def _test_NrgCingRdb(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
host = 'localhost'
if 1: # DEFAULT False
host = '143.210.218.192'
schema=RECOORD_DB_SCHEMA #@UnusedVariable
schema=NRG_DB_NAME
m = NrgCingRdb(host=host, schema=schema)
# self.assertFalse( m.showCounts())
# self.assertFalse( m.createScatterPlots())
self.assertFalse(m.createPlotsCompareBetweenDb(other_schema=NMR_REDO_DB_SCHEMA))
if False:
a = m.getPdbIdList()
nTdebug("pdbIdList length: %d %s" % (len(a), a))
self.assertTrue(a)
if 0 and a: # DEFAULT 0 watch out!
lToRemove = \
'1sae 1sah 1saj 1sak 1sal 1y0j 2k0a 2kiu 2ku2 2kx7 2ky5 2l0l 2l0m 2l0n 2l0o 2l2f 2l2x 2l3r 2l8m 2rqf 3sak'.split()
for entry_code in lToRemove:
self.assertFalse( m.removeEntry(entry_code))
def _test_NrgCingRdb(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
host = 'localhost'
if 1: # DEFAULT False
host = 'nmr.cmbi.umcn.nl'
schema=RECOORD_DB_SCHEMA #@UnusedVariable
schema=NRG_DB_NAME
m = NrgCingRdb(host=host,schema=schema)
# self.assertFalse( m.showCounts())
# self.assertFalse( m.createScatterPlots())
self.assertFalse( m.createPlotsCompareBetweenDb(other_schema=NMR_REDO_DB_SCHEMA))
if False:
a = m.getPdbIdList()
nTdebug("pdbIdList length: %d %s" % (len(a), a))
self.assertTrue(a)
if 0 and a: # DEFAULT 0 watch out!
lToRemove = \
'1sae 1sah 1saj 1sak 1sal 1y0j 2k0a 2kiu 2ku2 2kx7 2ky5 2l0l 2l0m 2l0n 2l0o 2l2f 2l2x 2l3r 2l8m 2rqf 3sak'.split()
for entry_code in lToRemove:
self.assertFalse( m.removeEntry(entry_code))
def __init__(
self,
useTopos=False,
getTodoList=True,
max_entries_todo=1,
max_time_to_wait=86400,
# one day. 2p80 took the longest: 5.2 hours.
# But <Molecule "2ku1" (C:7,R:1659,A:36876,M:30)> is taking longer. 2ku2 is taking over 12 hrs now.
processes_max=None,
prepareInput=False,
writeWhyNot=True,
writeTheManyFiles=False,
updateIndices=True,
# isProduction=True
):
kwds = NTdict(
useTopos=useTopos, # There must be an introspection possible for this.
getTodoList=getTodoList,
max_entries_todo=max_entries_todo,
max_time_to_wait=max_time_to_wait, # one day. 2p80 took the longest: 5.2 hours.
# But <Molecule "2ku1" (C:7,R:1659,A:36876,M:30)> is taking longer. 2ku2 is taking over 12 hrs now.
processes_max=processes_max,
prepareInput=prepareInput,
writeWhyNot=writeWhyNot,
writeTheManyFiles=writeTheManyFiles,
updateIndices=updateIndices,
# isProduction=isProduction,
)
kwds = kwds.toDict()
NrgCing.__init__(self, **kwds) # Steal most from super class.
self.results_base = results_base_recoord
self.entry_to_delete_count_max = 0 # can be as many as fail every time.
self.usedCcpnInput = 0 # For NMR_REDO it is not from the start.
self.validateEntryExternalDone = 0
self.nrgCing = NrgCing() # Use as little as possible thru this inconvenience variable.
self.archive_id = ARCHIVE_RECOORD_ID
self.validateEntryExternalDone = False # DEFAULT: True
# in the future and then it won't change but for NrgCing it is True from the start.
self.updateDerivedResourceSettings() # The paths previously initialized in NrgCing. Will also chdir.
