downstream references to iquod.db

Author: bkatiemills

filter-db.py

@@ -1,10 +1,10 @@
-# usage: python filter-db.py <full table name> <filtered table name> <number of good / bad profiles to pick>
+# usage: python filter-db.py <full table name> <filtered table name> <number of good / bad profiles to pick> <db filename>
 
 import sys, sqlite3
 
-if len(sys.argv) == 4:
+if len(sys.argv) == 5:
 
-    conn = sqlite3.connect('iquod.db', isolation_level=None)
+    conn = sqlite3.connect(sys.argv[4], isolation_level=None)
     cur = conn.cursor()
 
     query = "DROP TABLE IF EXISTS " + sys.argv[2]

plot-roc.py

@@ -78,13 +78,13 @@ def plotRow(row):
     pylab.savefig(dir + str(p.uid()) + '.png', bbox_inches='tight')
     plt.close()
 
-def plot_roc():
+def plot_roc(inputdb='iquod.db'):
 
     # get qc tests
     testNames = main.importQC('qctests')
 
     # connect to database
-    conn = sqlite3.connect('iquod.db', isolation_level=None)
+    conn = sqlite3.connect(inputdb, isolation_level=None)
     cur = conn.cursor()
 
     # extract matrix of test results and true flags into a dataframe

util/dbutils.py

@@ -83,10 +83,11 @@ def unpack_qc_results(results):
 def db_to_df(table,
              filter_on_wire_break_test=False, 
              filter_on_tests={},
-             n_to_extract=numpy.iinfo(numpy.int32).max):
+             n_to_extract=numpy.iinfo(numpy.int32).max,
+             inputdb='iquod.db'):
 
     '''
-    Reads the table from iquod.db into a pandas dataframe.
+    Reads the table from inputdb into a pandas dataframe.
     If filter_on_wire_break_test is True, the results from that test are used to exclude
          levels below a wire break from the test results and the wire break test is not returned.
     filter_on_tests is a generalised form of filter_on_wire_break and is used to exclude results; it takes a list of
@@ -99,7 +100,7 @@ def db_to_df(table,
     testNames.sort()
 
     # connect to database
-    conn = sqlite3.connect('iquod.db', isolation_level=None)
+    conn = sqlite3.connect(inputdb, isolation_level=None)
     cur = conn.cursor()
 
     # extract matrix of test results and true flags into a dataframe

util/main.py

@@ -167,15 +167,15 @@ def dictify(rows, keys):
 
   return dicts
 
-def dbinteract(command, values=[], tries=0):
+def dbinteract(command, values=[], tries=0, inputdb='iquod.db'):
   '''
   execute the given SQL command;
   catch errors and retry a maximum number of times;
   '''
 
   max_retry = 100
 
-  conn = sqlite3.connect('iquod.db', isolation_level=None, timeout=60)
+  conn = sqlite3.connect(inputdb, isolation_level=None, timeout=60)
   cur = conn.cursor()
 
   try:
@@ -201,13 +201,13 @@ def dbinteract(command, values=[], tries=0):
       print('database interaction failed after', max_retry, 'retries')
       return -1  
 
-def interact_many(query, values, tries=0):
+def interact_many(query, values, tries=0, inputdb='iquod.db'):
   # similar to dbinteract, but does executemany
   # intended exclusively for writes
 
   max_retry = 100
 
-  conn = sqlite3.connect('iquod.db', isolation_level=None, timeout=60)
+  conn = sqlite3.connect(inputdb, isolation_level=None, timeout=60)
   cur = conn.cursor()
 
   try: