function stringlengths 11 56k | repo_name stringlengths 5 60 | features list |
|---|---|---|
def debug_contents(self, indent=1, file=sys.stdout, _ids=None):
"""Print out interesting things about the object."""
klasses = list(self.__class__.__mro__)
klasses.reverse()
# print special attributes "bottom up"
previous_attrs = ()
for c in klasses:
attrs = getattr(c, '_debug_contents', ())
# if we have seen this list already, move to the next class
if attrs is previous_attrs:
continue
for attr in attrs:
file.write("%s%s = %s\n" % (" " * indent, attr, getattr(self, attr)))
previous_attrs = attrs
# build a list of property identifiers "bottom up"
property_names = []
properties_seen = set()
for c in klasses:
for prop in getattr(c, 'properties', []):
if prop.identifier not in properties_seen:
property_names.append(prop.identifier)
properties_seen.add(prop.identifier)
# print out the values
for property_name in property_names:
property_value = self._values.get(property_name, None)
# printing out property values that are None is tedious
if property_value is None:
continue
if hasattr(property_value, "debug_contents"):
file.write("%s%s\n" % (" " * indent, property_name))
property_value.debug_contents(indent+1, file, _ids)
else:
file.write("%s%s = %r\n" % (" " * indent, property_name, property_value)) | JoelBender/bacpypes | [
243,
121,
243,
107,
1436992431
] |
def stringInList_CaseInsens ( aString, aList ):
for s in aList:
u = s.upper()
if ( aString.upper() == u ): return ( 1 )
return ( 0 ) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def remapCategoricalFeatures(allClinDict):
print " "
print " in remapCategoricalFeatures "
keyList = allClinDict.keys()
keyList.sort()
for aKey in keyList:
aKey2 = aKey.lower()
if (aKey2 in remapDict.keys()):
numRemap = 0
print " "
print " looking at <%s> " % aKey2
tmpV = allClinDict[aKey]
# print " part of original vector : ", tmpV[:10]
newV = [0] * len(tmpV)
for kk in range(len(tmpV)):
bKey2 = tmpV[kk].lower()
if (bKey2.startswith("stage_")):
bKey2 = bKey2[6:]
if (bKey2.startswith("stage ")):
bKey2 = bKey2[6:]
try:
newV[kk] = remapDict[aKey2][bKey2]
if (newV[kk] != "NA" and newV[kk] != "na"):
if (newV[kk].lower() != bKey2):
# print " remapping ... ", aKey, aKey2, kk,
# bKey2, remapDict[aKey2][bKey2]
numRemap += 1
except:
if (0):
print " WARNING in remapCategoricalFeatures ... nothing to remap to ??? "
print " <%s> <%s> %d <%s> " % (aKey, aKey2, kk, bKey2)
print " <%s> " % remapDict[aKey2]
# sys.exit(-1)
newV[kk] = bKey2
if (numRemap > 0):
print " --> using remapped values for <%s> " % aKey
print " mapping dictionary : ", remapDict[aKey2]
print " part of original vector : ", tmpV[:10]
print " part of new vector : ", newV[:10]
allClinDict[aKey] = newV
return (allClinDict) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def getNumPatients(allClinDict):
aKey = allClinDict.keys()[0]
return ( len(allClinDict[aKey]) ) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def findProperKey(allClinDict, aString):
keyList = allClinDict.keys()
foundList = []
for aKey in keyList:
if ( aKey.lower().find(aString.lower()) >=0 ):
foundList += [ aKey ]
if ( len(foundList) == 0 ):
return ( "NO KEY" )
elif ( len(foundList) == 1 ):
return ( foundList[0] )
else:
## look for a perfect match ...
for mString in foundList:
mTokens = mString.split(':')
if ( len(mTokens) == 1 ):
if ( mTokens[0].lower() == aString.lower() ):
return ( mString )
elif ( len(mTokens) > 2 ):
try:
if ( mTokens[2].lower() == aString.lower() ):
return ( mString )
except:
print " findProperKey: ERROR in try ??? ", mString
print foundList
print " "
print " ERROR in findProperKey ??? multiple matches "
print " but none of them are perfect matches ... "
print aString
print foundList
print " "
sys.exit(-1) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def computeLymphnodesFraction(allClinDict):
aKey = findProperKey ( allClinDict, "number_of_lymphnodes_positive_by_he" )
bKey = findProperKey ( allClinDict, "number_of_lymphnodes_examined" )
if (aKey not in allClinDict.keys()):
print " "
print " skipping computeLymphnodesFraction "
return (allClinDict)
if (bKey not in allClinDict.keys()):
print " "
print " skipping computeLymphnodesFraction "
return (allClinDict)
print " "
print " in computeLymphnodesFraction ... "
numClin = getNumPatients(allClinDict)
newV = [0] * numClin
for kk in range(numClin):
if (allClinDict[bKey][kk] == "NA"):
newV[kk] = "NA"
elif (allClinDict[aKey][kk] == "NA"):
newV[kk] = "NA"
elif (int(allClinDict[bKey][kk]) == 0):
newV[kk] = "NA"
else:
newV[kk] = float(allClinDict[aKey][kk]) / \
float(allClinDict[bKey][kk])
allClinDict["N:SAMP:fraction_lymphnodes_positive_by_he:::::"] = newV
return (allClinDict) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def addTag2Key ( aKey, aTag ):
aTokens = aKey.split(':')
if ( len(aTokens) >= 7 ):
newKey = aTokens[0] + ':' + aTokens[1] + ':' + aTokens[2]
if ( aTag[0] == "_" ):
newKey += aTag
else:
newKey += "_" + aTag
for ii in range(3,len(aTokens)):
newKey += ":" + aTokens[ii]
else:
newKey = aKey
if ( aTag[0] == "_" ):
newKey += aTag
else:
newKey += "_" + aTag | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def checkBarcodes(allClinDict):
zKey = findProperKey (allClinDict, "bcr_patient_barcode" )
numClin = getNumPatients(allClinDict)
for ii in range(numClin):
if ( allClinDict[zKey][ii].find("_") >= 0 ):
print " BAD barcode !!! ", ii, allClinDict[zKey][ii]
sys.exit(-1) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def addFollowupInfo(allClinDict):
print " "
print " in addFollowupInfo ... "
# ------------------------------------------------------------------------
# FIRST: if there is a days_to_last_known_alive, then check that it is
# used consistently, otherwise create it
zKey = findProperKey (allClinDict, "bcr_patient_barcode")
aKey = findProperKey (allClinDict, "days_to_last_known_alive")
bKey = findProperKey (allClinDict, "days_to_last_followup")
cKey = findProperKey (allClinDict, "days_to_death")
haveA = (aKey in allClinDict.keys())
haveB = (bKey in allClinDict.keys())
haveC = (cKey in allClinDict.keys())
print " "
print " STEP #1 "
print " have flags A, B, and C : ", haveA, haveB, haveC
## print " allClinDict.keys() : "
## print allClinDict.keys()
if (haveA):
