def getCASP_NMR_DBMS():
csvFileDir = os.path.join(baseDir, 'Overview')
relationNames = glob1(csvFileDir, "*.csv")
relationNames = [ relationName[:-4] for relationName in relationNames]
dbms = DBMS()
dbms.readCsvRelationList(relationNames, csvFileDir)
return dbms
def getCASP_NMR_DBMS():
csvFileDir = os.path.join(baseDir, 'Overview')
relationNames = glob1(csvFileDir, "*.csv")
relationNames = [relationName[:-4] for relationName in relationNames]
dbms = DBMS()
dbms.readCsvRelationList(relationNames, csvFileDir)
return dbms
def testDBMSread(self):
csvFileDir = os.path.join(cingDirTestsData, "dbms", "Overview")
relationNames = glob("%s/*.csv" % csvFileDir)
# Truncate the extensions
relationNames = [relationName[:-4] for relationName in relationNames]
dbms = DBMS()
self.assertFalse(dbms.readCsvRelationList(relationNames, csvFileDir))
def testDBMSread(self):
csvFileDir = os.path.join(cingDirTestsData, "dbms", 'Overview')
relationNames = glob("%s/*.csv" % csvFileDir)
# Truncate the extensions
relationNames = [relationName[:-4] for relationName in relationNames]
dbms = DBMS()
self.assertFalse(dbms.readCsvRelationList(relationNames, csvFileDir))
def getCASD_NMR_DBMS():
csvFileDir = os.path.join(baseDir, 'Overview')
relationNames = glob1(csvFileDir, "*.csv")
relationNames = [ relationName[:-4] for relationName in relationNames]
if not relationNames:
nTerror('Failed to read any relation from %s' % baseDir)
dbms = DBMS()
dbms.readCsvRelationList(relationNames, csvFileDir)
return dbms
def getCASD_NMR_DBMS():
csvFileDir = os.path.join(baseDir, 'Overview')
relationNames = glob1(csvFileDir, "*.csv")
relationNames = [relationName[:-4] for relationName in relationNames]
if not relationNames:
nTerror('Failed to read any relation from %s' % baseDir)
dbms = DBMS()
dbms.readCsvRelationList(relationNames, csvFileDir)
return dbms
def getBmrbLinks():
""" Returns None for failure
Returns matches_many2one hash.
"""
dbms = DBMS()
# matchBmrbPdbDataDirLocal = os.path.join(cingRoot, matchBmrbPdbDataDir) # Needs to change to live resource as well.
matchBmrbPdbDataDirLocal = matchBmrbPdbDir
dbms.readCsvRelationList([ matchBmrbPdbTable ], matchBmrbPdbDataDirLocal)
mTable = dbms.tables[matchBmrbPdbTable]
# nTmessage("mTable:\n%s" % mTable.__str__(show_rows=False))
matches_many2one = mTable.getHash(useSingleValueOfColumn=1) # hashes by first column to the next by default already.
# nTmessage("Found %s matches from PDB to BMRB" % len(matches_many2one))
return matches_many2one
def getBmrbLinks():
""" Returns None for failure
Returns matches_many2one hash.
"""
dbms = DBMS()
# matchBmrbPdbDataDirLocal = os.path.join(cingRoot, matchBmrbPdbDataDir) # Needs to change to live resource as well.
matchBmrbPdbDataDirLocal = matchBmrbPdbDir
dbms.readCsvRelationList([matchBmrbPdbTable], matchBmrbPdbDataDirLocal)
mTable = dbms.tables[matchBmrbPdbTable]
# nTmessage("mTable:\n%s" % mTable.__str__(show_rows=False))
matches_many2one = mTable.getHash(
useSingleValueOfColumn=1
) # hashes by first column to the next by default already.
# nTmessage("Found %s matches from PDB to BMRB" % len(matches_many2one))
return matches_many2one
def getBmrbCsCounts():
dbms = DBMS()
bmrbCountTableName = 'BMRB_CS_counts'
dbms.readCsvRelationList([bmrbCountTableName], os.path.join(cingDirData, 'NRG'))
bmrbCountTable = dbms.tables[ bmrbCountTableName ]
bmrbCountTable.convertColumn(0) # default is integer data type converting the read strings
bmrbCountTable.convertColumn(2)
bmrbCountTableProper = bmrbCountTable.toTable()
# nTdebug("Found table: %r" % bmrbCountTableProper)
bmrbCountMap = NTdict()
# idxColumnKeyList = [0, 1, 2]
idxColumnKeyList = []
bmrbCountMap.appendFromTableGeneric(bmrbCountTableProper, *idxColumnKeyList)
return bmrbCountMap
def getNumberOfEntries():
nTmessage("Getting overall number of entry count")
if os.path.exists(psqlTmpCsvFile):
nTdebug('Removing previous copy of %s' % psqlTmpCsvFile)
os.unlink(psqlTmpCsvFile)
# end if
# without semi-colon
sqlSelectCmd = "select count(*) from pdbj.brief_summary"
# without semi-colon
sqlCopyCmd = "COPY (%s) TO STDOUT WITH CSV HEADER" % sqlSelectCmd
command = "psql -h %s --command='%s' pdbmlplus pdbj" % (PDBJ_DB_HOST,
sqlCopyCmd)
nTdebug("command: [%s]" % command)
psqlProgram = ExecuteProgram(command, redirectOutputToFile=psqlTmpCsvFile)
exitCode = psqlProgram()
if exitCode:
nTerrorT("Failed to run psql program with command: [%s]" % command)
return True
# end if
if not os.path.exists(psqlTmpCsvFile):
nTerror('Csv file %s not found' % psqlTmpCsvFile)
return True
