NCIP · msfitzsimons · Feb 7, 2018 · Feb 7, 2018 · Feb 7, 2018 · Feb 7, 2018
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,3 @@
 site/
-.DS_Store
+.DS_Store
+venv/
diff --git a/Data_Portal_UG.yml b/Data_Portal_UG.yml
@@ -19,6 +19,7 @@ pages:
   - 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'
   - Release Notes: 'Data_Portal/Release_Notes/Data_Portal_Release_Notes.md'
 extra:

diff --git a/Data_Submission_Portal_UG.yml b/Data_Submission_Portal_UG.yml
@@ -19,6 +19,7 @@ pages:
   - 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'
   - Release Notes: 'Data_Submission_Portal/Release_Notes/Data_Submission_Portal_Release_Notes.md'
 extra:

diff --git a/README.md b/README.md
@@ -1,87 +1,7 @@
 ![](https://gdc.cancer.gov/sites/all/themes/gdc_bootstrap/logo.png)
 
-# GDC Open Source code
+# THIS PROJECT HAS MOVED
 
-GDC is Open Source, Github Repositories containing source code of GDC Applications can be found on [GDC GitHub Organization page](https://github.com/NCI-GDC/).
-
-- GDC Data Portal: https://github.com/NCI-GDC/portal-ui
-- GDC Legacy Archive: https://github.com/NCI-GDC/portal-ui-legacy
-- GDC Data Transfer Tool: https://github.com/NCI-GDC/gdc-client
-- GDC Data Dictionary: https://github.com/NCI-GDC/gdcdictionary
-- GDC Data Model: https://github.com/NCI-GDC/gdcdatamodel
-- GDC Psqlgraph: https://github.com/NCI-GDC/psqlgraph 
-
-# Support
-
-Please direct technical questions to [GDC Support](https://gdc.cancer.gov/support).
-
-# GDC Documentation Site
-
-### Technology
-
- - Python 2.6, 2.7, 3.3, 3.4 and 3.5.
- - [mkdocs](http://www.mkdocs.org/)
- - [BSCodeTabs for mkdocs](https://github.com/mikecules/MarkdownBSCodeTabs#for-use-in-mkdocs)
-
-### Install & Run
-
- - `pip install -r requirements`
- - `mkdocs serve` (optionally set port `--dev-addr=0.0.0.0:<PORT>`)
-
-### Build
-
- - `mkdocs build --clean`
-
-### Repository Conventions
-
-- All Shared content in the "Commons" directory
-- One Directory per GDC product (API, Data_Portal, Data_Submission_Portal, Data_Transfer_Tool)
-- Each GDC product have a Users_Guide and Release_Notes directory
-
-### Linking
-
-To another documentation page
-```
-[Authentication and Authorization](../../Commons/Authentication.md)
-```
-
-Inside another documentation page
-
-```
-[Authentication and Authorization](../../Commons/Authentication.md#internal-section)
-```
-
-### Adding icons and PDFs
-The convention for this, when updating mkdocs.yml is the following:
-- <font-awesome-icon> <content> <url ending in .pdf>: 'index.md'
-example:
-- fa-file-pdf-o Download PDF /API/PDF/API_UG.pdf: 'index.md'
-
-### Documentation Conventions
-
-A detailed list of all conventions is available on [GDC Website](https://gdc.cancer.gov/conventions-page)
-
-
-### Build PDF
-
-Install mkdocs2pandoc, following instructions available here:
-```
-https://github.com/jgrassler/mkdocs-pandoc
-```
-
-Prepare a yml file dedicated to your Userguide, using Data_Portal_UG.yml as an example.
-
-Run the following commands to:
-* Convert the User Guide to Pandoc:
-* Tweak the pandoc file
-* Build a PDF
-
-```
-mkdocs2pandoc -f Data_Portal_UG.yml -o docs/Data_Portal/PDF/Data_portal_UG.pd
-sed -i -e 's/# / /g' docs/Data_Portal/PDF/Data_portal_UG.pd
-sed -i -e 's/### /## /g' docs/Data_Portal/PDF/Data_portal_UG.pd
-sed -i -e 's/\/site\//\/docs\//g' docs/Data_Portal/PDF/Data_portal_UG.pd
-pandoc --toc -V documentclass=report -V geometry:"top=2cm, bottom=1.5cm, left=1cm, right=1cm" -f markdown+grid_tables+table_captions -o docs/Data_Portal/PDF/Data_portal_UG.pdf docs/Data_Portal/PDF/Data_portal_UG.pd
-```
+Please join us at https://github.com/NCI-GDC/gdc-docs
 
 
diff --git a/docs/API/Release_Notes/API_Release_Notes.md b/docs/API/Release_Notes/API_Release_Notes.md
@@ -1,5 +1,131 @@
 # API Release Notes
 