# if we have the "days_to_last_known_alive" field, check that it
# is consistent with the other two fields ...
numClin = getNumPatients(allClinDict)
numNotNA = 0
for kk in range(numClin):
## if we have a 'days_to_death' field and it is not NA, then set 'days_to_last_known_alive' to that value
if (haveC):
if (str(allClinDict[cKey][kk]).upper() != "NA"):
allClinDict[aKey][kk] = allClinDict[cKey][kk]
## if we have a 'days_to_last_followup' field and it is not NA, then ...
if (haveB):
if (str(allClinDict[bKey][kk]).upper() != "NA"):
if (str(allClinDict[aKey][kk]).upper() == "NA"):
allClinDict[aKey][kk] = allClinDict[bKey][kk]
if (str(allClinDict[aKey][kk]).upper() != "NA"):
numNotNA += 1
print " UPDATED days_to_last_known_alive (%d) : " % numNotNA
print allClinDict[aKey]
else:
# create it ...
if ( aKey == "NO KEY" ): aKey = "N:CLIN:days_to_last_known_alive:::::"
numClin = getNumPatients(allClinDict)
newVec = [0] * numClin
numNotNA = 0
for kk in range(numClin):
newVec[kk] = "NA"
if (haveC):
if (str(allClinDict[cKey][kk]).upper() != "NA"):
newVec[kk] = allClinDict[cKey][kk]
if (haveB):
if (str(allClinDict[bKey][kk]).upper() != "NA"):
if (str(newVec[kk]).upper() == "NA"):
newVec[kk] = allClinDict[bKey][kk]
if (str(newVec[kk]).upper() != "NA"):
numNotNA += 1
print " NEW days_to_last_known_alive (%d) : " % numNotNA
## print newVec
allClinDict[aKey] = newVec
# ------------------------------------------------------------------------
# SECOND: if there is a "days_to_submitted_specimen_dx", then create
# a set of "days_to_" features that instead of being relative
# to "initial_pathologic_diagnosis" are relative to "submitted_specimen"
print " "
print " STEP #2 "
aKey = findProperKey (allClinDict, "days_to_submitted_specimen_dx")
tKey = findProperKey (allClinDict, "days_to_initial_pathologic_diagnosis")
if (aKey in allClinDict.keys()):
haveA = 1
else:
print " do not have [days_to_submitted_specimen_dx] in allClinDict "
haveA = 0
if (tKey in allClinDict.keys()):
haveT = 1
else:
print " do not have [days_to_initial_pathologic_diagnosis] in allClinDict "
haveT = 0
try:
numClin = getNumPatients(allClinDict)
for bKey in allClinDict.keys():
if (haveA == 0): continue
if (bKey == aKey): continue
if (bKey.find("days_to_") >= 0):
newKey = addTag2Key ( bKey, "relSS" )
print " --> making newKey <%s> from bKey <%s> [%d] " % (newKey, bKey, numClin)
newVec = [0] * numClin
numNotNA = 0
for kk in range(numClin):
## initialize to NA
newVec[kk] = "NA"
## skip if an important value is NA
if (str(allClinDict[aKey][kk]).upper() == "NA"): continue
if (str(allClinDict[bKey][kk]).upper() == "NA"): continue
if (haveT):
if (str(allClinDict[tKey][kk]).upper() == "NA"): continue
## deltaDays is either (days_to_submitted_specimen_dx) - (days_to_initial_pathologic_diagnosis)
## or just (days_to_submitted_specimen_dx)
if (haveT):
deltaDays = allClinDict[aKey][kk] - allClinDict[tKey][kk]
else:
deltaDays = allClinDict[aKey][kk]
## and then we subtract 'delta days' from the original key to make the new relative key
newVec[kk] = allClinDict[bKey][kk] - deltaDays
print " STEP2a ", kk, allClinDict[zKey][kk], allClinDict[bKey][kk], allClinDict[aKey][kk], deltaDays, newVec[kk]
numNotNA += 1
if ( numNotNA > 30 ):
print " adding new key (%d) : " % numNotNA, newKey
## print newVec[:5]
## print newVec[-5:]
allClinDict[newKey] = newVec
else:
print " NOT adding new key (%d) : ", numNotNA, newKey
if (bKey.find("age_at_") >= 0):
