Add .secrets.baseline

uc-cdis · Jan 10, 2025 · e092907 · e092907
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commit e092907
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Showing 5 changed files with 232 additions and 7 deletions.
diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml
@@ -13,4 +13,4 @@ jobs:
         DO_TEST_PUBLISH_FIRST: true
     secrets:
       PYPI_TEST_API_TOKEN: ${{ secrets.PYPI_TEST_API_TOKEN }}
-      PYPI_PROD_API_TOKEN: ${{ secrets.PYPI_PROD_API_TOKEN }}
+      PYPI_PROD_API_TOKEN: ${{ secrets.PYPI_PROD_API_TOKEN }}
diff --git a/.github/workflows/wool.yaml b/.github/workflows/wool.yaml
@@ -12,4 +12,4 @@ jobs:
 
     - uses: uc-cdis/wool@master
       env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -0,0 +1,225 @@
+{
+  "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": 3.0
+    },
+    {
+      "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_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": {
+    ".github/workflows/ci.yml": [
+      {
+        "type": "Secret Keyword",
+        "filename": ".github/workflows/ci.yml",
+        "hashed_secret": "3e26d6750975d678acb8fa35a0f69237881576b0",
+        "is_verified": false,
+        "line_number": 17
+      }
+    ],
+    ".travis.yml": [
+      {
+        "type": "Base64 High Entropy String",
+        "filename": ".travis.yml",
+        "hashed_secret": "a5550bd57663a78c1cd9ffd31148627d780a5e94",
+        "is_verified": false,
+        "line_number": 9
+      },
+      {
+        "type": "Base64 High Entropy String",
+        "filename": ".travis.yml",
+        "hashed_secret": "9367bab27f27511665862beae3dad6468998f4a5",
+        "is_verified": false,
+        "line_number": 10
+      }
+    ],
+    "gdcdictionary/examples/valid/aligned_reads_index.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/aligned_reads_index.json",
+        "hashed_secret": "a1ba33896d16eda8522e531edbaf3b625c1f4c31",
+        "is_verified": false,
+        "line_number": 6
+      }
+    ],
+    "gdcdictionary/examples/valid/experimental_metadata.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/experimental_metadata.json",
+        "hashed_secret": "daef34f66b6e909f3a22ffd063d48eb428067b6e",
+        "is_verified": false,
+        "line_number": 6
+      }
+    ],
+    "gdcdictionary/examples/valid/slide_image.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/slide_image.json",
+        "hashed_secret": "daef34f66b6e909f3a22ffd063d48eb428067b6e",
+        "is_verified": false,
+        "line_number": 6
+      }
+    ],
+    "gdcdictionary/examples/valid/submitted_aligned_reads.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/submitted_aligned_reads.json",
+        "hashed_secret": "e3f181b6b92d74e30d524d03029e785d0c7c7535",
+        "is_verified": false,
+        "line_number": 7
+      }
+    ],
+    "gdcdictionary/examples/valid/submitted_copy_number.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/submitted_copy_number.json",
+        "hashed_secret": "e3f181b6b92d74e30d524d03029e785d0c7c7535",
+        "is_verified": false,
+        "line_number": 6
+      }
+    ],
+    "gdcdictionary/examples/valid/submitted_methylation.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/submitted_methylation.json",
+        "hashed_secret": "e3f181b6b92d74e30d524d03029e785d0c7c7535",
+        "is_verified": false,
+        "line_number": 7
+      }
+    ],
+    "gdcdictionary/examples/valid/submitted_somatic_mutation.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/submitted_somatic_mutation.json",
+        "hashed_secret": "a1ba33896d16eda8522e531edbaf3b625c1f4c31",
+        "is_verified": false,
+        "line_number": 9
+      }
+    ],
+    "gdcdictionary/examples/valid/submitted_unaligned_reads.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": "gdcdictionary/examples/valid/submitted_unaligned_reads.json",
+        "hashed_secret": "88e3a7adc1779a311467797f00d2edc5e9697d9c",
+        "is_verified": false,
+        "line_number": 7
+      }
+    ]
+  },
+  "generated_at": "2025-01-10T20:22:28Z"
+}
diff --git a/NOTICE b/NOTICE
@@ -1 +1 @@
-Copyright 2015 University of Chicago, Ontario Institute for Cancer ResearchLicensed under the Apache License, Version 2.0 (the "License");you may not use this file except in compliance with the License.You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing,software distributed under the License is distributed on an "AS IS" BASIS,WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.See the License for the specific language governing permissions andlimitations under the License.Portions of this work, authored by University of Chicago andOntario Institute for Cancer Research employees, was funded in whole or in partby National Cancer Institute, National Institutes of Healthunder U.S. Government contract HHSN261200800001E.
+Copyright 2015 University of Chicago, Ontario Institute for Cancer ResearchLicensed under the Apache License, Version 2.0 (the "License");you may not use this file except in compliance with the License.You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing,software distributed under the License is distributed on an "AS IS" BASIS,WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.See the License for the specific language governing permissions andlimitations under the License.Portions of this work, authored by University of Chicago andOntario Institute for Cancer Research employees, was funded in whole or in partby National Cancer Institute, National Institutes of Healthunder U.S. Government contract HHSN261200800001E.