+
+| Version | Date |
+|---|---|
+| [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 |
+| [v1.14.0](API_Release_Notes.md#v1140) | April 23, 2018 |
+| [v1.13.0](API_Release_Notes.md#v1130) | February 15, 2018 |
+| [v1.12.0](API_Release_Notes.md#v1120) | December 21, 2017 |
+| [v1.11.0](API_Release_Notes.md#v1110) | November 16, 2017 |
+| [v1.10.0](API_Release_Notes.md#v1100) | August 22, 2017 |
+| [v1.9.0](API_Release_Notes.md#v190) | June 29, 2017 |
+| [v1.8.0](API_Release_Notes.md#v180) | May 9, 2017 |
+| [v1.7.1](API_Release_Notes.md#v171) | March 16, 2017 |
+| [v1.5.0](API_Release_Notes.md#v150) | October 31, 2016 |
+| [v1.4.0](API_Release_Notes.md#v140) | September 23, 2016 |
+| [v1.3.1](API_Release_Notes.md#v131) | September 7, 2016 |
+| [v1.2.0](API_Release_Notes.md#v120) | August 9, 2016 |
+| [v1.1.0](API_Release_Notes.md#v110) | May 25, 2016 |
+| [v1.0.1](API_Release_Notes.md#v101) | May 16, 2016 |
+
+## v1.16.0
+
+* __GDC Product__: Application Programming Interface (API)
+* __Release Date__: September 27, 2018
+
+### New Features and Changes
+
+* Tissue_type is now parsed from the BCR Biospecimen submission <!--TT-753-->
+
+
+### Bugs Fixed Since Last Release
+
+* Re-attach the /files path to the legacy blueprints in gdcapi <!--SV-1195-->
+* Fix Internal Server Error when exporting JSON in Data Portal <!--SV-1209-->
+
+### 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 -->
+
+
+
+
+## v1.15.0
+
+* __GDC Product__: Application Programming Interface (API)
+* __Release Date__: August 23, 2018
+
+### New Features and Changes
+
+* Added support for file versioning <!--TT-482-->
+* Added new API endpoints in support of versioning: history, files/versions, and files/versions/manifest  <!--PRTL-2015-->
+* Updated the submit and release process <!--TT-249-->
+* Created admin endpoint to allow for modifying file and project flags and states <!--API-368-->
+* Populate version and release information for all existing files <!--TT-154-->
+
+### 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 -->
+
+
+## v1.14.1
+
+* __GDC Product__: Application Programming Interface (API)
+* __Release Date__: May 21, 2018
+
+### New Features and Changes
+
+* None
+
+### Bugs Fixed Since Last Release
+
+* Update to XML submission to correctly import biospecimen relationnships <!--TT-578-->
+* GraphQL submission queries return incorrect information <!--SV-1086-->
+
+### Known Issues and Workarounds
+
+* The error message for not including a token is incorrect for controlled access API requests (e.g. bam slicing).  It states that your token is invalid, but it should request that a token be supplied. <!--API-495-->
+* 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 -->
+
+
+## v1.14.0
+
+* __GDC Product__: Application Programming Interface (API)
+* __Release Date__: April 23, 2018
+
+### New Features and Changes
+
+* Updated support of BCR XML submission for Next Generation Cancer Models <!--DAT-1207-->
+
+
+### 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 -->
+
+
+## v1.13.0
+
+* __GDC Product__: Application Programming Interface (API)
+* __Release Date__: February 15, 2018
+
+### New Features and Changes
+
+* Reduced number of submission portal timeouts by optimizing graphql API requests <!--API-317-->
+
+### Bugs Fixed Since Last Release
+
+* Fixed bug preventing submission of clinical data via BCR XML <!--SV-985-->
+
+### 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 -->
+
 ## v1.12.0
 
