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doc/server.md: new documentation on data migration 

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......@@ -908,156 +908,145 @@ python web2py -S vidjil -M db.auth_user[<user-id>].update_record(password=CRYPT(
# Migrating Data
## Database
The easiest way to perform a database migration is to first extract the
data with the following command:
Usually, when extracting data for a given user or group, the whole database should not be
copied over.
The `migrator` script allows the selective export and import of data,
whether it be a single patient/run/set or a list of them, or even all the sample sets
associated to a group (or to a user).
The script takes care both of database, but also of results and analysis files (see below for sequence files).
``` bash
mysqldump -u <user> -p <db> -c --no-create-info > <file>
```
See `server/web2py/applications/vidjil/scripts/migrator.py --help`
An important element to note here is the –no-create-info we add this
parameter because web2py needs to be allowed to create tables itself
because it keeps track of database migrations and errors will occur if
tables exist which it considers it needs to create.
## Exporting an archive
In order to import the data into an installation you first need to ensure
the tables have been created by Web2py this can be achieved by simply
accessing a non-static page.
(to be detailed)
/\!\\ If the database has been initialised from the interface you will
likely encounter primary key collisions or duplicated data, so it is best
to skip the initialisation altogether.
## Importing an archive
Once the tables have been created, the data can be imported as follows:
### Step 1 : extract the archive on your server
``` bash
mysql -u <user> -p <db> < <file>
```
The export directory must be on your server and accessible from your vidjil-server docker container.
You can define a new shared volume; or simply put the export directory on an already accessible location such as `[DOCKER DIRECTORY]/vidjil-server/conf/export/`
Please note that with this method you should have at least one admin user
that is accessible in the imported data. Since the initialisation is being
skipped, you will not have the usual admin account present.
It is also possible to create a user directly from the database although
this is not the recommended course of action.
### Step 2 : prepare the group that will own the data
## Files
Files can simply be copied over to the new installation, their filenames
are stored in the database and should therefore be accessible as long as
they are in the correct directories.
The permissions on a vidjil server are *group* based. Users and groups may be different from one server to another one. Before importing data on a server, one must have a group ready to receive the permissions to manage the imported files.
## Filtering data (soon deprecated)
From the admin web interface has, you can create a new group ("groups" -> "+new group" -> "add group"). The group ID is displayed between parenthesis next to its name on the group page, you will need it later. If you create such a group on a blank vidjil server, the ID is *4*.
When extracting data for a given user, the whole database should not be
copied over.
There are two courses of action:
### Step 3 : prepare your server analysis configs
- create a copy of the existing database and remove the users that are
irrelevant. The cascading delete should remove any unwanted data
barring a few exceptions (notably fused<sub>file</sub>, groups and sample<sub>setmembership</sub>)
*This step may require bioinformatics support depending on your data, the config previously used, and the ones you intend to use on your new installation. We can offer support via the [VidjilNet consortium](http://www.vidjil.net) for help on setting that.*
- export the relevant data directly from the database. This method
requires multiple queries which will not be detailed here.
Vidjil analysis configs should not be directly transferred between servers. Indeed, they depend on the setup of each server setup (software, paths...) and can collide with existing configs on your installation. Before importing, you thus need to create the missing analysis configs on your server and edit the `config.json` file provided in the export folder.
Once the database has been correctly extracted, a list of files can be
obtained from sequence<sub>file</sub>, fused<sub>file</sub>, results<sub>file</sub> and analysis<sub>file</sub>
with the following query:
This `config.json` file initially contains a list of the analysis configs from the original public server, such as:
``` sql
SELECT <filename field>
FROM <table name>
INTO OUTFILE 'filepath'
FIELDS TERMINATED BY ','
ENCLOSED BY ''
LINES TERMINATED BY '\n'
```
"2": {
"description": [
"IGH",
"vidjil",
"-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g:IGH,IGK,IGL,TRA,TRB,TRG,TRD -e 1 -w 50 -d -y all",
"-t 100 -d lenSeqAverage",
"multi-locus"
],
"link_local": 6
},
```
Note: We are managing filenames here which should not contain any
character such as quotes or commas so we can afford to refrain from
enclosing the data with quotes.
- `"2"` : the original config ID on the server from which the data was exported
- `"description"` : the original config parameters (only for information, they are ignoed in the import)
- `"link_local"` : the config ID that will be used on the new server
This query will output a csv file containing a filename on each line.
Copying the files is now just a matter of running the following script:
In the `config.json` file, you have to replace all` link_local` values with the corresponding config ID
of a similar config on your server (if you don't have a similar one you should create one).
