Merge pull request #1979 from antgonza/study-listing-no-ref

Thanks @antgonza ! Study listing brakes when no ref

.travis.yml

@@ -8,7 +8,7 @@ env:
     - TEST_ADD_STUDIES=True
 before_install:
   - redis-server --version
-  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
   - export PATH=/home/travis/miniconda3/bin:$PATH

qiita_db/analysis.py

@@ -857,20 +857,23 @@ def build_files(self,
 
             # figuring out if we are going to have duplicated samples, again
             # doing it here cause it's computational cheaper
-            # 1. merge samples per data_type, reference used and the command id
-            #    if not one of the tables is not 'Pick closed-reference OTUs'
-            #    it's safer to always rename. Note that grouped_samples is
-            #    basically how many biom tables we are going to create
+            # 1. merge samples per: data_type, reference used and
+            # the command id
+            # Note that grouped_samples is basically how many biom tables we
+            # are going to create
             rename_dup_samples = False
             grouped_samples = {}
             for k, v in viewitems(samples):
                 a = qdb.artifact.Artifact(k)
                 p = a.processing_parameters
-                c = p.command
-                if c.name != 'Pick closed-reference OTUs':
-                    rename_dup_samples = True
-                    break
-                l = "%s.%d.%d" % (a.data_type, p.values['reference'], c.id)
+                if p is not None and p.command is not None:
+                    ref = (str(p.values['reference'])
+                           if 'reference' in p.values else 'na')
+                    cid = str(p.command.id)
+                else:
+                    ref = 'na'
+                    cid = 'na'
+                l = "%s.%s.%s" % (a.data_type, ref, cid)
                 if l not in grouped_samples:
                     grouped_samples[l] = []
                 grouped_samples[l].append((k, v))

qiita_db/job.py

@@ -126,10 +126,12 @@ def exists(cls, datatype, command, options, analysis,
                         AND input_file_reference_id = %s
                         AND input_file_software_command_id = %s
                   """.format(cls._table)
+            rid = (input_file_reference.id
+                   if input_file_reference is not None else None)
+            cid = (input_file_software_command.id
+                   if input_file_software_command is not None else None)
             qdb.sql_connection.TRN.add(
-                sql, [datatype_id, command_id, opts_json,
-                      input_file_reference.id,
-                      input_file_software_command.id])
+                sql, [datatype_id, command_id, opts_json, rid, cid])
             analyses = qdb.sql_connection.TRN.execute_fetchindex()
 
             if not analyses and return_existing:
@@ -289,10 +291,12 @@ def create(cls, datatype, command, options, analysis,
                                             input_file_software_command_id)
                      VALUES (%s, %s, %s, %s, %s, %s)
                      RETURNING job_id""".format(cls._table)
+            rid = (input_file_reference.id
+                   if input_file_reference is not None else None)
+            cid = (input_file_software_command.id
+                   if input_file_software_command is not None else None)
             qdb.sql_connection.TRN.add(
-                sql, [datatype_id, 1, command_id, opts_json,
-                      input_file_reference.id,
-                      input_file_software_command.id])
+                sql, [datatype_id, 1, command_id, opts_json, rid, cid])
             job_id = qdb.sql_connection.TRN.execute_fetchlast()
 
             # add job to analysis
@@ -359,8 +363,8 @@ def options(self):
             db_comm = qdb.sql_connection.TRN.execute_fetchindex()[0]
 
             out_opt = loads(db_comm[1])
-            basedir = qdb.util.get_db_files_base_dir()
-            join_f = partial(join, join(basedir, "job"))
+            _, mp, _ = qdb.util.get_mountpoint('job', retrieve_subdir=True)[0]
+            join_f = partial(join, mp)
             for k in out_opt:
                 opts[k] = join_f("%s_%s_%s" % (self._id, db_comm[0],
                                                k.strip("-")))

qiita_db/support_files/patches/41.sql

@@ -0,0 +1,6 @@
+-- Oct 29, 2016
+-- Dropping command and reference NULL constraints from jobs so bioms
+-- without them can be analyzed
+
+ALTER TABLE qiita.job ALTER COLUMN input_file_reference_id DROP NOT NULL;
+ALTER TABLE qiita.job ALTER COLUMN input_file_software_command_id DROP NOT NULL;

qiita_db/support_files/qiita-db.dbs

@@ -876,8 +876,8 @@
 			<column name="log_id" type="bigint" jt="-5" >
 				<comment><![CDATA[Reference to error if status is error]]></comment>
 			</column>
-			<column name="input_file_reference_id" type="bigint" jt="-5" mandatory="y" />
-			<column name="input_file_software_command_id" type="bigint" jt="-5" mandatory="y" />
+			<column name="input_file_reference_id" type="bigint" jt="-5" />
+			<column name="input_file_software_command_id" type="bigint" jt="-5" />
 			<index name="pk_job" unique="PRIMARY_KEY" >
 				<column name="job_id" />
 			</index>
@@ -1916,12 +1916,12 @@ Controlled Vocabulary]]></comment>
 		<entity schema="qiita" name="processing_job_workflow" color="b2cdf7" x="2265" y="1710" />
 		<entity schema="qiita" name="processing_job_workflow_root" color="b2cdf7" x="2250" y="1590" />
 		<entity schema="qiita" name="processing_job" color="b2cdf7" x="1995" y="1350" />
-		<entity schema="qiita" name="job" color="d0def5" x="405" y="1155" />
 		<entity schema="qiita" name="prep_template_processing_job" color="b2cdf7" x="1740" y="960" />
 		<entity schema="qiita" name="software_artifact_type" color="b2cdf7" x="2040" y="945" />
 		<entity schema="qiita" name="software_type" color="b2cdf7" x="2625" y="930" />
 		<entity schema="qiita" name="software" color="b2cdf7" x="2400" y="930" />
 		<entity schema="qiita" name="software_command" color="b2cdf7" x="2175" y="1215" />
+		<entity schema="qiita" name="job" color="d0def5" x="405" y="1155" />
 		<group name="Group_analyses" color="c4e0f9" >
 			<comment>analysis tables</comment>
 			<entity schema="qiita" name="analysis" />