Transfer copy raw data

qiita_db/support_files/patches/python_patches/58.py

@@ -17,3 +17,9 @@
     parameters = {'artifact': ['artifact:["Demultiplexed"]', None]}
     Command.create(qiita_plugin, "submit_to_VAMPS",
                    "submits an artifact to VAMPS", parameters)
+
+    # Create the copy artifact command
+    parameters = {'artifact': ['artifact:["Demultiplexed"]', None],
+                  'prep_template': ['prep_template', None]}
+    Command.create(qiita_plugin, "copy_artifact",
+                   "Creates a copy of an artifact", parameters)

qiita_pet/handlers/api_proxy/artifact.py

@@ -15,14 +15,12 @@
 from qiita_core.util import execute_as_transaction
 from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_pet.handlers.api_proxy.util import check_access, check_fp
-from qiita_ware.context import safe_submit
-from qiita_ware.dispatchable import copy_raw_data
 from qiita_db.artifact import Artifact
 from qiita_db.user import User
 from qiita_db.metadata_template.prep_template import PrepTemplate
 from qiita_db.util import (
     get_mountpoint, get_visibilities, get_artifacts_information)
-from qiita_db.software import Command, Parameters
+from qiita_db.software import Command, Parameters, Software
 from qiita_db.processing_job import ProcessingJob
 
 PREP_TEMPLATE_KEY_FORMAT = 'prep_template_%s'
@@ -174,10 +172,15 @@ def artifact_post_req(user_id, filepaths, artifact_type, name,
     if access_error:
         return access_error
 
+    user = User(user_id)
+
     if artifact_id:
         # if the artifact id has been provided, import the artifact
-        job_id = safe_submit(user_id, copy_raw_data, prep, artifact_id)
-        is_qiita_job = False
+        qiita_plugin = Software.from_name_and_version('Qiita',  'alpha')
+        cmd = qiita_plugin.get_command('copy_artifact')
+        params = Parameters.load(cmd, values_dict={'artifact': artifact_id,
+                                                   'prep_template': prep.id})
+        job = ProcessingJob.create(user, params)
     else:
         uploads_path = get_mountpoint('uploads')[0][1]
         path_builder = partial(join, uploads_path, str(study_id))
@@ -210,18 +213,18 @@ def artifact_post_req(user_id, filepaths, artifact_type, name,
 
         command = Command.get_validator(artifact_type)
         job = ProcessingJob.create(
-            User(user_id),
+            user,
             Parameters.load(command, values_dict={
                 'template': prep_template_id,
                 'files': dumps(cleaned_filepaths),
                 'artifact_type': artifact_type
                 }))
-        job.submit()
-        job_id = job.id
-        is_qiita_job = True
+
+    # Submit the job
+    job.submit()
 
     r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep.id,
-                 dumps({'job_id': job_id, 'is_qiita_job': is_qiita_job}))
+                 dumps({'job_id': job.id, 'is_qiita_job': True}))
 
     return {'status': 'success', 'message': ''}
 

qiita_ware/dispatchable.py

@@ -13,39 +13,6 @@ def submit_to_ebi(preprocessed_data_id, submission_type):
     submit_EBI(preprocessed_data_id, submission_type, True)
 
 
-def copy_raw_data(prep_template, artifact_id):
-    """Creates a new raw data by copying from artifact_id
-
-    Parameters
-    ----------
-    prep_template : qiita_db.metadata_template.prep_template.PrepTemplate
-        The template to attach the artifact
-    artifact_id : int
-        The id of the artifact to duplicate
-
-    Returns
-    -------
-    dict of {str: str}
-        A dict of the form {'status': str, 'message': str}
-    """
-    from qiita_db.artifact import Artifact
-
-    status = 'success'
-    msg = ''
-
-    try:
-        Artifact.copy(Artifact(artifact_id), prep_template)
-    except Exception as e:
-        # We should hit this exception rarely (that's why it is an
-        # exception)  since at this point we have done multiple checks.
-        # However, it can occur in weird cases, so better let the GUI know
-        # that this failed
-        return {'status': 'danger',
-                'message': "Error creating artifact: %s" % str(e)}
-
-    return {'status': status, 'message': msg}
-
-
 def delete_artifact(artifact_id):
     """Deletes an artifact from the system
 

