Commits · 403b6db8a35b0ac825911552d92a2d48a114eb67 · vidjil / vidjil

20 Nov, 2020 40 commits
- 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
- 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
- single query permissions · ca9846bd
  Ryan Herbert authored Oct 19, 2020 and Mikaël Salson committed Nov 20, 2020
```
use auth.vidjil_accessible_query to include permissions
```
  ca9846bd
- add left join for auth_membership · b098e05d
  Ryan Herbert authored Oct 19, 2020 and Mikaël Salson committed Nov 20, 2020
```
the on query for anon permissions was causing a cross join with the
auth_membership table, which made the file_count and file_size fields
incorrect
```
  b098e05d
- cleanup debug prints · 01f7e36f
  Ryan Herbert authored Jan 13, 2020 and Mikaël Salson committed Nov 20, 2020
  
  01f7e36f
- fix issue wiith file count and size · 971e42cd
  Ryan Herbert authored Jan 13, 2020 and Mikaël Salson committed Nov 20, 2020
  
  971e42cd
- some dirty code to work for runs and sets · 42a919a9
  Ryan Herbert authored Jan 13, 2020 and Mikaël Salson committed Nov 20, 2020
  
  42a919a9
- add permissions and anon to single query · a12ba46c
  Ryan Herbert authored Jan 13, 2020 and Mikaël Salson committed Nov 20, 2020
  
  a12ba46c
- alter model to use work with group_concat · d0e1d58d
  Ryan Herbert authored Jan 13, 2020 and Mikaël Salson committed Nov 20, 2020
  
  d0e1d58d
- move group_concat to model · 8966ce35
  Ryan Herbert authored Jan 13, 2020 and Mikaël Salson committed Nov 20, 2020
  
  8966ce35
- Merge branch 'feature-t/4566-warnings-clone-multiple-denominations' into 'dev' · e7cca318
  Mathieu Giraud authored Nov 20, 2020
```
Resolve "Warnings, avoir un nouveau wrning si un clone a plusiuers dénomination sur différents samples"

Closes #4566

See merge request !850
```
  e7cca318