WIP: EBI-ENA test

.travis.yml

@@ -7,8 +7,7 @@ env:
   matrix:
     - TEST_ADD_STUDIES=False COVER_PACKAGE=qiita_db
     - TEST_ADD_STUDIES=False COVER_PACKAGE=qiita_pet
-    - TEST_ADD_STUDIES=True COVER_PACKAGE="qiita_core qiita_ware"
-    - secure: ta4qrBQleTSwDUml9+jtnJES1qHCgLtjUpOHKX25ZCdw3vi/SpXxyErn5yrXvdefIDYtspVv3OWpWesiwFf3Qq1PSWJBeIrxdYizqebRr6GuUcdPN+Mj8PQ09UDWY3GthMfb26oIKmWi9YyELjwqkb6zztSW/e276scrEWppsVI=
+    - TEST_ADD_STUDIES=True COVER_PACKAGE="qiita_core qiita_ware" secure: ta4qrBQleTSwDUml9+jtnJES1qHCgLtjUpOHKX25ZCdw3vi/SpXxyErn5yrXvdefIDYtspVv3OWpWesiwFf3Qq1PSWJBeIrxdYizqebRr6GuUcdPN+Mj8PQ09UDWY3GthMfb26oIKmWi9YyELjwqkb6zztSW/e276scrEWppsVI=
 before_install:
   - redis-server --version
   - redis-server --port 7777 &

qiita_pet/support_files/doc/source/gettingstartedguide/index.rst

@@ -131,6 +131,8 @@ Checking for Errors In Sample information
 
 * `Keemei <https://keemei.qiime2.org/>`__ is a Google Sheets add-on for validating sample metadata. Validation of sample metadata is important before beginning any analysis. Install Keemei and follow the instructions on its website to validate your sample information spread sheet.
 
+  * Keemei can only be used to validate sample information **not preparation information**
+
 **Remember that spelling and capitalization matters in Qiita**
 
 Attaching the Sample Information to the Study
@@ -318,12 +320,6 @@ additional column is required.
 |                  |             | and ``my-data.fastq`` becomes ``my-data``).                                                |
 +------------------+-------------+--------------------------------------------------------------------------------------------+
 
-Checking for Errors In Preparation information
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-* `Keemei <https://keemei.qiime2.org/>`__ is a Google Sheets add-on for validating sample metadata. Validation of sample metadata is important before beginning any analysis. Install Keemei and follow the instructions on its website to validate your sample information spread sheet.
-
-**Remember that spelling and capitalization matters in Qiita**
 
 Attaching Preparation Information to the Study
 ----------------------------------------------

qiita_ware/commands.py

@@ -21,20 +21,20 @@
 from qiita_ware.exceptions import ComputeError, EBISubmissionError
 
 
-def submit_EBI(preprocessed_data_id, action, send):
-    """Submit a preprocessed data to EBI
+def submit_EBI(artifact_id, action, send):
+    """Submit a artifact to EBI
 
     Parameters
     ----------
-    preprocessed_data_id : int
-        The preprocesssed data id
+    artifact_id : int
+        The artifact id
     action : %s
         The action to perform with this data
     send : bool
         True to actually send the files
     """
     # step 1: init and validate
-    ebi_submission = EBISubmission(preprocessed_data_id, action)
+    ebi_submission = EBISubmission(artifact_id, action)
 
     # step 2: generate demux fastq files
     ebi_submission.study.ebi_submission_status = 'submitting'
@@ -46,7 +46,7 @@ def submit_EBI(preprocessed_data_id, action, send):
             rmtree(ebi_submission.full_ebi_dir)
         ebi_submission.study.ebi_submission_status = 'failed: %s' % error_msg
         LogEntry.create('Runtime', error_msg,
-                        info={'ebi_submission': preprocessed_data_id})
+                        info={'ebi_submission': artifact_id})
         raise
 
