diff util/add_datatype.py @ 0:0bca8a6364a7 draft default tip

planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/add_datatype.py	Wed Dec 21 17:21:18 2016 -0500
@@ -0,0 +1,74 @@
+#!/usr/bin/python
+
+"""
+This script copy the huba datatype into your galaxy:
+    - Add under <registration>, the datatype_conf
+    - Add huba.xml under display_application/ucsc/
+    - Add hubAssembly.py inside lib/galaxy/datatypes
+Place yourself in the folder of the python script, and launch it
+- Based on the fact datatypes_conf
+"""
+
+import argparse
+import os
+import shutil
+import sys
+import xml.etree.ElementTree as ET
+
+
+def main(argv):
+    # Command Line parsing init
+    parser = argparse.ArgumentParser(description='Create a foo.txt inside the given folder.')
+
+    parser.add_argument('-g', '--galaxy_root', help='Galaxy root folder', required=True)
+
+    # Get the args passed in parameter
+    args = parser.parse_args()
+
+    galaxy_root_path = args.galaxy_root
+
+    add_datatype_conf(galaxy_root_path)
+    add_huba_xml(galaxy_root_path)
+    add_hubAssembly(galaxy_root_path)
+
+
+def add_datatype_conf(galaxy_root_path):
+    print "======= Add datatype ======="
+    datatype_conf_path = os.path.join(galaxy_root_path, 'config/datatypes_conf.xml')
+    # TODO: Not relative to this python file but based on a parameter galaxy_root
+    # TODO: Check if datatypes_conf.xml, if not create it by copying datatypes_conf.xml.sample
+    # TODO: For debug only
+    # tree = ET.parse('../test-data/add_datatype/datatypes_conf.xml.sample')
+    # TODO: UnComment for prod
+    tree = ET.parse(datatype_conf_path)
+    root = tree.getroot()
+    print root.tag
+    registration = root[0]
+    print registration.attrib
+
+    huba_datatype = ET.parse('../trackHub/datatypes_conf.xml').getroot()
+    # TODO: Verify the datatype is not already existing, else do not add / write. And in another version, check it
+    registration.append(huba_datatype)
+    tree.write(datatype_conf_path)
+    print "datatype added in %s" % datatype_conf_path
+    return
+
+
+def add_huba_xml(galaxy_root_path):
+    print "======= Add hub xml ======="
+    displayApp_ucsc_path = os.path.join(galaxy_root_path, "display_applications/ucsc/")
+    shutil.copy("../trackHub/huba.xml", displayApp_ucsc_path)
+    print "Content of %s now: %s" % (displayApp_ucsc_path, os.listdir(displayApp_ucsc_path))
+    return
+
+
+def add_hubAssembly(galaxy_root_path):
+    print "======= Add hubAssembly ======="
+    datatype_lib_path = os.path.join(galaxy_root_path, "lib/galaxy/datatypes/")
+    shutil.copy("../trackHub/hubAssembly.py", datatype_lib_path)
+    print "Content of %s now: %s" % (datatype_lib_path, os.listdir(datatype_lib_path))
+    return
+
+
+if __name__ == "__main__":
+    main(sys.argv)