to be used as "Input Datasets" when constructing a workflow from a history.
Fix problem with dynamic selects in histories (the values are now properly
wrapped with UnvalidatedValue).
A database change is necessary:
ALTER TABLE galaxy_user ADD COLUMN external boolean;
To use:
http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy
I've tried to be as friendly as possible with respect to enabling and
disabling $REMOTE_USER support. If you have an existing server and
enable use_remote_user, users whose external login matches their Galaxy
username will have access to their existing history/session. If the
logins don't match, any existing credentials they had are destroyed.
Likewise, when disabled, users who weren't created automatically may
continue to access their histories/sessions. Automatically created
users are logged out, and can't log in unless enabled by an administrator.
http://www.selenic.com/mercurial/
Developers can clone a fresh repository like this:
hg clone ssh://coltrane.bx.psu.edu//depot/projects/universe/hg galaxy_dist
That extra / between coltrane and depot is required.
Read-only access is available in many ways:
Via Mercurial: hg clone http://www.bx.psu.edu/hg/galaxy
Via Subversion: svn co http://www.bx.psu.edu/svn/galaxy
Via Tarball: wget http://www.bx.psu.edu/hg/galaxy/archive/tip.tar.gz
Note that the Subversion repo address is not the same as the old one.
This is unavoidable since to continue to support SVN checkouts, we had
to convert Subversion->Mercurial->Subversion.
Please let me know ASAP of any issues (especially errors on an 'hg
push' so I can get them fixed quickly.
read only for the recipient, however they can always run the latest version of
the workflow. They can also 'clone' the workflow to create their own editable
copy of the current version.
Make sure to backup your database before updating.
Also fix a long standing bug in the async controller dealing with updating output datasets upon job completion.
Credit for database migration directions go to Greg.
*** This is a significant change, be sure to follow the migration steps below exactly and in order: ***
---------------
0. Stop Galaxy server
---------------
1. Backup database and galaxy_root/database directory
---------------
2. The current validation_error table is not being used, it is left over from Ian's work that was not made functional. However, if we want to keep it around, we should drop the old version of the table so it will get re-created correctly when the Galaxy server is restarted:
any database - sql command(s):
------------------------------
DROP TABLE validation_error;
---------------
3. Stop server, perform svn update to get latest code, start server to create new history_dataset_association and implicitly_converted_dataset_association tables
---------------
4. Add new columns to dataset table:
postgres sql command(s):
------------------------
ALTER TABLE dataset ADD COLUMN purgable boolean DEFAULT 't';
ALTER TABLE dataset ADD COLUMN external_filename text;
ALTER TABLE dataset ADD COLUMN _extra_files_path text;
mysql sql command(s):
---------------------
ALTER TABLE dataset ADD COLUMN purgable boolean DEFAULT TRUE;
ALTER TABLE dataset ADD COLUMN external_filename text;
ALTER TABLE dataset ADD COLUMN _extra_files_path text;
sqlite sql command(s):
----------------------
ALTER TABLE dataset ADD COLUMN purgable boolean DEFAULT 0;
ALTER TABLE dataset ADD COLUMN external_filename text;
ALTER TABLE dataset ADD COLUMN _extra_files_path text;
---------------
5. Populate new columns:
postgres sql command(s):
------------------------
UPDATE
dataset
SET
external_filename = dataset_filename.filename,
_extra_files_path = dataset_filename.extra_files_path
FROM
dataset_filename
WHERE
dataset.filename_id = dataset_filename.id;
mysql or sqlite sql command(s):
-------------------------------
UPDATE
dataset,
dataset_filename
SET
dataset.external_filename = dataset_filename.filename,
dataset._extra_files_path = dataset_filename.extra_files_path
WHERE
dataset.filename_id = dataset_filename.id;
---------------
6. Populate dataset table with info from dataset_child_association table:
postgres sql command(s):
------------------------
UPDATE
dataset
SET
parent_id = dataset_child_association.parent_dataset_id
FROM
dataset_child_association
WHERE
dataset.id = dataset_child_association.child_dataset_id;
mysql or sqlite sql command(s):
-------------------------------
UPDATE
dataset,
dataset_child_association
SET
dataset.parent_id = dataset_child_association.parent_dataset_id
WHERE
dataset.id = dataset_child_association.child_dataset_id;
---------------
7. Drop dataset_child_association table:
any database - sql command(s):
------------------------------
DROP TABLE dataset_child_association;
---------------
8. Copy parts of the current dataset table to the new history_dataset_association table:
postgres sql command(s):
------------------------
INSERT INTO history_dataset_association
SELECT
id,
history_id,
id AS dataset_id,
create_time,
update_time,
hid,
name,
info,
blurb,
peek,
extension,
metadata,
parent_id,
designation,
deleted,
visible
FROM dataset
ORDER BY id;
mysql or sqlite sql command(s):
-------------------------------
INSERT INTO
history_dataset_association
(
history_id,
dataset_id,
create_time,
update_time,
hid,
name,
info,
blurb,
peek,
extension,
metadata,
parent_id,
designation,
deleted,
visible
)
SELECT
history_id,
id,
create_time,
update_time,
hid,
name,
info,
blurb,
peek,
extension,
metadata,
parent_id,
designation,
deleted,
visible
FROM
dataset
ORDER BY
id;
---------------
9. Update the nextval value of the primary key sequence in the history_dataset_association table
NOTE: THIS IS NOT NECESSARY FOR MYSQL OR SQLITE!