## make sure that this is not a "stage_at_" feature !!!
if ( bKey.find("stage_at_") >= 0 ): continue
newKey = addTag2Key ( bKey, "relSS" )
print " --> making newKey <%s> from bKey <%s> [%d] " % (newKey, bKey, numClin)
newVec = [0] * numClin
numNotNA = 0
for kk in range(numClin):
## initialize to NA
newVec[kk] = "NA"
## skip if an important value is NA
if (str(allClinDict[aKey][kk]).upper() == "NA"): continue
if (str(allClinDict[bKey][kk]).upper() == "NA"): continue
if (haveT):
if (str(allClinDict[tKey][kk]).upper() == "NA"): continue
## deltaDays is either (days_to_submitted_specimen_dx) - (days_to_initial_pathologic_diagnosis)
## or just (days_to_submitted_specimen_dx)
if (haveT):
deltaDays = allClinDict[aKey][kk] - allClinDict[tKey][kk]
else:
deltaDays = allClinDict[aKey][kk]
## and then we subtract 'delta days' from the original key to make the new relative key
## 04mar14 : actually we need to ADD here because "age" should go UP with deltaDays ...
newVec[kk] = allClinDict[bKey][kk] + ( float(deltaDays) / DAYS_PER_YEAR )
print " STEP2b ", kk, allClinDict[zKey][kk], allClinDict[bKey][kk], allClinDict[aKey][kk], deltaDays, newVec[kk]
numNotNA += 1
if ( numNotNA > 30 ):
print " adding new key (%d) : " % numNotNA, newKey
## print newVec[:5]
## print newVec[-5:]
allClinDict[newKey] = newVec
else:
print " NOT adding new key (%d) : ", numNotNA, newKey
except:
print " --> failed in this try (x) "
doNothing = 1
# ------------------------------------------------------------------------
# THIRD: if there is a "days_to_sample_procurement", then create
# a set of "days_to_" features that instead of being relative
# to "initial_pathologic_diagnosis" are relative to "sample_procurement
print " "
print " STEP #3 "
aKey = findProperKey (allClinDict, "days_to_sample_procurement")
tKey = findProperKey (allClinDict, "days_to_initial_pathologic_diagnosis")
if (aKey in allClinDict.keys()):
haveA = 1
else:
print " do not have [days_to_sample_procurement] in allClinDict "
haveA = 0
if (tKey in allClinDict.keys()):
haveT = 1
else:
haveT = 0
print " do not have a [days_to_initial_pathologic_diagnosis] key "
try:
numClin = getNumPatients(allClinDict)
for bKey in allClinDict.keys():
if (haveA == 0): continue
if (bKey == aKey): continue
if (bKey.find("days_to_") >= 0):
## make sure that this is not one of the relSS features just added !!!
if ( bKey.find("relSS") >= 0 ): continue
newKey = addTag2Key ( bKey, "relSP" )
print " --> making newKey <%s> from bKey <%s> [%d] " % (newKey, bKey, numClin)
newVec = [0] * numClin
numNotNA = 0
for kk in range(numClin):
## initialize to NA
newVec[kk] = "NA"
## skip if an important value is NA
if (str(allClinDict[aKey][kk]).upper() == "NA"): continue
if (str(allClinDict[bKey][kk]).upper() == "NA"): continue
if (haveT):
if (str(allClinDict[tKey][kk]).upper() == "NA"): continue
## deltaDays is either (days_to_sample_procurement) - (days_to_initial_pathologic_diagnosis)
## or just (days_to_sample_procurement)
if (haveT):
deltaDays = allClinDict[aKey][kk] - allClinDict[tKey][kk]
else:
deltaDays = allClinDict[aKey][kk]
## and then we subtract 'delta days' from the original key to make the new relative key
newVec[kk] = allClinDict[bKey][kk] - deltaDays
print " STEP3a ", kk, allClinDict[zKey][kk], allClinDict[bKey][kk], allClinDict[aKey][kk], deltaDays, newVec[kk]
numNotNA += 1
if ( numNotNA > 30 ):
print " adding new key (%d) : " % numNotNA, newKey
## print newVec[:5]
## print newVec[-5:]
allClinDict[newKey] = newVec
else:
print " NOT adding new key (%d) : ", numNotNA, newKey
if (bKey.find("age_at_") >= 0):
## make sure that this is not one of the relSS features just added !!!
if ( bKey.find("relSS") >= 0 ): continue
## make sure that this is not a "stage_at_" feature !!!
if ( bKey.find("stage_at_") >= 0 ): continue
newKey = addTag2Key ( bKey, "relSP" )
print " --> making newKey <%s> from bKey <%s> [%d] " % (newKey, bKey, numClin)
newVec = [0] * numClin
numNotNA = 0
for kk in range(numClin):
## initialize to NA
newVec[kk] = "NA"
## skip if an important value is NA
print " checking for important information ... ", aKey, bKey, tKey
print allClinDict[aKey][kk]
print allClinDict[bKey][kk]
if (str(allClinDict[aKey][kk]).upper() == "NA"): continue
if (str(allClinDict[bKey][kk]).upper() == "NA"): continue
if (haveT):
print allClinDict[tKey][kk]
if (str(allClinDict[tKey][kk]).upper() == "NA"): continue
## deltaDays is either (days_to_sample_procurement) - (days_to_initial_pathologic_diagnosis)
## or just (days_to_sample_procurement)
if (haveT):
deltaDays = allClinDict[aKey][kk] - allClinDict[tKey][kk]
else:
deltaDays = allClinDict[aKey][kk]
