Dependency update: Flask 1.1.1

Release Notes

For: uc-cdis/sheepdog

Notes since tag: 2.0.1

Notes to tag/commit: 2.1.0

Generated: 2019-09-26

Dependency Updates

• Flask 1.1.1, Werkzeug 0.16.0 (#300)

Fix indexd record and alias creation

Release Notes

For: uc-cdis/sheepdog

Notes since tag: 2.0.0

Notes to tag/commit: 2.0.1

Generated: 2019-09-24

Bug Fixes

• Fix bug with alias path building when we use a custom indexd base URL (#301)
• Fix authz resource path in newly created indexd records (#301)

Dependency Updates

• Bump indexclient to 1.6.2 (#301)

2.0.0

Release Notes

For: uc-cdis/sheepdog

Notes since tag: 1.1.13

Notes to tag/commit: 2.0.0

Generated: 2019-09-11

New Features

• Program and project creation automatically creates resources in arborist
  (#298)

Breaking Changes

• Use Arborist + gen3authz for auth requests (#298)

Dependency Updates

• Add gen3authz dependency for auth requests (#298)
• temporarily pin rx==1.6.1 until sheepdog is python 3 (#294)
• bump gdcdictionary to gen3dictionary 2.0.0 (#292)

Deployment Changes

• Optional configuration variable ARBORIST (arborist base URL) (#298)
• Requires Arborist to be deployed (#298)

Bug Fixes

• Update authz field in blank indexd record in data upload flow (#294)
• Sync new revision from indexd server after _update_acl_uploader_for_file
  (#294)

1.1.13

Release Notes

For: uc-cdis/sheepdog

Notes since tag: 1.1.12

Notes to tag/commit: 6fc107e

Generated: 2019-06-25

Dependency Updates

• bump sqlalchemy from 0.9.9 to 1.3.5 (#278)
• bump dictionaryutils from 2.0.4 to 2.0.7 (#278)
• bump psqlgraph to 2.0.2 (#278)
• bump gen3datamodel to 2.0.2 (#278)
• bump indexd from 1.0.8 to 1.1.2 (#278)
• bump authutils to 3.1.1 (#278)
• bump requests to 2.22.0 (#278)
• add rbac-client (#278)
• bump datamodelutils to 0.4.7 (#278)

New Features

• Accept consent codes during submission and include the consent codes in the
  indexd record's authz field. (#288)

1.1.12

Release Notes

For: uc-cdis/sheepdog

Notes since tag: 1.1.11

Notes to tag/commit: d13676f

Generated: 2019-06-18

Breaking Changes

• looks for INDEX_CLIENT instead of SIGNPOST in app.config and gets INDEX_CLIENT_HOST env var instead of SIGNPOST_HOST--you must therefore use the latest cloud automation or manually recreate your sheepdog secrets
• removes the USE_SIGNPOST backwards-compatibility workarounds and testing,
  since GDC forked sheepdog and signpost is dead (#291)
• deprecate "related cases" caching--not a problem if CASE_CACHE was False
  (#290)

Deployment Changes

• look for INDEX_CLIENT instead of SIGNPOST in app.config (#291)
• get INDEX_CLIENT_HOST env var instead of SIGNPOST_HOST (#291)

Dependency Updates

• remove signpost and signpostclient from requirements (#291)
• Remove cirrus from dev-requirements (#284)
• Remove fence from dev-requirements (#284)
• Remove userdatamodel from dev-requirements (#284)

Bug Fixes

• Fixed a bug in Indexd API calling when base_url has subpath (#287)
• Handle integrity Error when there are two transactions submit data to DB
  (#282)

Improvements

• stops importing and using signpost, and stops calling index client signpost
  where index client is already being used instead of signpost (#291)
• renames various vbbs and fns to not be signpost-specific, eg "signpost_obj"
  to "file_record" (#291)

1.1.11

Release Notes

For: uc-cdis/sheepdog
Notes since tag: 1.1.10
Notes to tag/commit: 2425220
Generated: 2019-04-29

Dependency Updates

• datamodelutils bumped to 0.4.5 (#277 #280)

Improvements

• Added missing index to make submission faster (#280)

1.1.10

For: uc-cdis/sheepdog
Notes since tag: 1.1.9
Notes to tag/commit: b13085d
Generated: 2019-04-18

Improvements

• added unique indexes for uniqueKeys (#259)
• Timeout is disabled for export endpoint (#275)

Deployment Changes

• Sheepdog will now create (or replace) the missing indexes during migration
  (#259)
• New unique indexes have been added to all nodes uc-cdis/gen3datamodel#12
  (#259)

1.1.9

Release Notes

For: uc-cdis/sheepdog
Notes since tag: 1.1.8
Notes to tag/commit: 1.1.9
Generated: 2019-04-02

Bug Fixes
  - fix the parsing of asterisks in properties for TSV and JSON metadata
    submission (#273)
  - Don't use lazy application initialization setting in uwsgi, which was
    causing multiple workers to try to open the database simultaneously (and
    fail if they couldn't). (#256)

Improvements
  - add tests for TSV and CSV submission (#273)
  - add tests for TSV and JSON submission with asterisks (#273)
  - Links are now case-insensitive (#272)
  - Use PyYaml safe_load() instead of load() (#271)

Breaking Changes
  - removed redundant building steps (#263)
  - changed uwsgi socket location (#263)

Dependency Updates
  - Upgrade PyYaml to 5.1 (#271)

1.1.8

For: uc-cdis/sheepdog
Notes since tag: 1.1.7
Notes to tag/commit: 1.1.8
Generated: 2019-02-25

Deployment Changes

• Now uWSGI worker process will kill itself (harakiri) and restart depending on reverse proxy timeout (#261)

Improvements

• Fixed inconsistent successful result when 504 Timeout (#261)
• fix(formatting): Black (#247)
• Fixed Swagger docs of export (#239)
• Also renamed program_id and project_id to program and project in Swagger docs of widely-used parameters program and project in URL path. (#239)

Bug Fixes

• Fix bug that POST submission may insert data with duplicate uniqueKeys successfully (#266)
• Align uWSGI timeout of /_status requests (#262)
• Make entity ID a separate and non-unique column on transaction snapshots. (#253)
• Change the ID column to be a real internal primary key. (#253)
• Fix the bug loading the wrong dictionary when running locally with run.py (#258)
• Removes the drop_all in the transaction log setup. This was wiping the transaction logs for the docker-compose version of Gen3. (#254)
• Make entity ID a separate and non-unique column on transaction snapshots. (#250)
• Change the ID column to be a real internal primary key. (#250)
• fix(assert): Not always true now (#247)
• fix encoding bug in sheepdog multiple node export (#243)
• fix asterisk bug in sheepdog single node export (#243)

Dependency Updates

• Upgrade to gdcdatamodel 1.3.9 (#266)
• Update to psqlgraph 1.2.3 (#266)
• fix(pyyaml): Version bump to 4.2 (#247)

Indexd update fix

fix/partial fail (#241)

* fix(partial-fail): error

* fix(partial-fail): update indexd before flush node to db

* fix(partial-fail): remove fake error

* fix(null-uploader): append to acl

* Revert "fix(null-uploader): append to acl"

This reverts commit a41d7bec80e1df2b99489f27808785845c3d7048.

* fix(null-uploader): submission succeeds if null uploader