 * __GDC Product__: Application Programming Interface (API)
@@ -15,7 +141,6 @@
 
 ### Known Issues and Workarounds
 
-* API queries to the cases or files endpoints will not return anything if the "size" parameter is set to over 10,000. For API queries expected to return results larger than 10,000 cases/files, use the "from" parameter to break up the results.  <!--SV-953-->
 * 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 -->
 

diff --git a/docs/API/Users_Guide/Appendix_A_Available_Fields.md b/docs/API/Users_Guide/Appendix_A_Available_Fields.md
@@ -10,21 +10,21 @@ The GDC API's [search and retrieval endpoints](Search_and_Retrieval.md) provide
 | --- |
 | dbgap_accession_number |
 | disease_type |
-| name |
+| name |  
 | primary_site |
 | project_id |
 | released |
 | state |
 | program.dbgap_accession_number |
-| program.name |
+| program.name |  
 | program.program_id |
 | summary.case_count |
 | summary.file_count |
 | summary.file_size |
 | summary.data_categories.case_count |
 | summary.data_categories.data_category |
 | summary.data_categories.file_count |
-| summary.experimental_strategies.case_count |
+| summary.experimental_strategies.case_count |  
 | summary.experimental_strategies.experimental_strategy |
 | summary.experimental_strategies.file_count |
 
@@ -38,8 +38,8 @@ The GDC API's [search and retrieval endpoints](Search_and_Retrieval.md) provide
 | aliquot_ids |
 | analyte_ids |
 | case_id |
-| created_datetime |
-| days_to_index |
+| created_datetime |  
+| days_to_index |  
 | portion_ids |
 | sample_ids |
 | slide_ids |
@@ -50,7 +50,7 @@ The GDC API's [search and retrieval endpoints](Search_and_Retrieval.md) provide
 | submitter_portion_ids |
 | submitter_sample_ids |
 | submitter_slide_ids |
-| updated_datetime |
+| updated_datetime |  
 | annotations.annotation_id |
 | annotations.case_id |
 | annotations.case_submitter_id |
@@ -122,7 +122,7 @@ The GDC API's [search and retrieval endpoints](Search_and_Retrieval.md) provide
 | exposures.weight |
 | exposures.years_smoked |
 | family_histories.created_datetime |
-| family_histories.family_history_id |
+| family_histories.family_history_id |  
 | family_histories.relationship_age_at_diagnosis |
 | family_histories.relationship_gender |
 | family_histories.relationship_primary_diagnosis |
@@ -425,8 +425,8 @@ The GDC API's [search and retrieval endpoints](Search_and_Retrieval.md) provide
 | files.cases.samples.portions.is_ffpe |
 | files.cases.samples.portions.portion_id |
 | files.cases.samples.portions.portion_number |
-| files.cases.samples.portions.state |
-| files.cases.samples.portions.submitter_id |
+| files.cases.samples.portions.state |  
+| files.cases.samples.portions.submitter_id |  
 | files.cases.samples.portions.updated_datetime |
 | files.cases.samples.portions.weight |
 | files.cases.samples.portions.analytes.a260_a280_ratio |
@@ -470,9 +470,9 @@ The GDC API's [search and retrieval endpoints](Search_and_Retrieval.md) provide
 | files.cases.samples.portions.analytes.aliquots.annotations.updated_datetime |
 | files.cases.samples.portions.analytes.aliquots.center.center_id |
 | files.cases.samples.portions.analytes.aliquots.center.center_type |
-| files.cases.samples.portions.analytes.aliquots.center.code |
-| files.cases.samples.portions.analytes.aliquots.center.name |
-| files.cases.samples.portions.analytes.aliquots.center.namespace |
+| files.cases.samples.portions.analytes.aliquots.center.code |  
+| files.cases.samples.portions.analytes.aliquots.center.name |  
+| files.cases.samples.portions.analytes.aliquots.center.namespace |  
 | files.cases.samples.portions.analytes.aliquots.center.short_name |
 | files.cases.samples.portions.analytes.annotations.annotation_id |
 | files.cases.samples.portions.analytes.annotations.case_id |
@@ -675,7 +675,7 @@ The GDC API's [search and retrieval endpoints](Search_and_Retrieval.md) provide
 | samples.annotations.entity_id |
 | samples.annotations.entity_submitter_id |
 | samples.annotations.entity_type |
-| samples.annotations.legacy_created_datetime |
+| samples.annotations.legacy_creat
 | samples.annotations.legacy_updated_datetime |
 | samples.annotations.notes |
 | samples.annotations.state |
@@ -1511,3 +1511,11 @@ The GDC API's [search and retrieval endpoints](Search_and_Retrieval.md) provide
 | --- |
 | project |
 | project.program |
+
+### GDC Conventions Supplemental
+| Field Group Name |
+| --- | --- |
+| File size | Listed in bytes |
+| Submitter id | String supplied by submitter |
+| Datetime | Combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss |    
+| Id | GDC supplied UUID ID |