Masifor240402

.gitignore

@@ -1,3 +1,4 @@
 site/
 .DS_Store
-venv/
+venv*/
+.vscode/

.pre-commit-config.yaml

@@ -0,0 +1,6 @@
+repos:
+-   repo: [email protected]:Yelp/detect-secrets
+    rev: v0.13.1
+    hooks:
+    -   id: detect-secrets
+        args: ['--baseline', '.secrets.baseline']

.secrets.baseline

@@ -0,0 +1,220 @@
+{
+  "exclude": {
+    "files": null,
+    "lines": null
+  },
+  "generated_at": "2023-11-30T17:33:04Z",
+  "plugins_used": [
+    {
+      "name": "AWSKeyDetector"
+    },
+    {
+      "name": "ArtifactoryDetector"
+    },
+    {
+      "base64_limit": 4.5,
+      "name": "Base64HighEntropyString"
+    },
+    {
+      "name": "BasicAuthDetector"
+    },
+    {
+      "name": "CloudantDetector"
+    },
+    {
+      "hex_limit": 3,
+      "name": "HexHighEntropyString"
+    },
+    {
+      "name": "IbmCloudIamDetector"
+    },
+    {
+      "name": "IbmCosHmacDetector"
+    },
+    {
+      "name": "JwtTokenDetector"
+    },
+    {
+      "keyword_exclude": null,
+      "name": "KeywordDetector"
+    },
+    {
+      "name": "MailchimpDetector"
+    },
+    {
+      "name": "PrivateKeyDetector"
+    },
+    {
+      "name": "SlackDetector"
+    },
+    {
+      "name": "SoftlayerDetector"
+    },
+    {
+      "name": "StripeDetector"
+    },
+    {
+      "name": "TwilioKeyDetector"
+    }
+  ],
+  "results": {
+    "docs/API/Users_Guide/Additional_Examples.md": [
+      {
+        "hashed_secret": "d9bbc424159a2c5ef89902e02caa2be6cff1817c",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 89,
+        "type": "Hex High Entropy String"
+      },
+      {
+        "hashed_secret": "34d2afab6dc6f76855d5f83cc2dbed2efd99ddfb",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 110,
+        "type": "Hex High Entropy String"
+      }
+    ],
+    "docs/API/Users_Guide/Getting_Started.md": [
+      {
+        "hashed_secret": "05b339a29ce9a548e1efbe032131cfcdde6727d8",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 91,
+        "type": "Hex High Entropy String"
+      }
+    ],
+    "docs/API/Users_Guide/Search_and_Retrieval.md": [
+      {
+        "hashed_secret": "8b0471397a6dec83405ee2ae28edde87d02271a0",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 386,
+        "type": "Hex High Entropy String"
+      },
+      {
+        "hashed_secret": "14f469780554b9dd75a3d03a267b3be725582499",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 409,
+        "type": "Hex High Entropy String"
+      },
+      {
+        "hashed_secret": "6b505580b5bc4fab5bd4b2e0e10d621fea0614ee",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 447,
+        "type": "Hex High Entropy String"
+      },
+      {
+        "hashed_secret": "98895ba87fa2e568b0f48b1afbddb9b45d8c8ec3",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 491,
+        "type": "Hex High Entropy String"
