Scripts to update metadata to the latest model.

Be sure to backup databases before executing.
2026-09-21 05:45:37 +08:00 · 2007-08-22 20:04:40 +00:00
parent 3f0579c7a4
commit b873d64859
2 changed files with 94 additions and 0 deletions
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+#!/usr/bin/env python2.4
+#Dan Blankenberg
+"""
+Updates metadata in the database to match rev 1891.
+
+Remember to backup your database before running.
+"""
+
+import sys, os, ConfigParser
+import galaxy.app
+from galaxy.util.bunch import Bunch
+import galaxy.datatypes.tabular
+
+
+def main():
+    ini_file = sys.argv.pop(1)
+    conf_parser = ConfigParser.ConfigParser({'here':os.getcwd()})
+    conf_parser.read(ini_file)
+    configuration = {}
+    for key, value in conf_parser.items("app:main"): configuration[key] = value
+    app = galaxy.app.UniverseApplication( global_conf = ini_file, **configuration )
+    
+    # Step through Database, turning metadata bunches into dictionaries.
+    print "Changing metadata bunches to dictionaries."
+    for row in app.model.Dataset.table.select().execute():
+        if isinstance (row.metadata, Bunch):
+            print row.id
+            app.model.Dataset.table.update(app.model.Dataset.table.c.id == row.id).execute( _metadata = row.metadata.__dict__ )
+    
+    print "Rewriting all metadata to database, setting metadata dbkey, to ensure JSONified storage."
+    #Make sure all metadata is jsonified
+    for row in app.model.Dataset.table.select().execute():
+        print row.id
+        data = app.model.Dataset.get(row.id)
+        dbkey = data.old_dbkey
+        if not dbkey or data.metadata.dbkey not in ["?", ["?"], None, []]:
+            dbkey = data.metadata.dbkey
+        if not dbkey: dbkey = "?"
+        #change dbkey then flush, then change to real value and flush, ensures that metadata is rewritten to database
+        data.dbkey="~"
+        data.flush()
+        data.dbkey=dbkey
+        data.flush()
+    
+    print "Seeking out tabular based files and setting number of columns."
+    #Search out tabular datatypes and make sure that number of columns is set.
+    for row in app.model.Dataset.table.select().execute():
+        data = app.model.Dataset.get(row.id)
+        if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('tabular'))):
+            print row.id
+            galaxy.datatypes.tabular.Tabular().set_meta( data ) #Call tabular set metadata method for all Classes, this will set number of columns.
+            data.flush()
+    
+    app.shutdown()
+    sys.exit(0)
+
+if __name__ == "__main__":
+    main()
@@ -0,0 +1,36 @@
+#!/bin/sh
+
+## Set MACHTYPE to something, 
+MACHTYPE=`uname -m`
+[ "$MACHTYPE" = "Power Macintosh" ] && MACHTYPE="powerpc"
+LC_ALL=POSIX
+export MACHTYPE LC_ALL
+
+KERNEL=`uname -s | tr "A-Z" "a-z"`
+ARCH="$KERNEL-$MACHTYPE"
+
+echo "Architecture appears to be $ARCH"
+
+UNIVERSE_HOME=`pwd`
+PYTHONPATH=$UNIVERSE_HOME/lib:$UNIVERSE_HOME/eggs
+export UNIVERSE_HOME PYTHONPATH
+
+## For PBS - if you need to force node paths (i.e. the arch the frontend
+## runs on is not the same arch as the compute nodes or Galaxy is
+## installed in a different path on the node).
+#NODEMACH="i686"
+#NODEARCH="linux-i686"
+#NODEPATH=$PATH
+
+## Certain tools (EMBOSS, PAML...) are not distributed with Galaxy.
+## If you have them installed, add their bin directories to the PATH.
+PATH=$PATH:/depot/apps/$MACHTYPE/bin:/home/universe/$ARCH/EMBOSS/bin:/home/universe/$ARCH/ImageMagick/bin:/home/universe/$ARCH/PAML/paml3.15/bin
+
+## NODEPATH defaults to $PATH
+: ${NODEPATH:=$PATH}
+
+export PATH NODEPATH
+
+echo "python path: $PYTHONPATH"
+
+python2.4 ./scripts/update_metadata.py universe_wsgi.ini $@