print " computed deltaDays : ", deltaDays
## and then we subtract 'delta days', scaled to years ...
## 03mar14 : actually we need to ADD here ...
newVec[kk] = allClinDict[bKey][kk] + ( float(deltaDays) / DAYS_PER_YEAR )
print " STEP3b ", kk, allClinDict[zKey][kk], allClinDict[bKey][kk], allClinDict[aKey][kk], deltaDays, newVec[kk]
numNotNA += 1
if ( numNotNA > 30 ):
print " adding new key (%d) : " % numNotNA, newKey
## print newVec[:5]
## print newVec[-5:]
allClinDict[newKey] = newVec
else:
print " NOT adding new key (%d) : ", numNotNA, newKey
except:
print " --> failed in this try (y) "
doNothing = 1
return (allClinDict) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def checkFollowupInfo(allClinDict):
print " "
print " in checkFollowupInfo ... "
# FIRST: if there is a days_to_last_known_alive, then check that it is
# used consistently, otherwise create it
zKey = findProperKey (allClinDict, "bcr_patient_barcode")
aKey = findProperKey (allClinDict, "days_to_last_known_alive")
bKey = findProperKey (allClinDict, "days_to_last_followup")
cKey = findProperKey (allClinDict, "days_to_death")
dKey = findProperKey (allClinDict, "vital_status")
haveA = (aKey in allClinDict.keys())
haveB = (bKey in allClinDict.keys())
haveC = (cKey in allClinDict.keys())
haveD = (dKey in allClinDict.keys())
print " have flags A, B, C and D : ", haveA, haveB, haveC, haveD
if ( not haveD ):
print " skipping this function ... requires vital_status "
return (allClinDict)
## print " allClinDict.keys() : "
## print allClinDict.keys()
numClin = getNumPatients(allClinDict)
# range of days_to_last_known_alive is typically something like [0,3196]
for kk in range(numClin):
if (str(allClinDict[dKey][kk]).upper() == "DEAD"):
if (str(allClinDict[cKey][kk]).upper() == "NA"):
print " ERROR !!! need to know when this person died !!! ", allClinDict[zKey][kk]
print kk
print aKey, allClinDict[aKey][kk]
print bKey, allClinDict[bKey][kk]
print cKey, allClinDict[cKey][kk]
print dKey, allClinDict[dKey][kk]
print " UPDATING vital_status to Alive ... "
print " "
## because we do not have a days_to_death value, we are going to call this person "Alive"
allClinDict[dKey][kk] = "Alive"
if (str(allClinDict[dKey][kk]).upper() == "ALIVE"):
if (str(allClinDict[aKey][kk]).upper() == "NA"):
if (str(allClinDict[bKey][kk]).upper() == "NA"):
print " ERROR !!! no information about follow-up ??? ", allClinDict[zKey][kk]
print kk
print aKey, allClinDict[aKey][kk]
print bKey, allClinDict[bKey][kk]
print cKey, allClinDict[cKey][kk]
print dKey, allClinDict[dKey][kk]
print " UPDATING days_to_last_known_alive and days_to_last_followup to 0 "
print " "
allClinDict[aKey][kk] = 0
allClinDict[bKey][kk] = 0
else:
print " ERROR in checkFollowupInfo ... how did we get here ??? "
sys.exit(-1) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def PreferredStage(reported, computed):
t = testTumorStage(reported, computed)
if (t == "AGREE"):
return(reported)
if (t == "Stage cannot be derived from TNM"):
return(reported)
if (t == "Derived stage is more specific"):
return(repStage(computed)) # For SupTab1 use return(computed)
if (t == "Stage can be derived from TNM"):
return(repStage(computed)) # For SupTab1 use return(computed)
if (t == "Stage more specific than TNM"):
return(reported)
if (t == "DISAGREE"):
return(reported) # assuming the reported one to be valid!
return("Error: Lack a preferred stage") | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def repStage(substage):
if (type(substage) is str):
return(substage)
if (type(substage) is list):
return(substage[0]) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def testTumorStage(reported, computed):
# Agreement includes "in" relationship and NA equivalence
if (type(computed) is list):
if (reported in computed):
return("AGREE")
if (type(computed) is str):
if (reported == computed):
return("AGREE")
if (((reported == "STAGE IVA") | (reported == "STAGE IVB")) & (computed == "STAGE IV")):
return("Stage more specific than TNM")
if ((reported == "NA") & (computed != "NA")):
return("Stage can be derived from TNM")
if ((reported != "NA") & (computed == "NA")):
return("Stage cannot be derived from TNM")
if (repStage(computed).startswith(reported)):
return("Derived stage is more specific")
return("DISAGREE") | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def getTumorStage(T, N, M):
print " WARNING ... this function should NOT be called ... "
sys.exit(-1)
T = T.upper()
N = N.upper()
M = M.upper()
if (M == "M1"):
# Seems to be TCGA choice if IVA, IVB not specified
return ("STAGE IV")
if (M == "M1A"):
return ("STAGE IVA")
if (M == "M1B"):
return ("STAGE IVB")
if (T == "TX"):
T = "NA"
if (N == "NX"):
N = "NA"
if (M == "MX"):
M = "NA"
if (T == "NA" or N == "NA" or M == "NA"):
return ("NA")
if (T == "T0" and N == "N0" and M == "M0"):
return ("STAGE 0")
if (T == "Tis" and N == "N0" and M == "M0"):
return ("STAGE 0")
if (T == "T1" and N == "N0" and M == "M0"):
return ("STAGE I")
if (T == "T1A" and N == "N0" and M == "M0"):
return ("STAGE I")