+      },
+      {
+        "hashed_secret": "20b3183bf913ad4ef0d5ecd59c1de5437a7e8a04",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 528,
+        "type": "Hex High Entropy String"
+      }
+    ],
+    "docs/API/Users_Guide/Submission.md": [
+      {
+        "hashed_secret": "93f5b94e262e685fee4a419438d60e82fafaf491",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 2468,
+        "type": "Hex High Entropy String"
+      },
+      {
+        "hashed_secret": "313355a8530a54c23567f7bbedd9f804bb269820",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 2561,
+        "type": "Hex High Entropy String"
+      },
+      {
+        "hashed_secret": "b47ceb76f45ab4e8b52da270875d85fdd9b7fc33",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 2623,
+        "type": "Hex High Entropy String"
+      }
+    ],
+    "docs/API/Users_Guide/System_Information.md": [
+      {
+        "hashed_secret": "ecb0642a6305ce066c2675dac1562535b530e5b0",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 70,
+        "type": "Hex High Entropy String"
+      }
+    ],
+    "docs/Data_Submission_Portal/Users_Guide/Best_Practices.md": [
+      {
+        "hashed_secret": "87d7b59b5af7c86ea71b60ed042d1e62175136fb",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 86,
+        "type": "Hex High Entropy String"
+      }
+    ],
+    "docs/Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough.md": [
+      {
+        "hashed_secret": "87d7b59b5af7c86ea71b60ed042d1e62175136fb",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 651,
+        "type": "Hex High Entropy String"
+      }
+    ],
+    "docs/Data_Submission_Portal/Users_Guide/Data_Upload_UG.md": [
+      {
+        "hashed_secret": "dbaf99f4789432509c1313aba5256a6ea4ddb986",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 482,
+        "type": "Hex High Entropy String"
+      },
+      {
+        "hashed_secret": "471568dffba5b4873ca000b88049046d5aa687d4",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 553,
+        "type": "Hex High Entropy String"
+      },
+      {
+        "hashed_secret": "87d7b59b5af7c86ea71b60ed042d1e62175136fb",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 765,
+        "type": "Hex High Entropy String"
+      }
+    ],
+    "theme/css/font-awesome-4.5.css": [
+      {
+        "hashed_secret": "51de2b835bd35a67eb32dbcd3d77d4b96e5aa39d",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 1734,
+        "type": "Secret Keyword"
+      }
+    ],
+    "theme/css/font-awesome.min-4.5.css": [
+      {
+        "hashed_secret": "3e4128ccd5d7d597667230af6326b3387fd18545",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 4,
+        "type": "Secret Keyword"
+      }
+    ]
+  },
+  "version": "0.13.1",
+  "word_list": {
+    "file": null,
+    "hash": null
+  }
+}

