Commits · ab65bf8d875d8bb008173ece1435622560b16171 · vidjil / vidjil

15 Jun, 2016 5 commits

patient.py patient/add.html patient group · ab65bf8d

HERBERT Ryan authored Jun 02, 2016

When adding a patient is it now necessary to select a group for this
patient in order to determine how the permissions will be propagated

ab65bf8d

group.py group/add.html Associate groups · 1c07b887

HERBERT Ryan authored Jun 02, 2016

It is now possible to select a parent group when creating a new one.
This will allow groups to inherit any read permission that is assigned
to the parent.

1c07b887

VidjilAuth.py Permissions Changes · 0f9bd03f

HERBERT Ryan authored Jun 02, 2016

In order to simplify the permissions system and improve performance as
well as make way for the new group associations. A single permission now
determines whether a group (or association of groups) has access to a
patient, run or sample_set

More advanced levels of access are now defined globally for a group.
Which means a group will always have the same permissions on files
accessible to it's association.

Furthermore groups are assigned in a parent/child manner. Only one group
can be a parent in an association, therefore associating a group to one
that already has a parent will associate said group to that parent.

A parent group will confer file readability to its children but the
children do not do the same for the parent and do not confer file
permissions with eachother.

0f9bd03f

VidjilAuth.py New group associated permissions management · 0ecc9f67
HERBERT Ryan authored May 31, 2016
```
Added some functions to manage permissions with group associations
```
0ecc9f67
db.py Add new table to associate groups · a79f1200
HERBERT Ryan authored May 31, 2016

a79f1200

13 Jun, 2016 3 commits

model.js: Save a .svg file rather than opening it · fcb47b0f

Mikaël Salson authored Jun 13, 2016

Once the tab is opened it is not that easy to save the SVG.
For instance FF adds <html> tags if one wants to save through the File > Save as button

fcb47b0f

graph.js: Clip the graph · fd180735

Mikaël Salson authored Jun 13, 2016

When exporting the graph the gray area extended to the bottom.
We use a <clipPath> tag to ensure that nothing goes outside.
All the other elements are put in an element which refers to this clip path.
Moreover the rectangle defining the clip path is resized with the other rectangle
when the graph needs be resized.

fd180735

germline_builder: 5, 4, 3 are now under the recombinations key · 04652b42
Mikaël Salson authored Jun 13, 2016
```
Fix 5f842de4
```
04652b42

10 Jun, 2016 4 commits
- core/segment.cpp: JUNCTION{start,end} initialization · b34cc22d
  Mathieu Giraud authored Jun 10, 2016
```
Thanks to Valgrind
```
  b34cc22d
- Maefile: temporarily bypass .should-vdj tests · 5815bf0d
  Mathieu Giraud authored Jun 10, 2016
```
(Same comment than ad0fe37e)
These tests were extended with many sequences that should be further checked.
Moreover they will be soon moved to their own git repository.
We have to find a new way to measure the quality of the build
even when some tests fail.
```
  5815bf0d
- doc/format-analysis.org: web application · 29894ba9
  Mathieu Giraud authored Jun 10, 2016
  
  29894ba9
- doc/format-analysis.org: typos · 0bc43e58
  Mathieu Giraud authored Jun 10, 2016
  
  0bc43e58
31 May, 2016 1 commit
- dev.org: server: permissions · 4f516bb0
  Mikaël Salson authored May 31, 2016
  
  4f516bb0
26 May, 2016 1 commit

css browser/index.html Uploads always visible · 1d849ec7

HERBERT Ryan authored May 26, 2016

Extracted the uploads recap from the top container in order to change
the z-index to a higher value than the db_div

1d849ec7

25 May, 2016 1 commit

model_loader.js remove analysis log · bd90e001

HERBERT Ryan authored May 25, 2016

Some analysis files contain a sample log entry. Added an exception to
the code to make sure this log does not replace the existing log as it
may be outdated

bd90e001

23 May, 2016 2 commits

controllers/default.py Out of index get_data · 99dcbf89

HERBERT Ryan authored May 23, 2016

Resolved a bug where opening a result file to which all the
sequence files have been deleted caused a server error. Instead we load
the file as normal but without all the information that is stored in
the sequence_file entry in the database

99dcbf89

should-vdj: 10 Vd2-Ja29 and 6 Db-Jb sequences from Prague · 98791511
Mathieu Giraud authored May 19, 2016

