Maf documentation

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'

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:

docs/API/Release_Notes/API_Release_Notes.md

@@ -3,6 +3,10 @@
 
 | Version | Date |
 |---|---|
+| [v1.20.0](API_Release_Notes.md#v1200) | April 17, 2019 |
+| [v1.19.0](API_Release_Notes.md#v1190) | February 20, 2019 |
+| [v1.18.0](API_Release_Notes.md#v1180) | December 18, 2018 |
+| [v1.17.0](API_Release_Notes.md#v1170) | November 7, 2018 |
 | [v1.16.0](API_Release_Notes.md#v1160) | September 27, 2018 |
 | [v1.15.0](API_Release_Notes.md#v1150) | August 23, 2018 |
 | [v1.14.1](API_Release_Notes.md#v1141) | May 21, 2018 |
@@ -21,6 +25,112 @@
 | [v1.1.0](API_Release_Notes.md#v110) | May 25, 2016 |
 | [v1.0.1](API_Release_Notes.md#v101) | May 16, 2016 |
 
+
+## v1.20.0 <!--REQ-385-->
+
+* __GDC Product__: Application Programming Interface (API)
+* __Release Date__:  April 17, 2019
+
+### New Features and Changes
+
+* Disallowed creation of multiple file versions in the same data release <!--API-585-->
+* Improved API concurrency performance and addressed random failures/4XX/5XX responses <!--GDCDEVOPS-187,GP-15-->
+* Improved API/Portal performances for querying large sets of data from the Elasticsearch indices <!--API-613-->
+* Updated BCR Clinical XML parser code to support future indexing of additional clinical data <!--DAT-2076-->
+    - Updated the mapping for:
+        - `days_to_death`	<!--DAT-2083-->
+        - `days_to_birth`	<!--DAT-2084-->
+        - `vital_status`	<!--DAT-2085-->
+        - `prior_malignancy` and `synchronous_malignancy`	<!--DAT-2094-->
+    - Added a mapping for:
+        - `pack_years_smoked`	<!--DAT-2086-->
+        - `prior_treatment`	<!--DAT-2095-->
+        - `age_at_index`	<!--DAT-2096-->
+        - `days_to_diagnosis`	<!--DAT-2097-->
+        - `icd_10_code`	<!--DAT-2098-->
+        - `year_of_diagnosis`	<!--DAT-2099-->
+    - Remove calculation for:
+        - `cigarettes_per_day`	<!--DAT-2091-->
+        - `year_of_birth`	<!--DAT-2092-->
+        - `year_of_death`	<!--DAT-2093-->
+        - `bmi`  <!--DAT-2087-->
+    - Updated XML Parser to pull the most Up-to-Date Survival Information	<!--DAT-2063-->
+
+### Bugs Fixed Since Last Release
+
+* None
+
+### Known Issues and Workarounds
+
+* None
+
+
+## v1.19.0 <!--REQ-381-->
+
+* __GDC Product__: Application Programming Interface (API)
+* __Release Date__:  February 20, 2019
+
+### New Features and Changes
+
+* Added API features to support controlled access DAVE <!--TT-393-->
+* Updated API query endpoints to handle filtering of queries based on tokens <!--TT-641-->
+* Created login notification Endpoint <!--API-586-->
+* Added hashing and logging for similar ES queries <!--API-569-->
+
+### Bugs Fixed Since Last Release
+
+* Fixed bug where quick search ES query grows with each request <!--API-580-->
+* Fixed bug where new file versions could be created when exactly the same existing metadata is uploaded <!--API-571-->
+* Fixed bug where submitting to specific projects produced error that data already existed <!--API-568-->
+
+
+
+## v1.18.0 <!--REQ-335-->
+
+* __GDC Product__: Application Programming Interface (API)
+* __Release Date__:  December 18, 2018
+
+### New Features and Changes
+
+* Update to auth for GDC Pre-Release Data Portal <!--TT-739-->
+
+### Bugs Fixed Since Last Release
+
+* None
+
+### Known Issues and Workarounds
+
+* Fields are not counted as missing if parent field is also missing.  This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter.  This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING". <!-- PGDC-2530 // https://github.com/NCI-GDC/gdcapi/pull/524  -->
+* Certain very large API requests will time out.  It is recommended to break up very large requests into a series of smaller requests. <!-- PGDC-2411 -->
+
+
+
+## v1.17.0
+
+* __GDC Product__: Application Programming Interface (API)
+* __Release Date__:  November 7, 2018
+
+### New Features and Changes
+
+* Created new index cnv_centric <!--TT743-->
+* Created new index cnv_occurrence_centric <!--TT-744-->
+* Created new REST API endpoints for CNV <!--TT-757-->
+* Created mapping from aliquot to case for occurrence on cnv_centric <!--TT-762-->
+* Created new graphql endpoints for CNV <!--TT-769-->
+* Updated index case_centric to add cnv <!--TT-745-->
+* Updated index gene_centric to add cnv <!--TT-747-->
+
+### Bugs Fixed Since Last Release
+
+* Fixed bug to prevent users from deleting files in state submitted or released <!--API-560-->
+
+### Known Issues and Workarounds
+
+* Fields are not counted as missing if parent field is also missing.  This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter.  This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING". <!-- PGDC-2530 // https://github.com/NCI-GDC/gdcapi/pull/524  -->
+* Certain very large API requests will time out.  It is recommended to break up very large requests into a series of smaller requests. <!-- PGDC-2411 -->
+
+
+
 ## v1.16.0
 
