_verified": false,
+        "line_number": 1462,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/API/Users_Guide/Submission.md",
+        "hashed_secret": "b47ceb76f45ab4e8b52da270875d85fdd9b7fc33",
+        "is_verified": false,
+        "line_number": 1533,
+        "is_secret": false
+      }
+    ],
+    "docs/API/Users_Guide/System_Information.md": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/API/Users_Guide/System_Information.md",
+        "hashed_secret": "ecb0642a6305ce066c2675dac1562535b530e5b0",
+        "is_verified": false,
+        "line_number": 82,
+        "is_secret": false
+      }
+    ],
+    "docs/Data_Dictionary/gdcmvs.md": [
+      {
+        "type": "Base64 High Entropy String",
+        "filename": "docs/Data_Dictionary/gdcmvs.md",
+        "hashed_secret": "bda4195ff28a812d14a7e4dd172299f68962d55a",
+        "is_verified": false,
+        "line_number": 7,
+        "is_secret": false
+      },
+      {
+        "type": "Base64 High Entropy String",
+        "filename": "docs/Data_Dictionary/gdcmvs.md",
+        "hashed_secret": "04a52a012e416f2d2b07b144a16e757e36da7ecd",
+        "is_verified": false,
+        "line_number": 8,
+        "is_secret": false
+      }
+    ],
+    "docs/Data_Dictionary/viewer.md": [
+      {
+        "type": "Base64 High Entropy String",
+        "filename": "docs/Data_Dictionary/viewer.md",
+        "hashed_secret": "406ff424dc0a82cba2f75fd2965c5862e89fc505",
+        "is_verified": false,
+        "line_number": 11,
+        "is_secret": false
+      }
+    ],
+    "docs/Data_Submission_Portal/Users_Guide/Best_Practices.md": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/Data_Submission_Portal/Users_Guide/Best_Practices.md",
+        "hashed_secret": "87d7b59b5af7c86ea71b60ed042d1e62175136fb",
+        "is_verified": false,
+        "line_number": 91,
+        "is_secret": false
+      }
+    ],
+    "docs/Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough.md": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough.md",
+        "hashed_secret": "87d7b59b5af7c86ea71b60ed042d1e62175136fb",
+        "is_verified": false,
+        "line_number": 475,
+        "is_secret": false
+      }
+    ],
+    "docs/Data_Submission_Portal/Users_Guide/Data_Upload_UG.md": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/Data_Submission_Portal/Users_Guide/Data_Upload_UG.md",
+        "hashed_secret": "87d7b59b5af7c86ea71b60ed042d1e62175136fb",
+        "is_verified": false,
+        "line_number": 446,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/Data_Submission_Portal/Users_Guide/Data_Upload_UG.md",
+        "hashed_secret": "dbaf99f4789432509c1313aba5256a6ea4ddb986",
+        "is_verified": false,
+        "line_number": 482,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/Data_Submission_Portal/Users_Guide/Data_Upload_UG.md",
+        "hashed_secret": "471568dffba5b4873ca000b88049046d5aa687d4",
+        "is_verified": false,
+        "line_number": 553,
+        "is_secret": false
+      }
+    ],
+    "docs/Data_Submission_Portal/Users_Guide/Troubleshooting.md": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/Data_Submission_Portal/Users_Guide/Troubleshooting.md",
+        "hashed_secret": "87d7b59b5af7c86ea71b60ed042d1e62175136fb",
+        "is_verified": false,
+        "line_number": 320,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/Data_Submission_Portal/Users_Guide/Troubleshooting.md",
+        "hashed_secret": "0aeed44f3796724f216cd8b44eed2ccf7e6027ab",
+        "is_verified": false,
+        "line_number": 397,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/Data_Submission_Portal/Users_Guide/Troubleshooting.md",
+        "hashed_secret": "02f935c708e5e6c25a7c6afc474791548137c14a",
+        "is_verified": false,
+        "line_number": 730,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/Data_Submission_Portal/Users_Guide/Troubleshooting.md",
+        "hashed_secret": "ac4ee19b19ebcbcb9ae0549646a038e7ee489b33",
+        "is_verified": false,
+        "line_number": 1004,
+        "is_secret": false
+      },
+      {
+        "type": "Hex High Entropy String",
+        "filename": "docs/Data_Submission_Portal/Users_Guide/Troubleshooting.md",
+        "hashed_secret": "2155632d48ada1352359f70362a44272a74fdf41",
+        "is_verified": false,
+        "line_number": 1275,
+        "is_secret": false
+      }
+    ],
+    "docs/Encyclopedia/index.md": [
+      {
+        "type": "Base64 High Entropy String",
+        "filename": "docs/Encyclopedia/index.md",
+        "hashed_secret": "bda4195ff28a812d14a7e4dd172299f68962d55a",
+        "is_verified": false,
+        "line_number": 5,
+        "is_secret": false
+      }
+    ]
+  },
+  "generated_at": "2025-05-19T17:56:04Z"
+}