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Automated processing of chemoproteomics data
This may require changes to ip2api.. can either give searches unique names (under the same experiment name on ip2), add a unique identifier to the experiment name, or store search ids in the experiment table.
Should probably just clear the folder when the app starts.
Need to modify ip2api
to add a method to login via a stored cookie. On page load check if cookie still works and if not, require that the user passes their username and password once again.
Though there's a check for the presence of credentials in the session prior to rendering of the main page, these credentials aren't actually checked. The end result is sometimes the input boxes for these credentials pop up after the user has submitted.
Perhaps checking credentials before rendering every request is a bit much, but perhaps the experience of them being rejected/stale can be made a bit less jarring.
Cues that require little processing such as IP2 submission should be allowed higher concurrency than intense cues like running cimage.
Should just retry sending the email with increasing cooldown times instead.
Task ctesi.core.tasks.convert_task[f17e0507-8f93-4405-a099-ddac4fe54a69] raised unexpected: OperationalError('(sqlite3.OperationalError) database is locked',)
Traceback (most recent call last):
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 724, in _commit_impl
self.engine.dialect.do_commit(self.connection)
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/engine/default.py", line 462, in do_commit
dbapi_connection.commit()
sqlite3.OperationalError: database is locked
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/celery/app/trace.py", line 382, in trace_task
R = retval = fun(*args, **kwargs)
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/celery/app/trace.py", line 641, in __protected_call__
return self.run(*args, **kwargs)
File "/home/ctesi/ctesi/ctesi/core/tasks.py", line 83, in convert_task
status_callback=lambda s: update_status(experiment_id, 'converting', meta=s),
File "/home/ctesi/ctesi/ctesi/core/convert.py", line 22, in convert
status_callback(status)
File "/home/ctesi/ctesi/ctesi/core/tasks.py", line 83, in <lambda>
status_callback=lambda s: update_status(experiment_id, 'converting', meta=s),
File "/home/ctesi/ctesi/ctesi/api/__init__.py", line 71, in update_experiment_status
db.session.commit()
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/orm/scoping.py", line 153, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/orm/session.py", line 943, in commit
self.transaction.commit()
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/orm/session.py", line 471, in commit
t[1].commit()
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 1643, in commit
self._do_commit()
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 1674, in _do_commit
self.connection._commit_impl()
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 726, in _commit_impl
self._handle_dbapi_exception(e, None, None, None, None)
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception
exc_info
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 265, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 248, in reraise
raise value.with_traceback(tb)
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 724, in _commit_impl
self.engine.dialect.do_commit(self.connection)
File "/home/ctesi/ctesi/venv/lib/python3.5/site-packages/sqlalchemy/engine/default.py", line 462, in do_commit
dbapi_connection.commit()
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked (Background on this error at: http://sqlalche.me/e/e3q8)
Otherwise if multiple diff-mods are entered it may be unclear to user which mass was assigned to which symbol
Probably would be best to break up tasks into smaller chunks. Should also consider allowing tasks to just retry.
Recently switched to 'nice' html error pages. There may be api consumers that expect a json response with an error
property.
Large datasets seem to time out as the zip operation takes too long.
For example:
Would be nicer than a lot of this:
experiment = api.Experiment.query.get(experiment_id)
if experiment.user_id == int(current_user.get_id()) or current_user.has_role('admin'):
// something that requires permissions
Possible issues with this after implementing batched file upload.
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