API_UG.yml

@@ -16,6 +16,7 @@ pages:
   - BAM Slicing: 'API/Users_Guide/BAM_Slicing.md'
   - Submission: 'API/Users_Guide/Submission.md'
   - Python Examples: 'API/Users_Guide/Python_Examples.md'
+  - GraphQL Examples: 'API/Users_Guide/GraphQL_Examples.md'
   - System Information: 'API/Users_Guide/System_Information.md'
   - Additional Examples: 'API/Users_Guide/Additional_Examples.md'
   - "Appendix A: Available Fields": 'API/Users_Guide/Appendix_A_Available_Fields.md'

Adding_write_to_file.md

@@ -0,0 +1,14 @@
+# Changes made 2-5-2021
+
+An extra script added to the following scripts, to redirect a copy of the output to a file:
+
+```
+- A Basic Query
+
+- A Filtered Query
+
+- Complex Filters
+
+- Basic Troubleshooting
+```
+Also the ```.PY``` files in ```scripts``` folder were updated accordingly.

Data_Portal_UG.yml

@@ -9,18 +9,22 @@ copyright: "© 2015-2016"
 theme_dir: theme
 pages:
 - Data Portal:
-  - Getting Started: 'Data_Portal/Users_Guide/Getting_Started.md'
+  - Getting Started: 'Data_Portal/Users_Guide/getting_started.md'
+  - Quick Start: 'Data_Portal/Users_Guide/quick_start.md'
+  - Cohort Builder: 'Data_Portal/Users_Guide/cohort_builder.md'
+  - Analysis Center: 'Data_Portal/Users_Guide/analysis_center.md'
+  - Repository: 'Data_Portal/Users_Guide/Repository.md'
   - Projects: 'Data_Portal/Users_Guide/Projects.md'
-  - Exploration: Data_Portal/Users_Guide/Exploration.md
-  - Repository: Data_Portal/Users_Guide/Repository.md
-  - Genes and Mutations: Data_Portal/Users_Guide/Genes_and_Mutations.md
-  - Custom Set Analysis: Data_Portal/Users_Guide/Custom_Set_Analysis.md  
-  - Annotations: 'Data_Portal/Users_Guide/Annotations.md'
-  - Advanced Search: 'Data_Portal/Users_Guide/Advanced_Search.md'
-  - Authentication: 'Data_Portal/Users_Guide/Authentication.md'
-  - File Cart: 'Data_Portal/Users_Guide/Cart.md'
-  - Image Viewer: 'Data_Portal/Users_Guide/Image_viewer.md'
-  - Legacy Archive: 'Data_Portal/Users_Guide/Legacy_Archive.md'
+  - BAM Slicing: 'Data_Portal/Users_Guide/BAMslicing.md'
+  - Clinical Data Analysis: 'Data_Portal/Users_Guide/clinical_data_analysis.md'
+  - Cohort Comparison: 'Data_Portal/Users_Guide/cohort_comparison.md'
+  - Gene Expression Clustering: 'Data_Portal/Users_Guide/gene_expression_clustering.md'
+  - Mutation Frequency: 'Data_Portal/Users_Guide/mutation_frequency.md'
+  - OncoMatrix: 'Data_Portal/Users_Guide/oncomatrix.md'
+  - ProteinPaint: 'Data_Portal/Users_Guide/proteinpaint_lollipop.md'
+  - Sequence Reads: 'Data_Portal/Users_Guide/proteinpaint_bam.md'
+  - Set Operations: 'Data_Portal/Users_Guide/set_operations.md'
+  - For Developers: 'Data_Portal/Users_Guide/Developers_Guide.md'
   - Release Notes: 'Data_Portal/Release_Notes/Data_Portal_Release_Notes.md'
 extra:
   project_root_dir: '/'

Data_Portal_V1_UG.yml

@@ -0,0 +1,27 @@
+#
+# GDC Docs - Config
+#
+
+site_name: GDC Docs
+site_url: http://docs.gdc.cancer.gov
+repo_url: https://github.com/NCI-GDC/gdc-docs
+copyright: "© 2015-2016"
+theme_dir: theme
+pages:
+- Data Portal v1.0:
+  - Getting Started: 'Data_Portal_V1/Users_Guide/Getting_Started.md'
+  - Projects: 'Data_Portal_V1/Users_Guide/Projects.md'
+  - Exploration: Data_Portal_V1/Users_Guide/Exploration.md
+  - Repository: Data_Portal_V1/Users_Guide/Repository.md
+  - Genes and Mutations: Data_Portal_V1/Users_Guide/Genes_and_Mutations.md
+  - Annotations: 'Data_Portal_V1/Users_Guide/Annotations.md'
+  - Advanced Search: 'Data_Portal_V1/Users_Guide/Advanced_Search.md'
+  - Authentication: 'Data_Portal_V1/Users_Guide/Authentication.md'
+  - File Cart: 'Data_Portal_V1/Users_Guide/Cart.md'
+  - Image Viewer: 'Data_Portal_V1/Users_Guide/Image_viewer.md'
+  - Release Notes: 'Data_Portal_V1/Release_Notes/Data_Portal_V1_Release_Notes.md'
+extra:
+  project_root_dir: '/'
+  project_org: 'GDC'
+  project_description: 'GDC Docs'
+  version: 1.0