if (T == "T1B" and N == "N0" and M == "M0"):
return ("STAGE I")
if (T == "T2" and N == "N0" and M == "M0"):
return ("STAGE I")
if (T == "T2A" and N == "N0" and M == "M0"):
return ("STAGE I")
if (T == "T2B" and N == "N0" and M == "M0"):
return ("STAGE I")
if (T == "T3" and N == "N0" and M == "M0"):
return ("STAGE IIA")
if (T == "T3A" and N == "N0" and M == "M0"):
return ("STAGE IIA")
if (T == "T3B" and N == "N0" and M == "M0"):
return ("STAGE IIB")
if (T == "T3C" and N == "N0" and M == "M0"):
return ("STAGE IIB")
if (T == "T4A" and N == "N0" and M == "M0"):
return ("STAGE IIB")
if (T == "T4B" and N == "N0" and M == "M0"):
return ("STAGE IIC")
if (T == "T4" and N == "N0" and M == "M0"):
return (["STAGE IIB", "STAGE IIC"])
if (T == "T1" and N == "N1" and M == "M0"):
return ("STAGE IIIA")
if (T == "T1A" and N == "N1" and M == "M0"):
return ("STAGE IIIA")
if (T == "T1B" and N == "N1" and M == "M0"):
return ("STAGE IIIA")
if (T == "T1" and N == "N1A" and M == "M0"):
return ("STAGE IIIA")
if (T == "T1" and N == "N1B" and M == "M0"):
return ("STAGE IIIA")
if (T == "T1" and N == "N1C" and M == "M0"):
return ("STAGE IIIA")
if (T == "T1" and N == "N2" and M == "M0"):
return (["STAGE IIIA", "STAGE IIIB"]) # CHOICE IIIA, IIIB
if (T == "T1B" and N == "N2" and M == "M0"):
return ("STAGE IIIB")
if (T == "T1" and N == "N2A" and M == "M0"):
return ("STAGE IIIA")
if (T == "T1" and N == "N3" and M == "M0"):
return ("STAGE IIIA")
if (T == "T2" and N == "N1" and M == "M0"):
return ("STAGE IIIA")
if (T == "T2A" and N == "N1" and M == "M0"):
return ("STAGE IIIA")
if (T == "T2B" and N == "N1" and M == "M0"):
return ("STAGE IIIA")
if (T == "T2" and N == "N1A" and M == "M0"):
return ("STAGE IIIA")
if (T == "T2" and N == "N1B" and M == "M0"):
return ("STAGE IIIA")
if (T == "T2" and N == "N1C" and M == "M0"):
return ("STAGE IIIA")
if (T == "T3" and N == "N1" and M == "M0"):
return ("STAGE IIIB")
if (T == "T3A" and N == "N1" and M == "M0"):
return ("STAGE IIIB")
if (T == "T3B" and N == "N1" and M == "M0"):
return ("STAGE IIIB")
if (T == "T3" and N == "N1A" and M == "M0"):
return ("STAGE IIIB")
if (T == "T3" and N == "N1B" and M == "M0"):
return ("STAGE IIIB")
if (T == "T3" and N == "N1C" and M == "M0"):
return ("STAGE IIIB")
if (T == "T4A" and N == "N1" and M == "M0"):
return ("STAGE IIIB")
if (T == "T4A" and N == "N1A" and M == "M0"):
return ("STAGE IIIB")
if (T == "T4A" and N == "N1B" and M == "M0"):
return ("STAGE IIIB")
if (T == "T4A" and N == "N1C" and M == "M0"):
return ("STAGE IIIB")
if (T == "T4" and N == "N1" and M == "M0"):
return (["STAGE IIIB", "STAGE IIIC"])
if (T == "T2" and N == "N2" and M == "M0"):
return ("STAGE IIIB")
if (T == "T2A" and N == "N2" and M == "M0"):
return ("STAGE IIIB")
if (T == "T2B" and N == "N2" and M == "M0"):
return ("STAGE IIIB")
if (T == "T2" and N == "N2A" and M == "M0"):
return ("STAGE IIIB")
if (T == "T2" and N == "N2B" and M == "M0"):
return ("STAGE IIIB")
if (T == "T2" and N == "N2C" and M == "M0"):
return ("STAGE IIIC")
if (T == "T2" and N == "N3" and M == "M0"):
return ("STAGE IIIC")
if (T == "T2B" and N == "N3" and M == "M0"):
return ("STAGE IIIC")
if (T == "T3" and N == "N2" and M == "M0"):
return (["STAGE IIIB", "STAGE IIIC"]) # CHOICE IIIB, IIIC
if (T == "T3" and N == "N2A" and M == "M0"):
return ("STAGE IIIB")
if (T == "T3" and N == "N2C" and M == "M0"):
return ("STAGE IIIC")
if (T == "T1" and N == "N2B" and M == "M0"):
return ("STAGE IIIB")
if (T == "T3" and N == "N2B" and M == "M0"):
return ("STAGE IIIC")
if (T == "T3" and N == "N3" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4" and N == "N2" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4A" and N == "N2" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4A" and N == "N2A" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4A" and N == "N2B" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4A" and N == "N2C" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4" and N == "N3" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4" and N == "N3A" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4A" and N == "N3" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4B" and N == "N1" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4B" and N == "N2" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4B" and N == "N1A" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4B" and N == "N1B" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4B" and N == "N1C" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4B" and N == "N2C" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4B" and N == "N2A" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4B" and N == "N2B" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4B" and N == "N2B" and M == "M0"):
return ("STAGE IIIC")
if (T == "T4B" and N == "N3A" and M == "M0"):
return ("STAGE IIIC")
# We reach this point if all values are non-NA, but combination is not in
# AJCC tumor table
print " ERROR in getTumorStage ??? ", T, N, M
return ("Not in AJCC Table?")