``` bash
sh copy_files <file source> <file destination> <input file>
```
If you much of your imported data was on `old` configs, that you do not intend to run anymore,
a solution is to create a generic `legacy` config for these old data.
## Exporting sample sets
<!--
The `config.json` could thus look like:
The migrator script allows the export and import of data, whether it be a
single patient/run/set or a list of them, or even all the sample sets
associated to a group.
XXXXXX mettre ici un config.json "par défaut" mappant les configs actuelles (de prod) de app sur les configs propres d'un nouveau serveur XXXX
-->
``` example
usage: migrator.py [-h] [-f FILENAME] [--debug] {export,import} ...
Export and import data
### Step 4 : prepare your server pre-process configs
positional arguments:
{export,import} Select operation mode
export Export data from the DB into a JSON file
import Import data from JSON into the DB
Proceed as in step 3 for pre-process configs. The file to edit is named `pprocess.json`.
optional arguments:
-h, --help show this help message and exit
-f FILENAME Select the file to be read or written to
--debug Output debug information
```
Export:
### Step 5 : import
``` example
usage: migrator.py export [-h] {sample_set,group} ...
The import takes place inside the vidjil-server container
```sh
docker exec -it docker_uwsgi_1 bash
cd usr/share/vidjil/server/web2py/applications/vidjil/scripts/
sh migrator.sh -p [RESULTS DIRECTORY] -s [EXPORT DIRECTORY] import --config [CONFIG.JSON FILE] --pre-process [PPROCESS.JSON FILE] [GROUP ID]
```
positional arguments:
{sample_set,group} Select data selection method
sample_set Export data by sample-set ids
group Extract data by groupid
- [RESULTS DIRECTORY] the results directory path inside the container, it should be defined in your docker-compose.yml, by default it is /mnt/result/results/
- [EXPORT DIRECTORY] the export directory you installed in step 1, if you set it up in docker/vidjil-server/conf/export/ is location inside the container should be /etc/vidjil/export/
- [CONFIG.JSON FILE] this file is located in the export folder and you should have edited it during step 3
- [PPROCESS.JSON FILE] this file is located in the export folder and you should have edited it during step 4
- [GROUP ID] ID of the group you should have created/selected during step 2
optional arguments:
-h, --help show this help message and exit
Usually, the command is thus:
```
sh migrator.sh -p /mnt/result/results/ -s /etc/vidjil/export/XXXX/ import --config/etc/vidjil/exportXXXX/config.json --pre-process /etc/vidjil/export/XXXX/pprocess.json 4
```
``` example
usage: migrator.py export sample_set [-h] {patient,run,generic} ID [ID
...]
positional arguments:
{patient,run,generic}
Type of sample
ID Ids of sample sets to be extracted
optional arguments:
-h, --help show this help message and exit
```
## Exporting/importing input sequence files
Note that web2py and the Vidjil server are robust to missing *input* files.
These files are not backuped and may be removed from the server at any time.
Most of the time, these large files won't be migrated along with the database, the results and the analysis files.
However, they can simply be copied over to the new installation. Their filenames
are stored in the database and should therefore be accessible as long as
they are in the correct directories.
``` example
usage: migrator.py export group [-h] groupid
positional arguments:
groupid The long ID of the group
optional arguments:
-h, --help show this help message and exit
## Exporting/importing a full database
When a full database migration is needed, it can be done with the following command:
``` bash
mysqldump -u <user> -p <db> -c --no-create-info > <file>
```
Import:
The `--no-create-info` option is important because web2py needs to be allowed to create tables itself.
Indeed, it keeps track of database migrations and errors will occur if
tables exist which it considers it needs to create.
``` example
usage: migrator.py import [-h] [--dry-run] [--config CONFIG] groupid
In order to import the data into an installation you first need to ensure
the tables have been created by Web2py this can be achieved by simply
accessing a non-static page.
/\!\\ If the database has been initialised from the interface you will
likely encounter primary key collisions or duplicated data, so it is best
to skip the initialisation altogether.
positional arguments:
groupid The long ID of the group
Once the tables have been created, the data can be imported as follows:
optional arguments:
-h, --help show this help message and exit
--dry-run With a dry run, the data will not be saved to the database
--config CONFIG Select the config mapping file
``` bash
mysql -u <user> -p <db> < <file>
```
At least the results and analysis files should thus be copied.
Please note that with this method you should have at least one admin user
that is accessible in the imported data. Since the initialization is being
skipped, the usual admin account won't be present.
It is also possible to create a user directly from the database although
this is not the recommended course of action.
# Using CloneDB [Under development]
The [CloneDB](https://gitlab.inria.fr/vidjil/clonedb) has to be installed
independently of the Vidjil platform.
......
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