     # step 3: generate and write xml files
@@ -60,7 +60,7 @@ def submit_EBI(preprocessed_data_id, action, send):
 
             LogEntry.create('Runtime',
                             ("Submitting sequences for pre_processed_id: "
-                             "%d" % preprocessed_data_id))
+                             "%d" % artifact_id))
             for cmd in ebi_submission.generate_send_sequences_cmd():
                 stdout, stderr, rv = system_call(cmd)
                 if rv != 0:
@@ -72,14 +72,13 @@ def submit_EBI(preprocessed_data_id, action, send):
             environ['ASPERA_SCP_PASS'] = old_ascp_pass
             LogEntry.create('Runtime',
                             ('Submission of sequences of pre_processed_id: '
-                             '%d completed successfully' %
-                             preprocessed_data_id))
+                             '%d completed successfully' % artifact_id))
 
         # step 5: sending xml and parsing answer
         xmls_cmds = ebi_submission.generate_curl_command()
         LogEntry.create('Runtime',
                         ("Submitting XMLs for pre_processed_id: "
-                         "%d" % preprocessed_data_id))
+                         "%d" % artifact_id))
         xml_content, stderr, rv = system_call(xmls_cmds)
         if rv != 0:
             error_msg = ("Error:\nStd output:%s\nStd error:%s" % (
@@ -88,8 +87,7 @@ def submit_EBI(preprocessed_data_id, action, send):
         else:
             LogEntry.create('Runtime',
                             ('Submission of sequences of pre_processed_id: '
-                             '%d completed successfully' %
-                             preprocessed_data_id))
+                             '%d completed successfully' % artifact_id))
         open(ebi_submission.curl_reply, 'w').write(
             'stdout:\n%s\n\nstderr: %s' % (xml_content, stderr))
 
@@ -99,7 +97,7 @@ def submit_EBI(preprocessed_data_id, action, send):
         except EBISubmissionError as e:
             le = LogEntry.create(
                 'Fatal', "Command: %s\nError: %s\n" % (xml_content, str(e)),
-                info={'ebi_submission': preprocessed_data_id})
+                info={'ebi_submission': artifact_id})
             ebi_submission.study.ebi_submission_status = (
                 "failed: XML parsing, log id: %d" % le.id)
             raise ComputeError("EBI Submission failed! Log id: %d" % le.id)

qiita_ware/test/test_commands.py

@@ -134,24 +134,20 @@ def generate_new_study_with_preprocessed_data(self):
         return ppd
 
     def test_submit_EBI_step_2_failure(self):
-        # see issue #406
-        # ppd = self.write_demux_files(PrepTemplate(1), False)
-        #
-        # with self.assertRaises(AttributeError):
-        #     submit_EBI(ppd.id, 'ADD', True)
-        pass
+        ppd = self.write_demux_files(PrepTemplate(1), False)
+
+        with self.assertRaises(AttributeError):
+            submit_EBI(ppd.id, 'VALIDATE', True)
 
     def test_submit_EBI_parse_EBI_reply_failure(self):
         ppd = self.write_demux_files(PrepTemplate(1))
         with self.assertRaises(ComputeError):
-            submit_EBI(ppd.id, 'ADD', True)
+            submit_EBI(ppd.id, 'VALIDATE', True)
 
     def test_full_submission(self):
-        # see issue #406
-        # ppd = self.generate_new_study_with_preprocessed_data()
-        #
-        # submit_EBI(ppd.id, 'ADD', True)
-        pass
+        ppd = self.generate_new_study_with_preprocessed_data()
+
+        submit_EBI(ppd.id, 'VALIDATE', True)
 
 
 FASTA_EXAMPLE = """>1.SKB2.640194_1 X orig_bc=X new_bc=X bc_diffs=0

scripts/qiita

@@ -187,16 +187,16 @@ def load_prep_template(fp, study, data_type):
 # #############################################################################
 
 @ebi.command()
-@click.option('--preprocessed_data_id', required=True, type=int)
+@click.option('--artifact-id', required=True, type=int)
 @click.option('--action', type=click.Choice(EBISubmission.valid_ebi_actions),
               default='submit', help='The generated XML files will specify '
               'this "action", which controls how the EBI servers handle the '
               'metadata')
 @click.option('--send/--no-send', default=False, help="Controls whether or "
               "not sequence files and metadata will actually be sent to EBI "
               "(default is to generate all the files, but not to send)")
-def submit(preprocessed_data_id, action, send):
-    _submit_EBI(preprocessed_data_id, action, send)
+def submit(artifact_id, action, send):
+    _submit_EBI(artifact_id, action, send)
 
 
 # #############################################################################