sys.exit(-1) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def checkTumorStage(allClinDict):
if ("tumor_stage" not in allClinDict.keys()):
print " skipping checkTumorStage ... "
return (allClinDict)
else:
print " running checkTumorStage ... "
numClin = getNumPatients(allClinDict)
print " total number of patients : ", numClin
if (0):
stringList = ["tumor", "stage", "spread"]
for aKey in allClinDict.keys():
for aString in stringList:
if (aKey.find(aString) >= 0):
print aKey
reqKeyList = [
"bcr_patient_barcode", "tumor_stage", "primary_tumor_pathologic_spread",
"lymphnode_pathologic_spread", "distant_metastasis_pathologic_spread"]
numNotFound = 0
for aKey in reqKeyList:
if (aKey not in allClinDict.keys()):
numNotFound += 1
if (numNotFound > 0):
print " skipping checkTumorStage ... "
return (allClinDict)
pKey = getProperKey ( allClinDict, "bcr_patient_barcode" )
sKey = getProperKey ( allClinDict, "tumor_stage" )
tKey = getProperKey ( allClinDict, "primary_tumor_pathologic_spread" )
nKey = getProperKey ( allClinDict, "lymphnode_pathologic_spread" )
mKey = getProperKey ( allClinDict, "distant_metastasis_pathologic_spread" )
for ii in range(numClin):
aCode = allClinDict[pKey][ii]
curTumorStage = allClinDict[sKey][ii]
curT = allClinDict[tKey][ii]
curN = allClinDict[nKey][ii]
curM = allClinDict[mKey][ii]
# print " checking tumor stage for <%s> <%s> <%s> <%s> <%s> " % (
# aCode, curTumorStage, curN, curM, curT )
## removing this 15aug2014 ...
if ( 0 ):
curTumorStage = curTumorStage.upper()
curTumorStage = curTumorStage.strip()
if (curTumorStage != "NA"):
if (not curTumorStage.startswith("STAGE ")):
curTumorStage = "STAGE " + curTumorStage
# as of 09nov12, NOT attempting to derive tumor stage from T, N, and M
if (0):
# get AJCC-derived tumor stage, compare to DCC value, and decide
# which to use
ajccStage = getTumorStage(curT, curN, curM)
newStage = PreferredStage(curTumorStage, ajccStage)
allClinDict[sKey][ii] = newStage
# report
if (type(ajccStage) is list):
ajccString = ' OR '.join(ajccStage)
else:
ajccString = ajccStage
print aCode.upper() + ', TNM:' + curT.upper() + ' ' + curN.upper() + ' ' + curM.upper() + ', DCC Stage:' \
+ curTumorStage + ', AJCC Stage:' + ajccString + ', Comparison:' \
+ \
testTumorStage(curTumorStage, ajccStage) + \
', Will use: ' + newStage
return (allClinDict) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def checkVitalStatus(allClinDict):
vsKey = findProperKey ( allClinDict, "vital_status" )
bcKey = findProperKey ( allClinDict, "bcr_patient_barcode" )
if ( vsKey == "NO KEY" ):
print " skipping checkVitalStatus ... "
return (allClinDict)
print " running checkVitalStatus ... "
numClin = getNumPatients(allClinDict)
print " total number of patients : ", numClin
numLC = 0
numDC = 0
for ii in range(numClin):
aCode = allClinDict[bcKey][ii]
curStatus = allClinDict[vsKey][ii]
doChange = 1
try:
newStatus = curStatus
except:
try:
if (curStatus == 0):
newStatus = "Alive"
numLC += 1
elif (curStatus == 1):
newStatus = "Dead"
numDC += 1
except:
doChange = 0
if (doChange):
allClinDict[vsKey][ii] = newStatus
if (numLC + numDC > 0):
print " WARNING: changed some vital status fields ... %d %d " % (numLC, numDC)
return (allClinDict) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def updateAge(allClinDict):
pKey = findProperKey ( allClinDict, "bcr_patient_barcode" )
aKey = findProperKey ( allClinDict, "age_at_initial_pathologic_diagnosis" )
bKey = findProperKey ( allClinDict, "days_to_birth" )
print " running updateAge ... "
numClin = getNumPatients(allClinDict)
print " total number of patients : ", numClin
for ii in range(numClin):
try:
aCode = allClinDict[pKey][ii]
curAge = allClinDict[aKey][ii]
curD2B = allClinDict[bKey][ii]
newAge = float(0 - int(curD2B)) / DAYS_PER_YEAR
# now we want to limit the 'precision' to two decimal places
newAge = float(int((100. * newAge) + 0.49)) / 100.