Data_Submission_Portal_UG.yml

@@ -9,19 +9,13 @@ copyright: "© 2015-2016"
 theme_dir: theme
 pages:
 - Data Submission Portal:
-  - Getting Started: 'Data_Submission_Portal/Users_Guide/Getting_Started.md'
-  - Submission Workflow: 'Data_Submission_Portal/Users_Guide/Submission_Workflow.md'
-  - Authentication: 'Data_Submission_Portal/Users_Guide/Authentication.md'
-  - Homepage: 'Data_Submission_Portal/Users_Guide/Homepage.md'
-  - Dashboard: 'Data_Submission_Portal/Users_Guide/Dashboard.md'
-  - Upload Data: 'Data_Submission_Portal/Users_Guide/Data_Upload_UG.md'
-  - Submit Data: 'Data_Submission_Portal/Users_Guide/Submit_Data.md'
-  - Release Data: 'Data_Submission_Portal/Users_Guide/Release_Data.md'
-  - Transactions: 'Data_Submission_Portal/Users_Guide/Transactions.md'
-  - Browse Data: 'Data_Submission_Portal/Users_Guide/Browse_Data.md'
-  - Pre-Release Data Review: 'Data_Submission_Portal/Users_Guide/Pre_Release_QC.md'
-  - Best Practices: 'Data_Submission_Portal/Users_Guide/Best_Practices.md'
+  - Before Submitting Data to the GDC Portal: 'Data_Submission_Portal/Users_Guide/Checklist.md'
+  - Data Submission Overview: 'Data_Submission_Portal/Users_Guide/Data_Submission_Overview.md'
+  - Data Submission Portal: 'Data_Submission_Portal/Users_Guide/Data_Submission_Process.md'
+  - Data Upload Walkthrough: 'Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough.md'
+  - Pre-Release Data Portal: 'Data_Submission_Portal/Users_Guide/Pre_Release_QC.md'
   - Release Notes: 'Data_Submission_Portal/Release_Notes/Data_Submission_Portal_Release_Notes.md'
+
 extra:
   project_root_dir: '/'
   project_org: 'GDC'

Data_Transfer_Tool_UG.yml

@@ -10,12 +10,10 @@ theme_dir: theme
 pages:
 - Data Transfer Tool:
   - Getting Started: 'Data_Transfer_Tool/Users_Guide/Getting_Started.md'
-  - Accessing Built-in Help: 'Data_Transfer_Tool/Users_Guide/Accessing_Built-in_Help.md'
   - Preparing for Data Download and Upload: 'Data_Transfer_Tool/Users_Guide/Preparing_for_Data_Download_and_Upload.md'
-  - Data Download and Upload - Command Line: 'Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload.md'
-  - Data Download - UI: 'Data_Transfer_Tool/Users_Guide/Data_Download_Upload_UI.md'
-  - Key Terms: 'Data_Transfer_Tool/Users_Guide/Appendix_A_-_Key_Terms.md'
+  - Data Transfer Tool Command Line Documentation: 'Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload.md'
   - Release Notes - Command Line: 'Data_Transfer_Tool/Release_Notes/DTT_Release_Notes.md'
+  - Data Transfer Tool UI Documentation: 'Data_Transfer_Tool/Users_Guide/Data_Download_DTT_UI.md'
   - Release Notes - UI: 'Data_Transfer_Tool/Release_Notes/DTT_UI_Release_Notes.md'
 
 extra:

Data_UG.yml

@@ -18,7 +18,9 @@ pages:
   - "Bioinformatics Pipeline: mRNA Analysis": 'Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline.md'
   - "Bioinformatics Pipeline: miRNA Analysis": 'Data/Bioinformatics_Pipelines/miRNA_Pipeline.md'
   - "Bioinformatics Pipeline: Copy Number Variation": 'Data/Bioinformatics_Pipelines/CNV_Pipeline.md'
-  - "Bioinformatics Pipeline: Methylation Liftover": 'Data/Bioinformatics_Pipelines/Methylation_LO_Pipeline.md'
+  - "Bioinformatics Pipeline: Methylation Analysis": 'Data/Bioinformatics_Pipelines/Methylation_Pipeline.md'
+  - "Bioinformatics Pipeline: Protein Expression": 'Data/Bioinformatics_Pipelines/RPPA_intro.md'
+  - Aligned Reads Summary Metrics: 'Data/Bioinformatics_Pipelines/Aligned_reads_summary_metrics.md'
   - Release Notes: 'Data/Release_Notes/Data_Release_Notes.md'
 extra:
   project_root_dir: '/'