Commits · f3a881370a54c16eb932b2b70e8f47af5c04dd48 · vidjil / vidjil

02 Dec, 2020 3 commits
- Merge branch 'dev' of gitlab.inria.fr:vidjil/vidjil into feature-c/4370-label-tooltip-graph · f3a88137
  flothoni authored Dec 02, 2020
  
  f3a88137
- Merge branch 'feature-ct/mrd_brasil_tool_and_client' into 'dev' · 4aabe687
  Mathieu Giraud authored Dec 02, 2020
```
Feature ct/mrd brasil tool and client

See merge request !781
```
  4aabe687
- Merge branch 'feature-s/4533-remove-compare-stats-main-page' into 'dev' · ea426df6
  Mathieu Giraud authored Dec 02, 2020
```
sample_set/all.html: remove now buttons for comparison/stats on the main page

See merge request !848
```
  ea426df6
30 Nov, 2020 1 commit
- screen_mrd.js : regroup screen_mrd functions in an object and extend clone prototype with it · 4c03088a
  marc duez authored Nov 20, 2020
  
  4c03088a
23 Nov, 2020 1 commit
- Merge branch 'feature-csdoc/sample-database' into 'dev' · 7311d943
  Mikaël Salson authored Nov 23, 2020
```
Sample database

See merge request !851
```
  7311d943
20 Nov, 2020 35 commits
- doc/user.md: typos, details · 1308da91
  Mathieu Giraud authored Nov 20, 2020
  
  1308da91
- doc/user.md: refer to the 'sample database', warning for healthcare data · cddb5d3e
  Mathieu Giraud authored Nov 20, 2020
```
Following !813.
```
  cddb5d3e
- browser/index.html: samples menu · 403b6db8
  Mathieu Giraud authored Nov 20, 2020
```
Any Vidjil server may be used to store sample sets that may be not patients.
Moreover, following !813, we don't want that people upload patient-related data on non-healthcare servers.
```
  403b6db8
- tests: update · 80374369
  Mathieu Giraud authored Nov 20, 2020
  
  80374369
- sample_set/all.html: move now button in devel_mode for comparison on the main page · f8e179fa
  Mathieu Giraud authored Nov 19, 2020
```
see #4533
```
  f8e179fa
- Merge branch 'feature-s/4506-healthcare-compliance-warning' into 'dev' · 7b78d8c9
  Mikaël Salson authored Nov 20, 2020
```
Healthcare-compliant servers : documentation, warnings

Closes #4506

See merge request !813
```
  7b78d8c9
- Merge branch 'feature-s/single-query-tests' into 'dev' · 172ac2d3
  Mikaël Salson authored Nov 20, 2020
```
Single query, improve set queries

Closes #3169

See merge request !832
```
  172ac2d3
- SampleSet.py group string: split on comma · 8191cc98
  Ryan Herbert authored Nov 13, 2020 and Mikaël Salson committed Nov 20, 2020
  
  8191cc98
- sample_set.py fix debug log · 17dc411d
  Ryan Herbert authored Nov 10, 2020 and Mikaël Salson committed Nov 20, 2020
  
  17dc411d
- sample_set stats fix sample_set_list references · 58b8d710
  Ryan Herbert authored Nov 10, 2020 and Mikaël Salson committed Nov 20, 2020
  
  58b8d710
- mysql trickiness for file sizes · b585d2e1
  Ryan Herbert authored Nov 10, 2020 and Mikaël Salson committed Nov 20, 2020
  
  b585d2e1
- SampleSetList tests: add missing select() · ce025c5b
  Ryan Herbert authored Nov 02, 2020 and Mikaël Salson committed Nov 20, 2020
  
  ce025c5b
- SampleSetList: fix typo · 26f49f71
  Ryan Herbert authored Nov 02, 2020 and Mikaël Salson committed Nov 20, 2020
  
  26f49f71
- SampleSetList new anon permissions · 47686009
  Ryan Herbert authored Nov 02, 2020 and Mikaël Salson committed Nov 20, 2020
```
since the anon permissions are no longer in the sample_set_list, we need
to adjust the test
```
  47686009
- fix admin permissions in sample_set list · b0dc4889
  Ryan Herbert authored Nov 02, 2020 and Mikaël Salson committed Nov 20, 2020
  
  b0dc4889
- add creator id to test data set · addb8ffa
  Ryan Herbert authored Oct 30, 2020 and Mikaël Salson committed Nov 20, 2020
  
  addb8ffa
- my account left join on creator · 05bd0fc5
  Ryan Herbert authored Oct 30, 2020 and Mikaël Salson committed Nov 20, 2020
  