if (abs(curAge - int(newAge)) > 0):
print " ERROR in updateAge ??? ", curAge, curD2B, newAge, aCode
allClinDict[aKey][ii] = newAge
except:
doNothing = 1
return (allClinDict) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def removeParens(oneKey):
print " in removeParens ... "
origUniqList = []
newUniqList = []
newKey = []
for aLabel in oneKey:
if (aLabel not in origUniqList):
origUniqList += [aLabel]
if (aLabel.find("(") >= 0):
print " --> found open paren ... at %d in <%s> " % (aLabel.find("("), aLabel)
bLabel = ""
copyOn = 1
for ii in range(len(aLabel)):
if (aLabel[ii] == "("):
copyOn = 0
if (copyOn):
bLabel += aLabel[ii]
if (aLabel[ii] == ")"):
copyOn = 1
if (bLabel.startswith("_")):
bLabel = bLabel[1:]
if (bLabel.endswith("_")):
bLabel = bLabel[:-1]
newKey += [bLabel]
if (bLabel not in newUniqList):
newUniqList += [bLabel]
else:
newKey += [aLabel]
if (aLabel not in newUniqList):
newUniqList += [aLabel]
print origUniqList
print newUniqList
if (len(newUniqList) == len(origUniqList)):
print " --> removing parenthetical strings "
print origUniqList
print newUniqList
return (newKey)
else:
print " NOT removing parenthetical strings "
return (oneKey) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def removeSpecialChars(oneKey):
okExceptions = ['4+']
# ran into a strange case here where most of the elements were strings
# like 'grade_1' but some were just integers like 3 :(
# so ... these next few blocks of code are TOTAL HACKS ...
numInt = 0
numNot = 0
aString = ''
aInt = 9999
for ii in range(len(oneKey)):
aLabel = str(oneKey[ii])
if (aLabel.upper() == "NA"):
continue
if (aLabel.upper() == "UNKNOWN"):
oneKey[ii] = "NA"
continue
try:
iVal = int(aLabel)
numInt += 1
aInt = iVal
except:
numNot += 1
aString = aLabel
print " number of integers = %d number NOT = %d " % (numInt, numNot)
if (numInt > 0 and numNot > 0):
# for now, we are just checking for 'grade' strings that are sometimes
# 'grade_3' and sometimes just '3'
if (aString.lower().startswith("grade_")):
for ii in range(len(oneKey)):
aLabel = str(oneKey[ii])
if (aLabel.upper() == "NA"):
continue
if (not aLabel.lower().startswith("grade_")):
try:
iVal = int(aLabel)
aString = "Grade_%d" % iVal
oneKey[ii] = aString
except:
print " FAILED to prepend grade ??? ", aLabel
sys.exit(-1)
# or if there are at least twice as many strings as integers, then we
# will cast the integers to strings ...
elif (numInt < (numNot / 2)):
for ii in range(len(oneKey)):
aLabel = str(oneKey[ii])
if (aLabel.upper() == "NA"):
continue
try:
iVal = int(aLabel)
oneKey[ii] = str(iVal)
except:
doNothing = 1
elif (aString not in okExceptions):
if ( 1 ):
print " WARNING ... something odd about this feature ... ", aInt, aString
print oneKey
## return ([])
## sys.exit(-1)
origUniqList = []
newUniqList = []
newKey = []
for aLabel in oneKey:
if (aLabel not in origUniqList):
origUniqList += [aLabel]
bLabel = ""
try:
for ii in range(len(aLabel)):
if (aLabel[ii] == ' '):
bLabel += "_"
elif (aLabel[ii] == "'"):
bLabel += "_"
elif (aLabel[ii] == '"'):
bLabel += "_"
elif (aLabel[ii] == ':'):
bLabel += "_"
elif (aLabel[ii] == '/'):
bLabel += "_"
# elif ( aLabel[ii] == '-' ):
## bLabel += "_"
elif (aLabel[ii] == '.'):
bLabel += "_"
elif (aLabel[ii] == ','):
bLabel += "_"
else:
bLabel += aLabel[ii]
except:
print " ERROR in removeSpecialChars ??? "
print " oneKey = <%s> " % (oneKey)
print " aLabel = <%s> " % (aLabel)
sys.exit(-1)
ii = bLabel.find("__")
while (ii >= 0):
bLabel = bLabel[:ii] + bLabel[ii + 1:]
ii = bLabel.find("__")
newKey += [bLabel]
if (bLabel not in newUniqList):
newUniqList += [bLabel]
print origUniqList
print newUniqList
if (len(newUniqList) == len(origUniqList)):
return (newKey)
else:
print " NOT removing parenthetical strings "
return (oneKey) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def getCommonPrefix(aLabel, bLabel):
nn = 0
while (aLabel[nn].lower() == bLabel[nn].lower()):
nn += 1
if (nn >= len(aLabel)):
return (aLabel[:nn])
if (nn >= len(bLabel)):
return (aLabel[:nn])
return (aLabel[:nn]) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def getCommonSuffix(aLabel, bLabel):
nn = -1
while (aLabel[nn].lower() == bLabel[nn].lower()):
nn -= 1
if (-nn > len(aLabel)):
return (aLabel)
if (-nn > len(bLabel)):
return (bLabel)
if (nn == -1):
return ("")
else:
return (aLabel[nn + 1:]) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def removeCommonPrefix(oneKey, labelList):
print " in removeCommonPrefix : ", labelList
madeChange = 0
nLabel = len(labelList)
for ii in range(nLabel):
for jj in range(ii + 1, nLabel):
commonPrefix = getCommonPrefix(labelList[ii], labelList[jj])
