Adding patches

Author: josenavas

qiita_db/support_files/patches/25.sql

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+-- May 19, 2015
+
+SELECT 42;

qiita_db/support_files/patches/python_patches/25.py

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+# May 19, 2015
+# We attach the prep template directly to the study. The raw data is no longer
+# attached to the study directly, the prep template point to them. This will
+# make the RawData to be effectively just a container for the raw files,
+# which is how it was acting previously.
+
+from qiita_db.sql_connection import SQLConnectionHandler
+from qiita_db.data import RawData
+from qiita_db.util import move_filepaths_to_upload_folder
+
+conn_handler = SQLConnectionHandler()
+queue = "PATCH_25"
+conn_handler.create_queue(queue)
+
+# the system may contain raw data with no prep template associated to it.
+# Retrieve all those raw data ids
+sql = """SELECT raw_data_id
+         FROM qiita.raw_data
+         WHERE raw_data_id NOT IN (
+            SELECT DISTINCT raw_data_id FROM qiita.prep_template);"""
+rd_ids = [x[0] for x in conn_handler.execute_fetchall(sql)]
+
+# We will delete those RawData. However, if they have files attached, we should
+# move them to the uploads folder of the study
+sql_detach = """DELETE FROM qiita.study_raw_data
+                WHERE raw_data_id = %s AND study_id = %s"""
+sql_unlink = "DELETE FROM qiita.raw_filepath WHERE raw_data_id = %s"
+sql_delete = "DELETE FROM qiita.raw_data WHERE raw_data_id = %s"
+move_files = []
+for rd_id in rd_ids:
+    rd = RawData(rd_id)
+    filepaths = rd.get_filepaths()
+    studies = sorted(rd.studies)
+    if filepaths:
+        # we need to move the files to a study. We chose the one with lower
+        # study id. Currently there is no case in the live database in which a
+        # RawData with no prep templates is attached to more than one study,
+        # but I think it is better to normalize this just in case
+        move_files.append((min(studies), filepaths))
+
+    # To delete the RawData we first need to unlink all the files
+    conn_handler.add_to_queue(queue, sql_unlink, (rd_id,))
+
+    # Then, remove the raw data from all the studies
+    for st_id in studies:
+        conn_handler.add_to_queue(queue, sql_detach, (rd_id, st_id))
+
+    conn_handler.add_to_queue(queue, sql_delete, (rd_id,))
+
+# We can now perform all changes in the DB. Although this changes can be
+# done in an SQL patch, they are done here because we need to execute the
+# previous clean up in the database before we can actually execute the SQL
+# patch.
+sql = """CREATE TABLE qiita.study_prep_template (
+    study_id             bigint  NOT NULL,
+    prep_template_id     bigint  NOT NULL,
+    CONSTRAINT idx_study_prep_template
+        PRIMARY KEY ( study_id, prep_template_id )
+ );
+
+CREATE INDEX idx_study_prep_template_0
+    ON qiita.study_prep_template ( study_id );
+
+CREATE INDEX idx_study_prep_template_1
+    ON qiita.study_prep_template ( prep_template_id );
+
+COMMENT ON TABLE qiita.study_prep_template IS
+    'links study to its prep templates';
+
+ALTER TABLE qiita.study_prep_template
+    ADD CONSTRAINT fk_study_prep_template_study
+    FOREIGN KEY ( study_id ) REFERENCES qiita.study( study_id );
+
+ALTER TABLE qiita.study_prep_template
+    ADD CONSTRAINT fk_study_prep_template_pt
+    FOREIGN KEY ( prep_template_id )
+    REFERENCES qiita.prep_template( prep_template_id );
+
+-- Connect the existing prep templates in the system with their studies
+DO $do$
+DECLARE
+    vals RECORD;
+BEGIN
+FOR vals IN
+    SELECT prep_template_id, study_id
+    FROM qiita.prep_template
+    JOIN qiita.study_raw_data USING (raw_data_id)
+LOOP
+    INSERT INTO qiita.study_prep_template (study_id, prep_template_id)
+    VALUES (vals.study_id, vals.prep_template_id);
+END LOOP;
+END $do$;
+
+--- Drop the study_raw__data table as it's not longer used
+DROP TABLE qiita.study_raw_data;
+"""
+conn_handler.add_to_queue(queue, sql)
+conn_handler.execute_queue(queue)
+
+# After the changes in the database have been performed, move the files
+# to the uploads folder
+errors = []
+for st_id, fps in move_files:
+    try:
+        move_filepaths_to_upload_folder(st_id, fps)
+    except Exception, e:
+        # An error here is unlikely. However, it's possible and there is no
+        # clean way that we can unroll all the previous changes in the DB.
+        errors.append((st_id, fps, str(e)))
+
+# Show the user any error that could have been generated during the files
+# movement
+if errors:
+    print ("The following errors where generated when trying to move files "
+           "to the upload folder")
+    for st_id, fps, e in errors:
+        print "Study: %d, Filepaths: %s, Error: %s" % (st_id, fps, e)