예제 #1
0
    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))
예제 #2
0
    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))
예제 #3
0
파일: recoord.py 프로젝트: jakesyl/cing
    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)
예제 #4
0
    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)