diff --git a/mutalyzer/entrypoints/admin.py b/mutalyzer/entrypoints/admin.py
index c235a93f39532434a42b6c17324b2357341cf281..f9eeff882b550e0e22302df34d26ca9133cb7a47 100644
--- a/mutalyzer/entrypoints/admin.py
+++ b/mutalyzer/entrypoints/admin.py
@@ -14,13 +14,14 @@ import os
import alembic.command
import alembic.config
from alembic.migration import MigrationContext
+import sqlalchemy
from sqlalchemy.orm.exc import NoResultFound
from . import _cli_string
from .. import announce
from .. import db
from ..db import session
-from ..db.models import Assembly, Chromosome
+from ..db.models import Assembly, BatchJob, BatchQueueItem, Chromosome
from .. import mapping
from .. import output
from .. import sync
@@ -151,6 +152,50 @@ def sync_cache(wsdl_url, url_template, history=7):
% (inserted, downloaded))
+def list_batch_jobs():
+ """
+ List batch jobs.
+ """
+ # For getting all batch jobs and their item counts, the following query
+ # might be more obvious at first thought. However, our current query below
+ # turns out to be more than twice as fast (and shorter).
+ #
+ # sq = session.query(
+ # BatchQueueItem.batch_job_id,
+ # sqlalchemy.func.count(BatchQueueItem.id).label('count')
+ # ).group_by(BatchQueueItem.batch_job_id).subquery()
+ # session.query(
+ # BatchJob,
+ # sq.c.count
+ # ).join(sq, BatchJob.id == sq.c.batch_job_id)
+ #
+ batch_jobs_with_counts = session.query(
+ BatchJob,
+ session.query(sqlalchemy.func.count('*')).filter(
+ BatchQueueItem.batch_job_id == BatchJob.id
+ ).label('count')
+ ).order_by(BatchJob.added.asc()).all()
+
+ lengths = {
+ 'id_len': max(len(str(j.id)) for j, _ in batch_jobs_with_counts),
+ 'type_len': max(len(j.job_type) for j, _ in batch_jobs_with_counts),
+ 'count_len': max(len(str(c)) for _, c in batch_jobs_with_counts),
+ 'email_len': max(len(j.email) for j, _ in batch_jobs_with_counts)
+ }
+
+ template = ('{id:{id_len}} {type:<{type_len}} {added:%Y-%m-%d %H:%M:%S}'
+ ' {count:<{count_len}} {email:{email_len}}')
+
+ for batch_job, count in batch_jobs_with_counts:
+ print template.format(
+ id=batch_job.id,
+ type=batch_job.job_type,
+ added=batch_job.added,
+ count=count,
+ email=batch_job.email,
+ **lengths)
+
+
def set_announcement(body, url=None):
"""
Set announcement to show to the user.
@@ -309,6 +354,12 @@ def main():
description=unset_announcement.__doc__.split('\n\n')[0])
p.set_defaults(func=unset_announcement)
+ # Subparser 'batch-jobs'.
+ p = subparsers.add_parser(
+ 'batch-jobs', help='list batch jobs',
+ description=list_batch_jobs.__doc__.split('\n\n')[0])
+ p.set_defaults(func=list_batch_jobs)
+
# Subparser 'sync-cache'.
p = subparsers.add_parser(
'sync-cache', help='synchronize cache with remote Mutalyzer',
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index a256831f1de687878e26fa1ecad06f23e256f94c..8281da387b4049ffbbdcc7d1410d07cf00d4db66 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -71,14 +71,20 @@ class MutalyzerService(ServiceBase):
super(MutalyzerService, self).__init__(environ)
#__init__
- @srpc(Mandatory.ByteArray, Unicode, Unicode, _returns=Unicode)
- def submitBatchJob(data, process='NameChecker', argument=''):
+ @srpc(Mandatory.ByteArray, Unicode, Unicode, Unicode, _returns=Unicode)
+ def submitBatchJob(data, process='NameChecker', argument='', email=None):
"""
Submit a batch job.
Input and output file formats for batch jobs are explained on the
website <https://mutalyzer.nl/batch>.
+ Batch jobs are processed using round-robin scheduling grouped by email
+ address. Per email address, jobs are processed sequentially in order
+ of submission. Jobs with no email address specified end up in a shared
+ group. This means your job is likely to be processed sooner if you
+ provide an email address.
+
On error an exception is raised:
- detail: Human readable description of the error.
- faultstring: A code to indicate the type of error.
@@ -90,6 +96,8 @@ class MutalyzerService(ServiceBase):
(default), SyntaxChecker, PositionConverter, SnpConverter.
@arg argument: Additional argument. Currently only used if batch_type
is PositionConverter, denoting the human genome build.
+ @arg email: Optional email address. Notification of job completion
+ will be sent to this address.
@return: Batch job identifier.
"""
@@ -139,7 +147,7 @@ class MutalyzerService(ServiceBase):
if job is None:
raise Fault('EPARSE', 'Could not parse input file, please check your file format.')
- result_id = scheduler.addJob('job@webservice', job, columns,
+ result_id = scheduler.addJob(email or 'job@webservice', job, columns,
batch_types[process], argument)
return result_id
diff --git a/mutalyzer/website/templates/batch-job-progress.html b/mutalyzer/website/templates/batch-job-progress.html
index 7f64c01fd0bcb95029c71e732da60fec3b4546a0..77511f9dd300f7f862eb95e2752dadb933ce38fb 100644
--- a/mutalyzer/website/templates/batch-job-progress.html
+++ b/mutalyzer/website/templates/batch-job-progress.html
@@ -10,6 +10,9 @@
<div id="if_items_left"{% if not items_left %} style="display:none"{% endif %}>
<p>Your job is in progress with <span id="items_left">{{ items_left }}</span> items remaining.</p>
<p>You will receive an email when the job is finished.</p>
+ <p>Please note that your jobs are processed in order of submission,
+ meaning you will not see any progress on this job until all your earlier
+ jobs have finished.</p>
</div>
<div id="ifnot_items_left"{% if items_left %} style="display:none"{% endif %}>
<p>Your job is finished, please download the results:
diff --git a/mutalyzer/website/templates/batch-jobs.html b/mutalyzer/website/templates/batch-jobs.html
index 4b4db65719e0f514114f19e4d7c55f4e51007991..6955a18a9e9bebf799397a434fe347382fa331bc 100644
--- a/mutalyzer/website/templates/batch-jobs.html
+++ b/mutalyzer/website/templates/batch-jobs.html
@@ -79,6 +79,8 @@
<p><a href="{{ url_for('.downloads', filename='batchtestnew.txt') }}">Download new style example file</a></p>
<h4>Old Style</h4>
+ <p><strong>Deprecation warning:</strong> Please don't use this format, it
+ is deprecated and will not be supported in the future.</p>
<p>This file format has a header-row, which consists of
three tab delimited fields. In each following row the
corressponding data is also tab delimited.</p>