Commits · feb4281d9967315f6f2901c6a896e303bf639984 · vidjil / vidjil

19 Oct, 2018 17 commits
- Merge branch 'feature-a/2828-output-airr' into 'dev' · feb4281d
  Mathieu Giraud authored Oct 19, 2018
```
Feature a/2828 output airr

See merge request !330
```
  feb4281d
- Merge branch 'feature-s/3367-two-factor-auth' into 'dev' · e91de594
  Mathieu Giraud authored Oct 19, 2018
```
2FA

See merge request !340
```
  e91de594
- db.py set group for two-step verification · 4a907455
  Ryan Herbert authored Oct 09, 2018
```
See #3367
```
  4a907455
- Merge branch 'feature-a/3575-warning-two-assignations' into 'dev' · dd14adbf
  Mikaël Salson authored Oct 19, 2018
```
Feature a/3575 warning two assignations

Closes #3575

See merge request !333
```
  dd14adbf
- tests: update · 8e36164d
  Mathieu Giraud authored Oct 17, 2018
  
  8e36164d
- tests: testing AIRR output on S22 and X5 · 1e497e54
  Mathieu Giraud authored Oct 16, 2018
  
  1e497e54
- core/output.cpp: getout(), returns a non-escaped string · 13f901e5
  Mathieu Giraud authored Oct 16, 2018
  
  13f901e5
- vidjil.cpp: use SampleOutputAIRR(), output .tsv AIRR · 9426c9a9
  Mathieu Giraud authored Oct 16, 2018
```
See #2828.
```
  9426c9a9
- core/output.{h,cpp}: define and use CloneOutput.reads() · 83e65abd
  Mathieu Giraud authored Oct 16, 2018
  
  83e65abd
- core/output.{h,cpp}: CloneOutputAIRR, SampleOutputAIRR · 657a89ce
  Mathieu Giraud authored Oct 17, 2018
```
See #2828 and #3457.
```
  657a89ce
- core/output.{h,cpp}: Output.get() · e0c43986
  Mathieu Giraud authored Oct 17, 2018
```
See #3358
```
  e0c43986
- tests: add test · 021fc442
  Mathieu Giraud authored Oct 17, 2018
```
Closes #3575.
```
  021fc442
- core/segment.cpp: warn when there are equally probable assignations · 6b4fabc2
  Mathieu Giraud authored Oct 17, 2018
```
See #3575.
```
  6b4fabc2
- doc/warnings.md: W69 · 5a5d92c2
  Mathieu Giraud authored Oct 17, 2018
```
See #3575.
```
  5a5d92c2
- Merge branch 'feature-a/3358-output' into 'dev' · 656ddd25
  Mikaël Salson authored Oct 19, 2018
```
Feature a/3358 output

See merge request !320
```
  656ddd25
- doc/server.md: docker, how to update? · 07961c01
  Mathieu Giraud authored Oct 18, 2018
  
  07961c01
- doc/server.md: details, typos · 719de28e
  Mathieu Giraud authored Oct 18, 2018
  
  719de28e
18 Oct, 2018 23 commits
- Merge branch 'feature-s/3533-set_tokens_everywhere' into 'dev' · 1753759c
  Mathieu Giraud authored Oct 18, 2018
```
Feature s/3533 set tokens everywhere

Closes #3533

See merge request !323
```
  1753759c
- .gitlab-ci.yml docker TYPE you have to echo it... · f959661a
  Ryan Herbert authored Oct 18, 2018
  
  f959661a
- .gitlab-ci.yml fix docker_deploy TYPE assignment · 22fb65b0
  Ryan Herbert authored Oct 18, 2018
  
  22fb65b0
- Merge branch 'feature-s/init_public_tags' into 'dev' · 2bf8e676
  Ryan Herbert authored Oct 18, 2018
```
vidjil_utils.py add default tags to db init

See merge request !335
```
  2bf8e676
- tests/unit/controllers/tag.py update expected tags · 6d6a5164
  Ryan Herbert authored Oct 18, 2018
```
We've added default tags to the database initialisation, so now they
will appear when requesting tags

See #3577
```
  6d6a5164
- Merge branch 'feature-s/fix-deploy-docker' into 'dev' · a875fcd2
  Mathieu Giraud authored Oct 18, 2018
```
Feature s/fix deploy docker

See merge request !336
```
  a875fcd2
- .gitlab-ci.yml docker deploy get sha1 first 8 · 9e87a8a3
  Ryan Herbert authored Oct 18, 2018
```
Only extract the first 8 characters from the commit sha1 reference
```
  9e87a8a3
- .gitlab-ci.yml deploy docker fix syntax · a7b55e16
  Ryan Herbert authored Oct 17, 2018
  
  a7b55e16
- vidjil_utils.py init_db_helper fix var ref · db997c4d
  Ryan Herbert authored Oct 18, 2018
```
See #3577
```
  db997c4d
- vidjil_utils.py add default tags to db init · 6f929f98
  Ryan Herbert authored Oct 18, 2018
```
See #3577
```
  6f929f98
- tests: update tests · 932b88af
  Mathieu Giraud authored Oct 18, 2018
  
  932b88af
- vidjil.cpp: always use .toOutput(), even with non segmented sequences · 2ea82b2b
  Mathieu Giraud authored Oct 18, 2018
```
Following a discussion with @mikael-s.
We want to have meaningfull names when the sequence is not segmented.
See !320 (comment 126622)
```
  2ea82b2b
- core/segment.cpp: set clone name in FineSegmenter.toOutput() · de88a137
  Mathieu Giraud authored Oct 18, 2018
  
  de88a137
- vidjil.cpp: -c segment, format unique id · 2f78933e
  Mathieu Giraud authored Oct 18, 2018
  
  2f78933e
- tests: add tests · a34cd291
  Mathieu Giraud authored Oct 18, 2018
  
  a34cd291
- core/tools.{h,cpp}: string_of_int(..., pad_to_width) · 18797367
  Mathieu Giraud authored Oct 18, 2018
  
  18797367
- docker-compose.yml: by default, SSL certificates in vidjil-client/ssl/ · 7c89fe3a
  Mathieu Giraud authored Oct 18, 2018
  
  7c89fe3a
- vidjil-server/conf/defs.py: comments · eac97499
  Mathieu Giraud authored Oct 18, 2018
  
  eac97499
- doc/server.md: details · 72758624
  Mathieu Giraud authored Oct 18, 2018
  
  72758624
- doc/server.md: details · 16e4c912
  Mathieu Giraud authored Oct 18, 2018
  
  16e4c912
- doc/server.md: adding software, details · b592b503
  Mathieu Giraud authored Oct 18, 2018
  
  b592b503
- doc/server.md: SSL, details · d1786c0e
  Mathieu Giraud authored Oct 18, 2018
  
  d1786c0e
- Merge branch 'more_docker_docs' into 'dev' · 1d6dc183
  Mathieu Giraud authored Oct 18, 2018
```
More docker docs

See merge request !334
```
  1d6dc183