 * __GDC Product__: Application Programming Interface (API)

docs/API/Users_Guide/Additional_Examples.md

@@ -668,7 +668,7 @@ curl 'https://api.gdc.cancer.gov/cases?filters=%7b%0d%0a+++%22op%22+%3a+%22%3d%2
 
 #### Example: Filter using a range
 
-This is an example of filtering for age at diagnosis. The request is for cases where the age at diagnosis is between 40 and 70 years. *Note:* `age_at_diagnosis` is expressed in days.
+This is an example of filtering for age at diagnosis. The request is for cases where the age at diagnosis is between 40 and 70 years. >**Note:** `age_at_diagnosis` is expressed in days.
 
 ```Filter
 {

docs/API/Users_Guide/Appendix_C_Format_of_Submission_Requests_and_Responses.md

@@ -123,4 +123,4 @@ API responses will contain a status for each entity specified in the request:
 
 **`error`**: The desired transaction was not sucessful, and the transaction was aborted because of this entity. This entity did not pass validation or an internal error occured when attempting to complete the transaction. The error state will be accompanied by a list of errors recorded about the entity (see label-error-messages).
 
-**Note:** GDC API requests are transactional. An error with processing a node specified in the transaction will abort the transaction and will result in no changes being applied for any node involved in the transaction.
+>**Note:** GDC API requests are transactional. An error with processing a node specified in the transaction will abort the transaction and will result in no changes being applied for any node involved in the transaction.

docs/API/Users_Guide/BAM_Slicing.md

@@ -21,11 +21,11 @@ Please note the following:
 The following query parameters and JSON fields are supported:
 
 | Description | Query Parameter | JSON Field | Query format |
-|---|---|---|
+|---|---|---|---|
 | entire chromosome, or a position or region on the chromosome, specified using chromosomal coordinates | region | regions | region=<chr>(:<start>(-<stop>)?)?</stop></start></chr> |
 | region specified using a [HGNC](http://www.genenames.org/) / [GENCODE v22](http://www.gencodegenes.org/) gene name |  gencode | gencode | gencode=<gene_name> |
 
-**NOTE:** The successfully sliced BAM will contain all reads that overlap (entirely or partially) with the specified region or gene. It is possible to specify an open-ended region, e.g. `chr2:10000`, which would return all reads that (completely or partially) overlap with the region of chromosome 2 from position 10,000 to the end of the chromosome.
+>**NOTE:** The successfully sliced BAM will contain all reads that overlap (entirely or partially) with the specified region or gene. It is possible to specify an open-ended region, e.g. `chr2:10000`, which would return all reads that (completely or partially) overlap with the region of chromosome 2 from position 10,000 to the end of the chromosome.
 
 ### JSON Schema