Transfer submit to vamps

qiita_db/__init__.py

@@ -26,12 +26,11 @@
 import study
 import user
 import processing_job
-import private
 
 __version__ = "0.2.0-dev"
 
 __all__ = ["analysis", "artifact", "base", "commands", "environment_manager",
            "exceptions", "investigation", "logger", "meta_util",
            "ontology", "portal", "reference", "search",
            "software", "sql_connection", "study", "user", "util",
-           "metadata_template", "processing_job", "private"]
+           "metadata_template", "processing_job"]

qiita_db/support_files/patches/58.sql

@@ -0,0 +1,4 @@
+-- Aug 31, 2017
+-- Remove MOI and transfer all jobs to internal QIITA plugin
+
+SELECT 42;

qiita_db/support_files/patches/python_patches/58.py

@@ -0,0 +1,19 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from qiita_db.sql_connection import TRN
+from qiita_db.software import Software, Command
+
+with TRN:
+    # Retrieve the Qiita plugin
+    qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
+
+    # Create the submit to VAMPS command
+    parameters = {'artifact': ['artifact:["Demultiplexed"]', None]}
+    Command.create(qiita_plugin, "submit_to_VAMPS",
+                   "submits an artifact to VAMPS", parameters)

qiita_pet/handlers/study_handlers/vamps_handlers.py

@@ -10,10 +10,10 @@
 from tornado.web import authenticated, HTTPError
 from qiita_files.demux import stats as demux_stats
 
-from qiita_ware.context import submit
-from qiita_ware.dispatchable import submit_to_VAMPS
 from qiita_db.exceptions import QiitaDBUnknownIDError
 from qiita_db.artifact import Artifact
+from qiita_db.software import Software, Parameters
+from qiita_db.processing_job import ProcessingJob
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_core.util import execute_as_transaction
 
@@ -99,23 +99,23 @@ def post(self, preprocessed_data_id):
                             user.id)
         msg = ''
         msg_level = 'success'
-        study = Artifact(preprocessed_data_id).study
-        study_id = study.id
-        state = study.ebi_submission_status
-        if state == 'submitting':
-            msg = "Cannot resubmit! Current state is: %s" % state
-            msg_level = 'danger'
-        else:
-            channel = user.id
-            job_id = submit(channel, submit_to_VAMPS,
-                            int(preprocessed_data_id))
 
-            self.render('compute_wait.html',
-                        job_id=job_id, title='VAMPS Submission',
-                        completion_redirect=('/study/description/%s?top_tab='
-                                             'preprocessed_data_tab&sub_tab=%s'
-                                             % (study_id,
-                                                preprocessed_data_id)))
-            return
+        plugin = Software.from_name_and_version('Qiita', 'alpha')
+        cmd = plugin.get_command('submit_to_VAMPS')
+        artifact = Artifact(preprocessed_data_id)
+
+        # Check if the artifact is already being submitted to VAMPS
+        is_being_submitted = any(
+            [j.status in ('queued', 'running')
+             for j in artifact.jobs(cmd=cmd)])
 
-        self.display_template(preprocessed_data_id, msg, msg_level)
+        if is_being_submitted == 'submitting':
+            msg = "Cannot resubmit! Data is already being submitted"
+            msg_level = 'danger'
+            self.display_template(preprocessed_data_id, msg, msg_level)
+        else:
+            params = Parameters.load(
+                cmd, values_dict={'artifact': preprocessed_data_id})
+            job = ProcessingJob.create(user, params)
+            job.submit()
+            self.redirect('/study/description/%s' % artifact.study.study_id)

qiita_ware/dispatchable.py

@@ -5,19 +5,14 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
-from qiita_ware.commands import submit_EBI, submit_VAMPS
+from qiita_ware.commands import submit_EBI
 
 
 def submit_to_ebi(preprocessed_data_id, submission_type):
     """Submit a study to EBI"""
     submit_EBI(preprocessed_data_id, submission_type, True)
 
 
-def submit_to_VAMPS(preprocessed_data_id):
-    """Submit a study to VAMPS"""
-    return submit_VAMPS(preprocessed_data_id)
-
-
 def copy_raw_data(prep_template, artifact_id):
     """Creates a new raw data by copying from artifact_id
 

qiita_db/private.py → qiita_ware/private_plugin.py

@@ -12,6 +12,7 @@
 import traceback
 
 import qiita_db as qdb
+from qiita_ware.commands import submit_VAMPS
 
 
 def build_analysis_files(job):
@@ -66,8 +67,21 @@ def release_validators(job):
         job._set_status('success')
 
 
+def submit_to_VAMPS(job):
+    """Submits an artifact to VAMPS
+
+    Parameters
+    ----------
+    job : qiita_db.processing_job.ProcessingJob
+        The processing job performing the task
+    """
+    with qdb.sql_connection.TRN:
+        submit_VAMPS(job.parameters.values['artifact'])
+
+
 TASK_DICT = {'build_analysis_files': build_analysis_files,
-             'release_validators': release_validators}
+             'release_validators': release_validators,
+             'submit_to_VAMPS': submit_to_VAMPS}
 
 
 def private_task(job_id):

scripts/qiita-private-plugin

@@ -10,7 +10,7 @@
 
 import click
 
-import qiita_db as qdb
+from qiita_ware.private_plugin import private_task
 
 
 @click.command()
@@ -23,7 +23,7 @@ def execute(url, job_id, output_dir):
     The parameters url and output_dir are ignored, but they are added for
     compatibility with the plugin system.
     """
-    qdb.private.private_task(job_id)
+    private_task(job_id)
 
 
 if __name__ == '__main__':