fix 55.py (#2168)

* fix 55.py

* fixing small bug in test env

* addressing @ElDeveloper comments

* config_test.cfg

* rm /test_data/ from folders

* fixing

* releases

* working_dir/releases

* working_dir/

Author: antgonza

qiita_core/support_files/config_test.cfg

@@ -26,10 +26,10 @@ REQUIRE_APPROVAL = True
 BASE_URL = https://localhost:21174
 
 # Download path files
-UPLOAD_DATA_DIR = /tmp/
+UPLOAD_DATA_DIR = /home/travis/miniconda3/envs/qiita/lib/python2.7/site-packages/qiita_db/support_files/test_data/uploads/
 
 # Working directory path
-WORKING_DIR = /tmp/
+WORKING_DIR = /home/travis/miniconda3/envs/qiita/lib/python2.7/site-packages/qiita_db/support_files/test_data/working_dir/
 
 # Maximum upload size (in Gb)
 MAX_UPLOAD_SIZE = 100

qiita_db/artifact.py

@@ -11,14 +11,16 @@
 from itertools import chain
 from datetime import datetime
 from os import remove, makedirs
-from os.path import isfile, exists
+from os.path import isfile, exists, relpath
 from shutil import rmtree
 from functools import partial
 
 import networkx as nx
 
 import qiita_db as qdb
 
+from qiita_core.qiita_settings import qiita_config
+
 
 class Artifact(qdb.base.QiitaObject):
     r"""Any kind of file (or group of files) stored in the system and its
@@ -154,11 +156,17 @@ def create_type(name, description, can_be_submitted_to_ebi,
             qdb.sql_connection.TRN.add(sql, sql_args, many=True)
 
             # When creating a type is expected that a new mountpoint is created
-            # for that type
+            # for that type, note that we are going to check if there is an
+            # extra path for the mountpoint, which is useful for the test
+            # environment
+            qc = qiita_config
+            mp = relpath(qc.working_dir, qc.base_data_dir).replace(
+                'working_dir', '')
+            mp = mp + name if mp != '/' and mp != '' else name
             sql = """INSERT INTO qiita.data_directory
                         (data_type, mountpoint, subdirectory, active)
                         VALUES (%s, %s, %s, %s)"""
-            qdb.sql_connection.TRN.add(sql, [name, name, True, True])
+            qdb.sql_connection.TRN.add(sql, [name, mp, True, True])
 
             # We are intersted in the dirpath
             dp = qdb.util.get_mountpoint(name)[0][1]

qiita_db/support_files/patches/55.sql

@@ -1,21 +1,4 @@
 -- Jul 6, 2017
 -- DELETE all sample/prep CONSTRAINTs
 
--- Step 1, remove all FK constraints from study_sample
-CREATE OR REPLACE FUNCTION qiita.delete_study_sample_constraints(cname text, tname text) RETURNS void AS $$
-    BEGIN
-      EXECUTE 'ALTER TABLE ' || tname || ' DROP CONSTRAINT ' || cname;
-    END;
-$$ LANGUAGE plpgsql;
-
-WITH query AS (
-  SELECT constraint_name AS cname, 'qiita.' || table_name AS tname
-    FROM information_schema.table_constraints
-    WHERE constraint_type ='FOREIGN KEY' AND (
-        (constraint_name LIKE 'fk_sample_%' AND table_name LIKE 'sample_%') OR
-        (constraint_name LIKE 'fk_prep_%' AND table_name LIKE 'prep_%')) AND
-        table_name NOT IN ('prep_template', 'prep_template_sample',
-                           'prep_template_filepath', 'prep_template_processing_job'))
-SELECT qiita.delete_study_sample_constraints(cname, tname) FROM query;
-
-DROP FUNCTION qiita.delete_study_sample_constraints(cname text, tname text);
+SELECT 42;

qiita_db/support_files/patches/python_patches/55.py

@@ -0,0 +1,21 @@
+from qiita_db.sql_connection import TRN
+
+sql = """
+    SELECT constraint_name AS cname, 'qiita.' || table_name AS tname
+    FROM information_schema.table_constraints
+    WHERE constraint_type ='FOREIGN KEY' AND (
+        (constraint_name LIKE 'fk_sample_%' AND table_name LIKE 'sample_%') OR
+        (constraint_name LIKE 'fk_prep_%' AND table_name LIKE 'prep_%')) AND
+        table_name NOT IN (
+            'prep_template', 'prep_template_sample', 'prep_template_filepath',
+            'prep_template_processing_job')"""
+
+with TRN:
+    TRN.add(sql)
+    to_delete = TRN.execute_fetchindex()
+
+for cname, tname in to_delete:
+    with TRN:
+        sql = "ALTER TABLE %s DROP CONSTRAINT %s" % (tname, cname)
+        TRN.add(sql)
+        TRN.execute()