split the library script into a reusable database/reporting layer

[htsworkflow.git] / scripts / library.py

diff --git a/scripts/library.py b/scripts/library.py
index 6263c9ae0916e28a5047b7c192a78586014aa353..eeeed90e3f47e9f7b2fedafcfaef20a0a5d4f77d 100644 (file)
--- a/scripts/library.py
+++ b/scripts/library.py
@@ -1,97 +1,22 @@
-import datetime
+"""
+Provide some quick and dirty access and reporting for the fctracker database.
+
+The advantage to this code is that it doesn't depend on django being
+installed, so it can run on machines other than the webserver.
+"""
 from optparse import OptionParser
-from pprint import pprint
-import sqlite3
 import sys
-import time
-
-class fctracker:
-    def __init__(self):
-        self.conn = sqlite3.connect('fctracker.db')
-        self._get_library()
-        self._get_species()
-
-    def _make_dict_from_table(self, table_name, pkey_name):
-        table = {}
-        c = self.conn.cursor()
-        c.execute('select * from %s;' % (table_name))
-        # extract just the field name
-        description = [ f[0] for f in c.description]
-        for row in c:
-            row_dict = dict(zip(description, row))
-            table[row_dict[pkey_name]] = row_dict
-        c.close()
-        return table
-
-    def _get_library(self):
-        self.library = self._make_dict_from_table(
-                         'fctracker_library', 
-                         'library_id')
-                                                  
-        
-    def _get_species(self):
-        self.species = self._make_dict_from_table(
-                         'fctracker_species',
-                         'id'
-                       )
-        
-    def _get_flowcells(self, where=None):
-        if where is None:
-            where = ""
-        self.flowcells = {}
-        c = self.conn.cursor()
-        c.execute('select * from fctracker_flowcell %s;' % (where))
-        # extract just the field name
-        description = [ f[0] for f in c.description ]
-        for row in c:
-            row_dict = dict(zip(description, row))
-            for lane in [ 'lane_%d_library' % (i) for i in range(1,9) ]:
-                lane_library = self.library[row_dict[lane+"_id"]]
-                species_id = lane_library['library_species_id']
-                lane_library['library_species'] = self.species[species_id]
-                row_dict[lane] = lane_library
-            # some useful parsing
-            run_date = time.strptime(row_dict['run_date'],  '%Y-%m-%d %H:%M:%S')
-            run_date = datetime.datetime(*run_date[:6])
-            row_dict['run_date'] = run_date
-            self.flowcells[row_dict['flowcell_id']] = row_dict
-        return self.flowcells
 
-
-def flowcell_gone(name):
-    if 'failed' in name:
-        return True
-    if 'deleted' in name:
-        return True
-    if 'not run' in name:
-        return True
-    return False
-
-def report(flowcells):
-    flowcell_list = []
-    for key, cell in flowcells.items():
-        flowcell_list.append( (cell['run_date'], key) )
-    flowcell_list.sort()
-    for run_date, flowcell_id in flowcell_list:
-        cell = flowcells[flowcell_id]
-        if flowcell_gone(cell['flowcell_id']):
-            continue
-        #pprint(cell)
-        #print cell['flowcell_id'], cell['run_date']
-        for l in range(1,9):
-            lane = 'lane_%d' % (l)
-            print cell['run_date'].strftime('%y-%b-%d'),
-            print cell['flowcell_id'],
-            #print "  ",
-            print l,cell['%s_library'%(lane)]['library_name'],
-            print '(%s)' % (cell['%s_library_id'%(lane)]),
-            print cell['%s_library'%(lane)]['library_species']['scientific_name']
+from gaworkflow.util import fctracker
 
 def make_parser():
     """
     Make parser
     """
     parser = OptionParser()
+    parser.add_option("-d", "--database", dest="database",
+                      help="path to the fctracker.db",
+                      default=None)
     parser.add_option("-w", "--where", dest="where",
                       help="add a where clause",
                       default=None)
@@ -104,10 +29,10 @@ def main(argv=None):
 
     opt, args = parser.parse_args(argv)
     
-    fc = fctracker()
+    fc = fctracker.fctracker(opt.database)
     cells = fc._get_flowcells(opt.where)
 
-    report(cells)
+    print fctracker.recoverable_drive_report(cells)
     return 0
 
 if __name__ == "__main__":