98791511

19 May, 2016 4 commits
- gb-to-should.py: argparse, -t · 7692c139
  Mathieu Giraud authored May 19, 2016
  
  7692c139
- gb-to-should.py: quick translation of some .gb files into .should-vdj.fa · e9b231e6
  Mathieu Giraud authored May 19, 2016
  
  e9b231e6
- should-vdj-to-tap.py: allows any character between succesive terms · c7a80b6d
  Mathieu Giraud authored May 19, 2016
```
'TRDV2 TRAJ29' should match 'TRDV2 13/CCCGAC/34 TRAJ29' (but not the opposite, unless -N is given)
```
  c7a80b6d
- builder.js: Display 'open patient' only when needed · 87974900
  Mikaël Salson authored May 19, 2016
```
Fix 1a02b2d8
```
  87974900
18 May, 2016 1 commit
- scripts/count-patients.py count-samples.py worker-status.py monitor scripts · 508e06ad
  HERBERT Ryan authored May 18, 2016
```
Adding scripts for monitoring purposes
```
  508e06ad
17 May, 2016 1 commit
- conf.js.sample: typo · 0c38a1a2
  Mikaël Salson authored May 17, 2016
  
  0c38a1a2
14 May, 2016 2 commits
- models/task.py, controllers/{file,patient}.py: streamline log messages · 9813eefc
  Mathieu Giraud authored May 14, 2016 and Vidjil Team committed May 14, 2016
  
  9813eefc
- models/task.py, controllers/file.py: pre_process, strealine log messages · 49c47f2e
  Mathieu Giraud authored May 14, 2016 and Vidjil Team committed May 14, 2016
  
  49c47f2e
13 May, 2016 2 commits
- sample_set/index.html: display sequence_file.id for admins · 708f0d8b
  Mathieu Giraud authored May 13, 2016 and Vidjil Team committed May 13, 2016
  
  708f0d8b
- file/add.html: reword, 'file 1'/'file 2' · 73095290
  Mathieu Giraud authored May 13, 2016 and Vidjil Team committed May 13, 2016
  
  73095290
11 May, 2016 1 commit
- css: more space for .db_table_split · a0c77528
  Mathieu Giraud authored May 11, 2016 and Vidjil Team committed May 11, 2016
  
  a0c77528
10 May, 2016 12 commits
- server: name encoding · 3a4698a9
  Mikaël Salson authored May 10, 2016
```
Safe encoding for first names and last names systematically.
Not only when we cannot view the full names.
```
  3a4698a9
- vidjil_utils: character encoding · fab1dccd
  Mikaël Salson authored May 10, 2016
```
Prefer using unicode(s).encode('utf-8') than unicode(s, 'utf-8'). Why? Don't know.
```
  fab1dccd
- sample_set/index.html: Fix 9e4d68e3 · ea001d55
  Mikaël Salson authored May 10, 2016
  
  ea001d55
- README.org: update, appnote submission · 7501d30a
  Mathieu Giraud authored May 10, 2016
  
  7501d30a
- doc/algo.org: update, appnote submission · d249e875
  Mathieu Giraud authored May 10, 2016
  
  d249e875
- doc/browser.org: update, app.vidjil.org, web application, appnote submission · 4cb78da9
  Mathieu Giraud authored May 10, 2016
  
  4cb78da9
- sample_set/index.html: Character encoding, fix 80eea121 · 9e4d68e3
  Mikaël Salson authored May 10, 2016
```
80eea121 could create problem in some situations [which ones?].
Now we try to encode in UTF-8 if it fails we let the string as is.
```
  9e4d68e3
- vidjil_utils: extract safe encoding · adf944d8
  Mikaël Salson authored May 10, 2016
```
It can be (and will be) useful elsewhere.
```
  adf944d8
- README.org: badges, remove coveralls, add landscape · 875000ff
  Mathieu Giraud authored May 10, 2016
```
gcov is now working on travis, but data are not properly sent to coveralls.
Landscape is working.
```
  875000ff
- .travis.yml: cache apt · ccd8bd36
  Mathieu Giraud authored May 10, 2016
```
greatly reduce build time
```
  ccd8bd36
- .travis.yml, Makefile: use gcov-4.8 for coveralls · 07ea4312
  Mathieu Giraud authored May 10, 2016
```
https://github.com/eddyxu/cpp-coveralls/issues/64
```
  07ea4312
- tests/Makefile: do not override CXX when it is defined · be11a796
  Mathieu Giraud authored May 10, 2016
```
as in algo/Makefile
```
  be11a796