diff --git a/README.md b/README.md
@@ -4,9 +4,9 @@ The data dictionary provides the first level of validation for all data
 stored in and generated by the BPA. Written in YAML, JSON schemas define all the individual entities
 (nodes) in the data model. Moreover, these schemas define all of the relationships (links)
 between the nodes. Finally, the schemas define the valid key-value pairs that can be used to
-describe the nodes. 
+describe the nodes.
 
-## Data Dictionary Structure 
+## Data Dictionary Structure
 
 The Data Model covers all of the nodes within the as well as the relationships between
 the different types of nodes. All of the nodes in the data model are strongly typed and individually
@@ -37,13 +37,13 @@ characterize the data they represent. Some properties are categorized as `requir
 If a submission lacks a required property, it cannot be accepted. Preferred properties can denote
 two things: the property is being highlighted as it has become more desired by the community or
 the property is being promoted to required. All properties not designated either `required` or
-`preferred` are still sought by BPA, but submissions without them are allowed. 
+`preferred` are still sought by BPA, but submissions without them are allowed.
 
 The properties have further validation through their entries. Legal values are defined in each
 property. For the most part these are represented in the `enum` categories although some keys,
 such as `submitter_id`, will allow any string value as a valid entry. Other numeric properties
 can have maximum and minimum values to limit valid entries.  For examples of what a valid entry
-would look like, each node has a mock submission located in the `examples/valid/` directory. 
+would look like, each node has a mock submission located in the `examples/valid/` directory.
 
 ## Contributing
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		Copyright 2015 University of Chicago, Ontario Institute for Cancer ResearchLicensed under the Apache License, Version 2.0 (the "License");you may not use this file except in compliance with the License.You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing,software distributed under the License is distributed on an "AS IS" BASIS,WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.See the License for the specific language governing permissions andlimitations under the License.Portions of this work, authored by University of Chicago andOntario Institute for Cancer Research employees, was funded in whole or in partby National Cancer Institute, National Institutes of Healthunder U.S. Government contract HHSN261200800001E.
		Copyright 2015 University of Chicago, Ontario Institute for Cancer ResearchLicensed under the Apache License, Version 2.0 (the "License");you may not use this file except in compliance with the License.You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing,software distributed under the License is distributed on an "AS IS" BASIS,WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.See the License for the specific language governing permissions andlimitations under the License.Portions of this work, authored by University of Chicago andOntario Institute for Cancer Research employees, was funded in whole or in partby National Cancer Institute, National Institutes of Healthunder U.S. Government contract HHSN261200800001E.
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