Merge branch 'fix-analysis-tests' into fix-qiita-ware-tests

Author: josenavas

qiita_db/analysis.py

@@ -29,11 +29,11 @@
 from qiita_core.exceptions import IncompetentQiitaDeveloperError
 from .sql_connection import SQLConnectionHandler
 from .base import QiitaStatusObject
-from .data import ProcessedData, RawData
+from .data import ProcessedData
 from .study import Study
 from .exceptions import QiitaDBStatusError, QiitaDBError
 from .util import (convert_to_id, get_work_base_dir,
-                   get_mountpoint, get_table_cols, insert_filepaths)
+                   get_mountpoint, insert_filepaths)
 
 
 class Analysis(QiitaStatusObject):

qiita_db/support_files/patches/23.sql

@@ -49,11 +49,10 @@ LOOP
 
     -- Copy the values from the required_sample_info table to the dynamic table
     EXECUTE '
-        WITH sample_values AS (SELECT *
-                               FROM qiita.required_sample_info
-                               JOIN qiita.required_sample_info_status
-                                    USING (required_sample_info_status_id)
-                               WHERE study_id = ' || st_id || ')
+        WITH sv AS (SELECT * FROM qiita.required_sample_info
+                    JOIN qiita.required_sample_info_status
+                        USING (required_sample_info_status_id)
+                    WHERE study_id = ' || st_id || ')
         UPDATE ' || dyn_table || '
             SET physical_specimen_location=sv.physical_location,
                 physical_specimen_remaining=sv.has_physical_specimen,
@@ -65,7 +64,7 @@ LOOP
                 latitude=sv.latitude,
                 longitude=sv.longitude,
                 required_sample_info_status=sv.status
-            FROM sample_values sv
+            FROM sv
             WHERE ' || dyn_table || '.sample_id = sv.sample_id;';
 
 END LOOP;
@@ -125,15 +124,14 @@ LOOP
 
     -- Copy the values from the common_prep_info table to the dynamic table
     EXECUTE '
-        WITH sample_values AS (SELECT *
-                               FROM qiita.common_prep_info
-                                    JOIN qiita.emp_status USING (emp_status_id)
-                               WHERE prep_template_id = ' || prep_id || ')
+        WITH sv AS (SELECT * FROM qiita.common_prep_info
+                        JOIN qiita.emp_status USING (emp_status_id)
+                    WHERE prep_template_id = ' || prep_id || ')
         UPDATE ' || dyn_table || '
             SET center_name=sv.center_name,
                 center_project_name=sv.center_project_name,
                 emp_status=sv.emp_status
-            FROM sample_values sv
+            FROM sv
             WHERE ' || dyn_table || '.sample_id=sv.sample_id;';
 
 END LOOP;

qiita_db/support_files/patches/python_patches/23.py

@@ -2,6 +2,7 @@
 # Need to re-generate the files, given that some headers have changed
 
 from qiita_db.sql_connection import SQLConnectionHandler
+from qiita_db.metadata_template import SampleTemplate, PrepTemplate
 
 conn_handler = SQLConnectionHandler()