Rename all the scripts to start with htsw-

[htsworkflow.git] / scripts / mark_archived_data

diff --git a/scripts/mark_archived_data b/scripts/mark_archived_data
deleted file mode 100755 (executable)
index 288ec1a..0000000
--- a/scripts/mark_archived_data
+++ /dev/null
@@ -1,123 +0,0 @@
-#!/usr/bin/env python
-
-from htsworkflow.util.hdquery import get_hd_serial_num
-from htsworkflow.frontend import settings
-
-from optparse import OptionParser
-import os
-import re
-import sys
-import urllib2
-import urlparse
-
-runfolder_pattern = re.compile(r'[0-9]{6}_[-A-Za-z\d]+_\d+_(?P<flowcell>[A-Z\d]+)\.tgz')
-
-def extract_flowcell(runfolder_name):
-    path, basename = os.path.split(runfolder_name)
-    match = runfolder_pattern.match(basename)
-    if match is not None:
-        return match.group('flowcell')
-    else:
-        return None
-    
-def construct_parser():
-    """
-    """
-    msg = "usage: %prog [-d </dev/sdX> | -s <serial_number] [-f <flowcell>] [archived dirs]"
-    parser = OptionParser()
-    parser.add_option('-u', '--url', default=None,
-                      help="Alternate url for marking archived flowcells")
-    parser.add_option("-f", "--flowcell",  type="string", help="flowcell being archived")
-    parser.add_option("-d", "--device", type="string",
-                      help="device flowcell is being archived to")
-    parser.add_option("-s", "--serial", type="string", help="serial num. of archive device")
-    parser.add_option("-v", "--verbose", action="store_true", default=False)
-    
-    return parser
-
-
-def update_db(root_url, flowcells, serial, debug=False):
-    """
-    Creates link between flowcell and storage device over http
-    """
-    for fc in flowcells:
-        url = urlparse.urljoin(root_url, '%s/%s/' % (fc, serial))
-        
-        req = urllib2.Request(url)
-        try:
-            response = urllib2.urlopen(req)
-        except urllib2.URLError, e:
-            print 'ERROR - HTTP OUTPUT (Return Code: %s); use -v/--verbose for more details.' % (e.code)
-            if debug:
-                print e.read()
-            sys.exit(e.code)
-        
-        print "DB Update of %s & %s succeeded" % (fc, serial)
-        print response.read()
-    
-
-def process_args(parser):
-    """
-    returns flowcell and serial#
-    """
-    options, args = parser.parse_args()
-    
-    msg = []
-    
-    # Only provide device or serial
-    if options.device is not None and options.serial is not None:
-        parser.error("Please provide only --device or --serial.\n"\
-                     "The serial number is extracted automatically if the"\
-                     "device is provided.")
-
-    # allow user to override the default destination URL
-    if options.url is not None:
-        root_url = options.url
-    else:
-        root_url = settings.LINK_FLOWCELL_STORAGE_DEVICE_URL
-
-    # if device and serial missing:
-    if options.device is None and options.serial is None:
-        parser.error('One of --device or --serial is required')
-
-    flowcells = []
-    
-    # sanitize args    
-    for runfolder in args:
-        flowcell_id = extract_flowcell(runfolder)
-        if flowcell_id is None:
-            parser.error('archive names must look like YYMMDD_MACHINE_RUN_FLOWCELLID.tgz\n'\
-                         '(got %s)' % (runfolder,))
-        else:
-            flowcells.append(flowcell_id)
-            
-    if options.flowcell is not None:
-        flowcells.append(options.flowcell)
-        
-    if len(flowcells) == 0:
-        parser.error('please specify a  --flowcell or list of runfolder archives\n'\
-                     'for archival. I need something to do.')
-
-    # Update db records
-    if options.device is not None:
-        serial = get_hd_serial_num(options.device)
-        update_db(root_url, flowcells, serial=serial, debug=options.verbose)
-    elif options.serial is not None:
-        update_db(root_url, flowcells, serial=options.serial, debug=options.verbose)
-    else:
-        msg ="FATAL should not happen error occured; i.e. the best kind!"
-        raise ValueError, msg
-    
-    
-
-def main():
-    """
-    """
-    parser = construct_parser()
-    process_args(parser)
-    
-    #print "Database Updated."
-    sys.exit(0)
-
-if __name__ == '__main__':
-    main()