Commit 7f426d91 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'doc/typos' into 'dev'

Doc/typos

See merge request !698
parents e3b958d2 d7f2632b
Pipeline #147499 failed with stages
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......@@ -332,14 +332,14 @@ webpage.
`browser/tests/functional`, with Watir.
The functional tests are built using two base files:
- vidjil<sub>browser</sub>.rb
- `vidjil_browser.rb`
abstracts the vidjil browser (avoid using IDs or
class names that could change in the test). The tests must rely as
much as possible on vidjil<sub>browser</sub>. If access to some
much as possible on `vidjil_browser`. If access to some
data/input/menus are missing they must be addded there.
- browser<sub>test</sub>.rb
- `browser_test.rb`
prepares the environment for the tests. Each test
file will extend this class (as can be seen in test<sub>multilocus</sub>.rb)
file will extend this class (as can be seen in `test_multilocus.rb`)
The file `segmenter_test.rb` extends the class in `browser_test.rb` to adapt
it to the purpose of testing the analyze autonomous app.
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......@@ -340,24 +340,27 @@ A click on the `out` link at the right of every sample give access to the raw ou
## Groups
Each patient, run or set is assigned to at least one group.
Users are assigned to diffrent groups and therefore gain access to any patients, runs or sets that said group has access to.
Users are assigned to different groups and therefore gain access to any patients, runs or sets that said group has access to.
There are also groups that may be clustered together. Usually this represents an organisation, such as a Hospital.
The organisation has a group to which subgroups are associated. This allows users with different sets of permissions
to gain access to files uploaded to the organisation's group automatically.
Groups may be nested.
For example, a group may represents an organization, such as a hospital or a network of hospitals.
Subgroups may be created for individual labs and/or for different roles in the labs.
This allows users to have different sets of permissions
while accessing to some of the files uploaded to the organization's group.
Users may be a part of several groups. By default Users are assigned their personnal group to which they can upload files
Users may be a part of several groups. By default Users are assigned their personal group to which they can upload files
and be the sole possessor of an access to this file.
Different groups implies different sets of permissions. A user may not have the same permissions on a file accessed
from an organisation's group as (s)he does on files from her/his personnal group, or even from a group associated to
another organisation.
Different groups imply different sets of permissions.
A user may not have the same permissions on a file accessed
from an organization's group as (s)he does on files from her/his personal group, or even from a group associated to
another organization.
The different permissions that can be attributed are:
- Read: Permissions to view patients/runs/sets to which a group or organisation has access to
- Read: Permissions to view patients/runs/sets to which a group or organization has access to
- Create: Permissions to create patients/runs/sets
- Upload: Permissions to upload samples to the patients/runs/sets of a group
- Run: Permissions to run vidjil on an uploaded samples to the patients/runs/sets of a group
- Run: Permissions to run Vidjil on an uploaded samples to the patients/runs/sets of a group
- View Details: Permissions to view patient/run/set data in an unencrypted manner for the patients/runs/sets of a group
- Save: Permissions to save an analysis for the patients/runs/sets of a group
......
......@@ -695,7 +695,7 @@ We also propose in [fuse.py](/tools) a way to convert AIRR format to the `.vidji
Note that Vidjil-algo is designed to efficiently gather reads from large datasets into clones.
By default (`-c clones`), we thus report in the AIRR format *clones*.
See also [What is a clone ?](vidjil-format/#what-is-a-clone).
See also [What is a clone ?](/vidjil-format/#what-is-a-clone).
Using `-c designations` trigger a separate analysis for each read, but this is usually not advised for large datasets.
......
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