postgres sql command(s):
------------------------
SELECT
setval('history_dataset_association_id_seq', max(id))
FROM
history_dataset_association;
---------------
10. Update dataset table to mark dataset_associated_file dataset as deleted:
postgres sql command(s):
------------------------
UPDATE dataset
SET
deleted = 't'
WHERE
id IN
(SELECT dataset_id FROM dataset_associated_file ORDER BY dataset_id DESC);
mysql or sqlite sql command(s):
-------------------------------
UPDATE dataset
SET
deleted = TRUE
WHERE
id IN
(SELECT dataset_id FROM dataset_associated_file ORDER BY dataset_id DESC);
---------------
11. Drop the dataset_associated_file table:
any database - sql command(s):
------------------------------
DROP TABLE dataset_associated_file;
---------------
12. Alter foreign keys on job_to_input_dataset table:
postgres or sqlite sql command(s):
------------------------
ALTER TABLE
job_to_input_dataset
DROP CONSTRAINT
job_to_input_dataset_dataset_id_fkey;
ALTER TABLE
job_to_input_dataset
ADD CONSTRAINT job_to_input_dataset_dataset_id_fkey
FOREIGN KEY
(dataset_id)
REFERENCES
history_dataset_association(id);
mysql sql command(s):
-------------------------------
ALTER TABLE
job_to_input_dataset
DROP FOREIGN KEY
ix_job_to_input_dataset_dataset_id;
ALTER TABLE
job_to_input_dataset
ADD FOREIGN KEY
ix_job_to_input_dataset_dataset_id (dataset_id)
REFERENCES
history_dataset_association(id);
---------------
13. Alter foreign keys on job_to_output_dataset table:
postgres or sqlite sql command(s):
------------------------
ALTER TABLE
job_to_output_dataset
DROP CONSTRAINT
job_to_output_dataset_dataset_id_fkey;
ALTER TABLE
job_to_output_dataset
ADD CONSTRAINT
job_to_output_dataset_dataset_id_fkey
FOREIGN KEY (dataset_id)
REFERENCES history_dataset_association(id);
mysql sql command(s):
-------------------------------
ALTER TABLE
job_to_output_dataset
DROP FOREIGN KEY
ix_job_to_output_dataset_dataset_id;
ALTER TABLE
job_to_output_dataset
ADD FOREIGN KEY
ix_job_to_output_dataset_dataset_id
FOREIGN KEY (dataset_id)
REFERENCES history_dataset_association(id);
---------------
14. Eliminate columns from the dataset table previously copied to history_dataset_association:
any database - sql command(s):
------------------------------
ALTER TABLE dataset DROP COLUMN hid;
ALTER TABLE dataset DROP COLUMN history_id;
ALTER TABLE dataset DROP COLUMN name;
ALTER TABLE dataset DROP COLUMN info;
ALTER TABLE dataset DROP COLUMN blurb;
ALTER TABLE dataset DROP COLUMN peek;
ALTER TABLE dataset DROP COLUMN extension;
ALTER TABLE dataset DROP COLUMN dbkey;
ALTER TABLE dataset DROP COLUMN metadata;
ALTER TABLE dataset DROP COLUMN parent_id;
ALTER TABLE dataset DROP COLUMN designation;
ALTER TABLE dataset DROP COLUMN visible;
ALTER TABLE dataset DROP COLUMN filename_id;
Greg Von Kuster