qiita_ware/private_plugin.py

@@ -77,11 +77,30 @@ def submit_to_VAMPS(job):
     """
     with qdb.sql_connection.TRN:
         submit_VAMPS(job.parameters.values['artifact'])
+        job._set_status('success')
+
+
+def copy_artifact(job):
+    """Creates a copy of an artifact
+
+    Parameters
+    ----------
+    job : qiita_db.processing_job.ProcessingJob
+        The processing job performing the task
+    """
+    with qdb.sql_connection.TRN:
+        param_vals = job.parameters.values
+        orig_artifact = qdb.artifact.Artifact(param_vals['artifact'])
+        prep_template = qdb.metadata_template.prep_template.PrepTemplate(
+            param_vals['prep_template'])
+        qdb.artifact.Artifact.copy(orig_artifact, prep_template)
+        job._set_status('success')
 
 
 TASK_DICT = {'build_analysis_files': build_analysis_files,
              'release_validators': release_validators,
-             'submit_to_VAMPS': submit_to_VAMPS}
+             'submit_to_VAMPS': submit_to_VAMPS,
+             'copy_artifact': copy_artifact}
 
 
 def private_task(job_id):

qiita_ware/test/test_dispatchable.py

@@ -17,8 +17,7 @@
 from qiita_core.util import qiita_test_checker
 from qiita_ware.dispatchable import (
     create_sample_template, update_sample_template, delete_sample_template,
-    update_prep_template, delete_artifact, copy_raw_data,
-    delete_sample_or_column)
+    update_prep_template, delete_artifact, delete_sample_or_column)
 from qiita_db.study import Study
 from qiita_db.artifact import Artifact
 from qiita_db.exceptions import QiitaDBUnknownIDError, QiitaDBWarning
@@ -42,13 +41,6 @@ def tearDown(self):
             if exists(fp):
                 remove(fp)
 
-    def test_copy_raw_data(self):
-        obs = copy_raw_data(PrepTemplate(1), 1)
-        exp = {'status': 'danger',
-               'message': "Error creating artifact: Prep template 1 already "
-                          "has an artifact associated"}
-        self.assertEqual(obs, exp)
-
     def test_delete_artifact(self):
         obs = delete_artifact(1)
         exp = {'status': 'danger',

qiita_ware/test/test_private_plugin.py

@@ -0,0 +1,63 @@
+# -----------------------------------------------------------------------------
+# 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 unittest import TestCase, main
+
+import pandas as pd
+
+from qiita_core.util import qiita_test_checker
+from qiita_db.software import Software, Parameters
+from qiita_db.processing_job import ProcessingJob
+from qiita_db.user import User
+from qiita_db.study import Study
+from qiita_db.metadata_template.prep_template import PrepTemplate
+from qiita_ware.private_plugin import private_task
+
+
+@qiita_test_checker()
+class TestPrivatePlugin(TestCase):
+    def _create_job(self, cmd, values_dict):
+        user = User('test@foo.bar')
+        qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
+        cmd = qiita_plugin.get_command('copy_artifact')
+        params = Parameters.load(cmd, values_dict=values_dict)
+        job = ProcessingJob.create(user, params)
+        job._set_status('queued')
+        return job
+
+    def test_copy_artifact(self):
+        # Failure test
+        job = self._create_job('copy_artifact',
+                               {'artifact': 1, 'prep_template': 1})
+
+        private_task(job.id)
+        self.assertEqual(job.status, 'error')
+        self.assertIn("Prep template 1 already has an artifact associated",
+                      job.log.msg)
+
+        # Success test
+        metadata_dict = {
+            'SKB8.640193': {'center_name': 'ANL',
+                            'primer': 'GTGCCAGCMGCCGCGGTAA',
+                            'barcode': 'GTCCGCAAGTTA',
+                            'run_prefix': "s_G1_L001_sequences",
+                            'platform': 'ILLUMINA',
+                            'instrument_model': 'Illumina MiSeq',
+                            'library_construction_protocol': 'AAAA',
+                            'experiment_design_description': 'BBBB'}}
+        metadata = pd.DataFrame.from_dict(metadata_dict, orient='index',
+                                          dtype=str)
+        prep = PrepTemplate.create(metadata, Study(1), "16S")
+        job = self._create_job('copy_artifact', {'artifact': 1,
+                                                 'prep_template': prep.id})
+        private_task(job.id)
+        self.assertEqual(job.status, 'success')
+
+
+if __name__ == '__main__':
+    main()