# end if
if not os.path.getsize(psqlTmpCsvFile):
nTerror('Csv file %s is empty' % psqlTmpCsvFile)
return True
# end if
relationNames = [psqlTmpCsvFile]
# Truncate the .csv extensions
relationNames = [relationName[:-4] for relationName in relationNames]
dbms = DBMS()
if dbms.readCsvRelationList(relationNames):
nTerror("Failed to read relation: %s" % str(relationNames))
return True
# end if
entryCountTable = dbms.tables[relationNames[0]]
# nTdebug('\n'+str(entryCountTable))
entryCountColumnName = entryCountTable.columnOrder[0]
if entryCountColumnName != 'count':
nTerrorT("Failed to find count column name from DB")
return True
# end if
entryCountList = entryCountTable.getColumnByIdx(0)
entryCount = entryCountList[0]
nTmessage("Currently found %s number of entries in pdbmlplus" % entryCount)
return entryCount
def getNumberOfEntries():
nTmessage("Getting overall number of entry count")
if os.path.exists(psqlTmpCsvFile):
nTdebug('Removing previous copy of %s' % psqlTmpCsvFile)
os.unlink(psqlTmpCsvFile)
# end if
# without semi-colon
sqlSelectCmd = "select count(*) from pdbj.brief_summary"
# without semi-colon
sqlCopyCmd = "COPY (%s) TO STDOUT WITH CSV HEADER" % sqlSelectCmd
command = "psql -h %s --command='%s' pdbmlplus pdbj" % ( PDBJ_DB_HOST, sqlCopyCmd)
nTdebug("command: [%s]" % command)
psqlProgram = ExecuteProgram(command, redirectOutputToFile=psqlTmpCsvFile)
exitCode = psqlProgram()
if exitCode:
nTerrorT("Failed to run psql program with command: [%s]" % command)
return True
# end if
if not os.path.exists( psqlTmpCsvFile ):
nTerror('Csv file %s not found' % psqlTmpCsvFile)
return True
# end if
if not os.path.getsize(psqlTmpCsvFile):
nTerror('Csv file %s is empty' % psqlTmpCsvFile)
return True
# end if
relationNames = [ psqlTmpCsvFile ]
# Truncate the .csv extensions
relationNames = [ relationName[:-4] for relationName in relationNames]
dbms = DBMS()
if dbms.readCsvRelationList(relationNames):
nTerror("Failed to read relation: %s" % str(relationNames))
return True
# end if
entryCountTable = dbms.tables[relationNames[0]]
# nTdebug('\n'+str(entryCountTable))
entryCountColumnName = entryCountTable.columnOrder[0]
if entryCountColumnName != 'count':
nTerrorT("Failed to find count column name from DB")
return True
# end if
entryCountList = entryCountTable.getColumnByIdx(0)
entryCount = entryCountList[0]
nTmessage("Currently found %s number of entries in pdbmlplus" % entryCount)
return entryCount
def getBmrbCsCounts():
dbms = DBMS()
bmrbCountTableName = 'BMRB_CS_counts'
dbms.readCsvRelationList([bmrbCountTableName],
os.path.join(cingDirData, 'NRG'))
bmrbCountTable = dbms.tables[bmrbCountTableName]
bmrbCountTable.convertColumn(
0) # default is integer data type converting the read strings
bmrbCountTable.convertColumn(2)
bmrbCountTableProper = bmrbCountTable.toTable()
# nTdebug("Found table: %r" % bmrbCountTableProper)
bmrbCountMap = NTdict()
# idxColumnKeyList = [0, 1, 2]
idxColumnKeyList = []
bmrbCountMap.appendFromTableGeneric(bmrbCountTableProper,
*idxColumnKeyList)
return bmrbCountMap
def _test_writeCsvNRG(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
myLoL = [ [0,1,2], [3,4,5] ]
dbms = DBMS()
r = Relation('mTable', dbms, columnList=['x', 'y'])
r.fromLol(myLoL)
r.writeCsvFile('myLoL')
def testDBMShashing(self):
dbms = DBMS()
mTable = Relation('mTable', dbms, columnList=['pdb_id', 'bmrb_id'])
_pdbIdNewMany2OneList = mTable.getColumn('pdb_id')
_bmrbIdNewMany2OneList = mTable.getColumn('bmrb_id')
_pdbIdNewMany2OneList += '2kz0 2rop'.split()
_bmrbIdNewMany2OneList += [16995, 11041]
mTableHash = mTable.getHash()
rowList = mTableHash['2rop']
self.assertEqual(11041, rowList[1])
nTdebug('\n' + str(mTable))
def _test_BMRBcounts(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
dbms = DBMS()
bmrbCountTableName = 'BMRB_CS_counts'
dbms.readCsvRelationList([bmrbCountTableName], os.path.join(cingDirData, 'NRG'))
bmrbCountTable = dbms.tables[ bmrbCountTableName ]
bmrbCountTable.convertColumn(0) # default is integer data type converting the read strings
bmrbCountTable.convertColumn(2)
bmrbCountTableProper = bmrbCountTable.toTable()
# nTdebug("Found table: %r" % bmrbCountTableProper)
bmrbCountMap = NTdict()
# idxColumnKeyList = [0, 1, 2]
idxColumnKeyList = []
bmrbCountMap.appendFromTableGeneric(bmrbCountTableProper, *idxColumnKeyList)
bmrb_id = 4020
self.assertEqual( getDeepByKeysOrAttributes( bmrbCountMap, bmrb_id, '1H' ), 183)
self.assertEqual( getDeepByKeysOrAttributes( bmrbCountMap, bmrb_id, '13C' ), 73)
self.assertEqual( getDeepByKeysOrAttributes( bmrbCountMap, bmrb_id, '15N' ), None)