if 1:
nTmessage("Going to use specific entry_list_todo in prepare")
# self.entry_list_done = readLinesFromFile('/Library/WebServer/Documents/NRG-CING/list/entry_list_recoord_nrgcing_shuffled.csv')
m = NrgCingRdb(schema=self.schema_id)
self.entry_list_done = m.getPdbIdList(fromCing=True)
self.entry_list_done = NTlist(*self.entry_list_done)
if 0:
self.entry_list_todo.clear()
# Random set of 10 from RECOORD still present in PDB.
# self.entry_list_todo += "1mmc 1ks0 1b4r 1nxi 1eww 1hp3 1iox 2u2f 1kjs 1orx".split()
self.entry_list_todo += "1brv".split()
if 0: # DEFAULT: 0
nTmessage("Going to use specific entry_list_todo in prepare")
self.entry_list_todo = readLinesFromFile(
"/Library/WebServer/Documents/NRG-CING/list/entry_list_recoord_nrgcing_shuffled.csv"
)
self.entry_list_todo = NTlist(*self.entry_list_todo)
def __init__(
self,
useTopos=False,
getTodoList=True,
max_entries_todo=1,
max_time_to_wait=86400,
# one day. 2p80 took the longest: 5.2 hours.
# But <Molecule "2ku1" (C:7,R:1659,A:36876,M:30)> is taking longer. 2ku2 is taking over 12 hrs now.
processes_max=None,
prepareInput=False,
writeWhyNot=True,
writeTheManyFiles=False,
updateIndices=True,
# isProduction=True
):
kwds = NTdict(
useTopos=
useTopos, # There must be an introspection possible for this.
getTodoList=getTodoList,
max_entries_todo=max_entries_todo,
max_time_to_wait=
max_time_to_wait, # one day. 2p80 took the longest: 5.2 hours.
# But <Molecule "2ku1" (C:7,R:1659,A:36876,M:30)> is taking longer. 2ku2 is taking over 12 hrs now.
processes_max=processes_max,
prepareInput=prepareInput,
writeWhyNot=writeWhyNot,
writeTheManyFiles=writeTheManyFiles,
updateIndices=updateIndices,
# isProduction=isProduction,
)
kwds = kwds.toDict()
NrgCing.__init__(self, **kwds) # Steal most from super class.
self.results_base = results_base_recoord
self.entry_to_delete_count_max = 0 # can be as many as fail every time.
self.usedCcpnInput = 0 # For NMR_REDO it is not from the start.
self.validateEntryExternalDone = 0
self.nrgCing = NrgCing(
) # Use as little as possible thru this inconvenience variable.
self.archive_id = ARCHIVE_RECOORD_ID
self.validateEntryExternalDone = False # DEFAULT: True
# in the future and then it won't change but for NrgCing it is True from the start.
self.updateDerivedResourceSettings(
) # The paths previously initialized in NrgCing. Will also chdir.
if 1:
nTmessage("Going to use specific entry_list_todo in prepare")
# self.entry_list_done = readLinesFromFile('/Library/WebServer/Documents/NRG-CING/list/entry_list_recoord_nrgcing_shuffled.csv')
m = NrgCingRdb(schema=self.schema_id)
self.entry_list_done = m.getPdbIdList(fromCing=True)
self.entry_list_done = NTlist(*self.entry_list_done)
if 0:
self.entry_list_todo.clear()
# Random set of 10 from RECOORD still present in PDB.
# self.entry_list_todo += "1mmc 1ks0 1b4r 1nxi 1eww 1hp3 1iox 2u2f 1kjs 1orx".split()
self.entry_list_todo += "1brv".split()
if 0: # DEFAULT: 0
nTmessage("Going to use specific entry_list_todo in prepare")
self.entry_list_todo = readLinesFromFile(
'/Library/WebServer/Documents/NRG-CING/list/entry_list_recoord_nrgcing_shuffled.csv'
)
self.entry_list_todo = NTlist(*self.entry_list_todo)