Number of jobs today - displays the total number of jobs for today
Number of jobs per Internet domain - displays the number of jobs that have been submitted per Internet domain
Number of registered users - displays the total number of registered users
Number of jobs per day for current month - displays days of the current month with the total number of jobs for each day
Number of jobs in error per day for current month - displays days of the current month with the total number of jobs in error for each day
All unfinished jobs - displays jobs that are currently in a "new" state, a "queued" state or a "running" state
Number of jobs per month - displays a list of months with the total number of jobs for each month
Number of jobs in error per month - displays a list of months with the total number of jobs in error for each month
Number of jobs per user - displays users sorted in descending order by the number of jobs they have submitted
Number of jobs per tool - displays tools sorted in alphabetical order by tool id and the number of jobs created by the tool
SQL commands for schema changes:
ALTER TABLE galaxy_session ADD COLUMN current_history_id INTEGER;
ALTER TABLE galaxy_session ADD FOREIGN KEY (current_history_id) REFERENCES history(id);
ALTER TABLE galaxy_session ADD COLUMN session_key VARCHAR(255) UNIQUE;
ALTER TABLE galaxy_session ADD COLUMN is_valid BOOLEAN DEFAULT false;
ALTER TABLE galaxy_session ADD COLUMN prev_session_id INTEGER;
Galaxy config change:
In the [app:main] section, add:
# Galaxy session security
id_secret = changethisinproductiontoo
1) The "universe", "universe_user" and "universe_session" cookies are deprecated and replaced with 1 new cookie named galaxysession". The deprecated cookies are still supported and will be for at least 90 days, but when a valid one is found, the value is taken and used to create a new "galaxysession" cookie and the deprecated cookie is immediately expired.
2) The value of the new "galaxysession" cookie is an encrypted unique, high entropy 128 bit random number. The decoded value is the value stored in the new session_key column of the galaxy_session table.
3) Whenever a user logs in or out they get a new GalaxySession, and the old one in the database is marked as invalidated, so a compromised cookie won't survive across login/logout. Also, when creating the new session, a reference to the previous one is saved ( via the new prev_session_id column in the galaxy_session table ) so we have a way to chain them together.
There was a case where a dataset could have been converted multiple times if the conversion took place in a previous input in the same tool.
Also several other miscellaneous bug fixes.
Now we only support FastqSolexa variants.
If the quality scores are presented as characters,
the integer values are obtained by their ascii code subtract 64.
Cron scripts on test and main will need to be updated when the server is.
GOPS complement tool and annotation profiler will now correctly use chromosome lengths files if available.
MAF tool interfaces now support the use of index species and all species existing in cached alignment sets.
Until main is updated and the old maf_location files can be overwritten, these symbolic links are required:
maf_index.loc -> /depot/data2/galaxy/maf_index_new.loc
maf_pairwise.loc -> /depot/data2/galaxy/maf_pairwise_new.loc
to set the displayed name of created datasets. This is a template, and can
use the incoming parameters, the tool, and the special "on_string" value
created from the names of the data inputs.
Fixed all references to 'qualityscore' file extensions to be 'qual', since that is the extension in the QualityScore class.
Added functional test to the fastq2fasta converter.
James Taylor