changeset 6:8d405ac8a837 draft

Deleted selected files

--- a/galaxy-tools/biobank/updater/update_titerplates.py	Thu Sep 22 09:29:21 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-'''
-From a file like this
-label         barcode    container_status  rows  columns
-A_TITERPLATE  XXYYZZ111  INSTOCK           8     12
-B_TITERPLATE  XXYYZZ112  INSTOCK           8     12
-C_TITERPLATE  XXYYZZ113  READY             8     12
-
-updates barcode, status and geography of given titerplates
-'''
-import sys, csv, argparse
-
-from bl.vl.kb import KnowledgeBase as KB
-import bl.vl.utils.ome_utils as vlu
-from bl.vl.utils import get_logger, LOG_LEVELS
-from bl.vl.kb.drivers.omero.objects_collections import ContainerStatus
-
-
-def make_parser():
-    parser = argparse.ArgumentParser(description='update titerplates')
-    parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
-    parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
-                        help='logging level (default=INFO)', default='INFO')
-    parser.add_argument('-H', '--host', type=str, help='omero hostname')
-    parser.add_argument('-U', '--user', type=str, help='omero user')
-    parser.add_argument('-P', '--passwd', type=str, help='omero password')
-    parser.add_argument('-O', '--operator', type=str, help='operator',
-                        required=True)
-    parser.add_argument('-i', '--in_file', type=str, required=True,
-                        help='input file with information to update')
-    parser.add_argument('--overwrite', dest='overwrite', action='store_true', 
-                        help='enable overwrite of data. Default is disabled ')
-    parser.set_defaults(overwrite=False)
-    return parser
-
-
-def update_titerplates(titerplate, barcode, container_status, rows, columns,
-                       overwrite, logger):
-    logger.info("Updating {}".format(titerplate.label))
-    r = False
-    if overwrite:
-        if barcode is not None:
-            titerplate.barcode = barcode
-        if container_status is not None:
-            titerplate.status = getattr(ContainerStatus, container_status)
-        if rows is not None:
-            titerplate.rows = rows
-        if columns is not None:
-            titerplate.columns = columns
-        r = True
-    else:
-        if titerplate.barcode is None and barcode is not None:
-            titerplate.barcode = barcode
-            r = True
-        if titerplate.status is None and container_status is not None:
-            titerplate.status = getattr(ContainerStatus, container_status)
-            r = True
-        if titerplate.rows is None and rows is not None:
-            titerplate.rows = rows
-            r = True
-        if titerplate.columns is None and columns is not None:
-            titerplate.columns = columns
-            r = True
-
-    if r:
-        return titerplate
-    else:
-        logger.info('Update denied for titerplate {}'.format(
-            titerplate.label))
-        return None
-
-
-def main(argv):
-    parser = make_parser()
-    args = parser.parse_args(argv)
-
-    logger = get_logger('update_titerplates', level=args.loglevel,
-                        filename=args.logfile)
-
-    try:
-        host = args.host or vlu.ome_host()
-        user = args.user or vlu.ome_user()
-        passwd = args.passwd or vlu.ome_passwd()
-    except ValueError, ve:
-        logger.critical(ve)
-        sys.exit(ve)
-
-    kb = KB(driver='omero')(host, user, passwd)
-
-    with open(args.in_file) as in_file:
-        to_be_updated = []
-        reader = csv.DictReader(in_file, delimiter='\t')
-        barcode = None
-        container_status = None
-        rows = None
-        columns = None
-        if 'label' in reader.fieldnames:
-            for row in reader:
-                tp_label = row['label']
-                tp = kb.get_by_label(kb.TiterPlate, tp_label)
-                if tp != None:
-                    if 'barcode' in reader.fieldnames:
-                        barcode = row['barcode']
-                    if 'container_status' in reader.fieldnames:
-                        container_status = row['container_status']
-                    if 'rows' in reader.fieldnames:
-                        rows = row['rows']
-                    if 'columns' in reader.fieldnames:
-                        columns = row['columns']
-
-                    tp_up = update_titerplates(tp, barcode,
-                                               container_status,rows,
-                                               columns, args.overwrite,
-                                               logger)
-                    if tp_up:
-                        to_be_updated.append(tp_up)            
-        else:
-            msg = 'Missing required field "label"'
-            logger.critical(msg)
-            sys.exit(msg)
-                
-    logger.info('%d titerplates are going to be updated' % len(to_be_updated))
-    kb.save_array(to_be_updated)
-    logger.info('Update complete')
-
-if __name__ == '__main__':
-    main(sys.argv[1:])

--- a/galaxy-tools/biobank/updater/update_titerplates.xml	Thu Sep 22 09:29:21 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-<tool id="vl_tools_update_titerplates_data" name="VLU.update_titerplates_data">
-  <description>
-    Update titerplates infodata
-  </description>
-  <command interpreter="python">
-    #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #update_titerplates.py
-    #else #unauthorized_access.py
-    #end if    
-    #if $advanced_configuration.configuration_level == 'advanced'
-      --host=${advanced_configuration.vl_host}
-      --user=${advanced_configuration.vl_user}
-      --passwd=${advanced_configuration.vl_passwd}
-    #end if
-    --in_file=${input1}
-    --operator=$__user_email__
-    --loglevel=$__app__.config.vl_loglevel
-    --logfile=${logfile}
-  </command>  
-  <inputs>   
-    <param format="tabular" name="input1" type="data"
-           label="A tabular dataset. See below."/>
-    <!-- ************************************************** -->
-    <conditional name="advanced_configuration">
-      <param name="configuration_level" type="select" 
-	     label="Configuration level">
-	<option value="default" selected="true">Default configuration</option>	
-	<option value="advanced">Advanced configuration</option>
-      </param>
-      <when value="default"/>
-      <when value="advanced">
-	<param name="vl_host" size="40" type="text" value="biobankxx.crs4.it"
-	       label="Omero/VL host"/>
-	<param name="vl_user" size="20" type="text" value="user"
-	       label="Omero/VL user"/>
-	<param name="vl_passwd" size="20" type="text" value="What?Me worry?" 
-	       label="Omero/VL passwd"/>
-      </when>
-    </conditional>
-  </inputs>
-
-  <outputs>
-    <data format="txt" name="logfile"     label="${tool.name}.logfile"/>
-  </outputs>
-<help>
-
-It will update titerplates data using informations from a file like this::
-
-    label	barcode	        container_status    rows    columns
-    A_TP	55555555	DISCARDED	    8       12
-    B_TP	66666666	DISCARDED	    8       12
-
-
-The first column is mandatory, the others only for the information that you want to update.
-
-For example, if you want to update a barcode data only that column is required
-  
-
-  </help>
-
-</tool>