  05bd0fc5
- force inner joins on sample_set query · b1d8a08a
  Ryan Herbert authored Oct 26, 2020 and Mikaël Salson committed Nov 20, 2020
  
  b1d8a08a
- remove patient permission from sample_set_list · 5d681766
  Ryan Herbert authored Oct 23, 2020 and Mikaël Salson committed Nov 20, 2020
```
Since we don't use them to display the list, we'll save a little time
```
  5d681766
- add index creation on auth_permission · 989c31ca
  Ryan Herbert authored Oct 23, 2020 and Mikaël Salson committed Nov 20, 2020
  
  989c31ca
- alter sql_mode to fix patient search · 56235507
  Ryan Herbert authored Oct 23, 2020 and Mikaël Salson committed Nov 20, 2020
```
setting the sql_mode caused an issue with escaped characters. It would
seem I had overwritten an option required for web2py
```
  56235507
- SampleSetList update unit tests · 0933247d
  Ryan Herbert authored Oct 22, 2020 and Mikaël Salson committed Nov 20, 2020
  
  0933247d
- match sqlite syntax · fc95ea04
  Ryan Herbert authored Oct 22, 2020 and Mikaël Salson committed Nov 20, 2020
```
Set MySQL to use pipes for concat just like SQLITE.
```
  fc95ea04
- SampleSetList fix file size counting · 4a234b5c
  Ryan Herbert authored Oct 22, 2020 and Mikaël Salson committed Nov 20, 2020
  
  4a234b5c
- SampleSet model change separator for GROUP_CONCAT · 05931d1e
  Ryan Herbert authored Oct 22, 2020 and Mikaël Salson committed Nov 20, 2020
```
The syntax for specifying the GROUP_CONCAT separator seems to differ
between SQLITE and MySQL.
```
  05931d1e
- update usages of SampleSetList to use helpers · aef0e801
  Ryan Herbert authored Oct 22, 2020 and Mikaël Salson committed Nov 20, 2020
  
  aef0e801
- count distinct sequence_file ids · 20d114a8
  Ryan Herbert authored Oct 22, 2020 and Mikaël Salson committed Nov 20, 2020
```
fixes issue with sequence_file count for sample_sets accessible to
multiple groups
```
  20d114a8
- SampleSetList add non-sample-set permissions · 65cd899d
  Ryan Herbert authored Oct 22, 2020 and Mikaël Salson committed Nov 20, 2020
```
Add a second left join for performance reasons to include permissions
regarding 'patient', 'run' and 'generic'.
```
  65cd899d
- comment for clarity · b82a9ae3
  Ryan Herbert authored Oct 22, 2020 and Mikaël Salson committed Nov 20, 2020
  
  b82a9ae3
- add in-search filtering · bd79a951
  Ryan Herbert authored Oct 21, 2020 and Mikaël Salson committed Nov 20, 2020
  
  bd79a951
- SampleSetList: refactor some type-specific fields · adcf7e89
  Ryan Herbert authored Oct 21, 2020 and Mikaël Salson committed Nov 20, 2020
```
Pass a helper instance to SampleSetList instead of a set type
```
  adcf7e89
- restore tag functionality · e7985084
  Ryan Herbert authored Oct 21, 2020 and Mikaël Salson committed Nov 20, 2020
  
  e7985084
- SampleSetList fix len function · 18f6fb93
  Ryan Herbert authored Oct 21, 2020 and Mikaël Salson committed Nov 20, 2020
  
  18f6fb93
- remove unused code · 180a79db
  Ryan Herbert authored Oct 21, 2020 and Mikaël Salson committed Nov 20, 2020
  
  180a79db
- move most used config to index · 593cb188
  Ryan Herbert authored Oct 19, 2020 and Mikaël Salson committed Nov 20, 2020
```
rather than calculate the most used config in the sample_set list,
calculate in the index.
```
  593cb188