# if the commonPrefix is *ever* the entire string, then
# we cannot really use this ...
if (commonPrefix == labelList[ii]):
continue
if (commonPrefix == labelList[jj]):
continue
if (len(commonPrefix) > 4):
print ii, jj, commonPrefix
newKey = []
for cLabel in oneKey:
if (cLabel.lower().startswith(commonPrefix)):
dLabel = cLabel[len(commonPrefix):]
if (len(dLabel) < 4):
dLabel = cLabel
else:
madeChange += 1
else:
dLabel = cLabel
if (dLabel[0] == '_'):
dLabel = dLabel[1:]
newKey += [dLabel]
newList = []
for cLabel in labelList:
if (cLabel.lower().startswith(commonPrefix)):
dLabel = cLabel[len(commonPrefix):]
if (len(dLabel) < 4):
dLabel = cLabel
else:
madeChange += 1
else:
dLabel = cLabel
if (dLabel[0] == '_'):
dLabel = dLabel[1:]
newList += [dLabel]
if (len(labelList) == len(newList)):
labelList = newList
oneKey = newKey
if (madeChange > 0):
print " after removeCommonPrefix : ", madeChange, labelList
return (oneKey, labelList) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def removeCommonSuffix(oneKey, labelList):
print " in removeCommonSuffix : ", labelList
madeChange = 0
nLabel = len(labelList)
for ii in range(nLabel):
for jj in range(ii + 1, nLabel):
commonSuffix = getCommonSuffix(labelList[ii], labelList[jj])
# if the commonSuffix is *ever* the entire string, then
# we cannot really use this ...
if (commonSuffix == labelList[ii]):
continue
if (commonSuffix == labelList[jj]):
continue
if (len(commonSuffix) > 4):
print ii, jj, commonSuffix
newKey = []
for cLabel in oneKey:
if (cLabel.lower().endswith(commonSuffix)):
dLabel = cLabel[:-len(commonSuffix)]
if (len(dLabel) < 4):
dLabel = cLabel
else:
madeChange += 1
else:
dLabel = cLabel
if (dLabel[-1] == '_'):
dLabel = dLabel[:-1]
newKey += [dLabel]
newList = []
for cLabel in labelList:
if (cLabel.lower().endswith(commonSuffix)):
dLabel = cLabel[:-len(commonSuffix)]
if (len(dLabel) < 4):
dLabel = cLabel
else:
madeChange += 1
else:
dLabel = cLabel
if (dLabel[-1] == '_'):
dLabel = dLabel[:-1]
newList += [dLabel]
if (len(labelList) == len(newList)):
labelList = newList
oneKey = newKey
if (0):
print " removeCommonSuffix has not yet been fully tested ... "
print labelList
print oneKey
sys.exit(-1)
if (madeChange > 0):
print " after removeCommonSuffix : ", madeChange, labelList
return (oneKey, labelList) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def abbrevCategStrings(allClinDict):
print " "
print " in abbrevCategStrings ... "
print " "
keyList = allClinDict.keys()
keyList.sort()
for aKey in keyList:
if (aKey.find("bcr_patient_barcode") >= 0):
print " all barcodes : "
print allClinDict[aKey]
print " done "
continue
(keyType, nCount, nNA, nCard, labelList, labelCount) = miscClin.lookAtKey(allClinDict[aKey])
print aKey, keyType, nCount, nNA
if (keyType == "NOMINAL"):
# remove weird characters from the strings ...
print " calling removeSpecialChars ... <%s> " % (aKey)
allClinDict[aKey] = removeSpecialChars(allClinDict[aKey])
# if we get nothing back, then skip ...
if (allClinDict[aKey] == []):
print " WARNING ... got nothing back ??? ", aKey
continue
# otherwise, look at cardinality, type, etc ...
(keyType, nCount, nNA, nCard, labelList, labelCount) = miscClin.lookAtKey(allClinDict[aKey])
maxLen = 0
skipFlag = 0
for aLabel in labelList:
try:
maxLen = max(maxLen, len(aLabel))
except:
print " what is up with this key ??? ", aKey, labelList
skipFlag = 1
if (skipFlag):
continue
if (maxLen > 10):
## print aKey, labelList, maxLen
# first try at making the labels a bit shorter by removing
# parenthetical elements ...
allClinDict[aKey] = removeParens(allClinDict[aKey])
(keyType, nCount, nNA, nCard, labelList,
labelCount) = miscClin.lookAtKey(allClinDict[aKey])
maxLen = 0
for aLabel in labelList:
maxLen = max(maxLen, len(aLabel))
## print aKey, labelList, maxLen
# removing this step for now (04dec12)
if (0):
# next try to remove common prefixes or suffixes ...
if (maxLen > 10):
(allClinDict[aKey], labelList) = removeCommonPrefix(
allClinDict[aKey], labelList)
(allClinDict[aKey], labelList) = removeCommonSuffix(
allClinDict[aKey], labelList)
maxLen = 0
for aLabel in labelList:
maxLen = max(maxLen, len(aLabel))
## print aKey, labelList, maxLen
if (maxLen > 25):
print " --> strings are still rather long, but not sure what to do about this ... "
print labelList, maxLen
print " "
print " "
return (allClinDict) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def checkPrefix(labelList, aPrefix):
nLabel = len(labelList)
nHas = 0
for aLabel in labelList:
bLabel = aLabel.upper()
if (bLabel == "NA"):
nLabel -= 1
continue
if (bLabel.startswith(aPrefix)):
nHas += 1
if ((nHas + 2) >= nLabel): return (1)
return (0) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def translateArabic(aLabel, usePrefix):
# print " in translateArabic ... "
pLen = len(usePrefix)
bLabel = aLabel.upper()
if (bLabel.startswith(usePrefix)):
bLabel = bLabel[pLen:]
if (bLabel[0] == "_"):
bLabel = bLabel[1:]
bLen = len(bLabel)
found = 0
for iLen in range(bLen, 0, -1):
# print found, iLen, bLabel[:iLen]
if (not found):
try:
curN = int(bLabel[:iLen])
found = 1
except:
doNothing = 1
if (not found):
# X means that it could not be assessed, so returning NA
if (bLabel == "X"):
return ("NA")
# B means 'borderline' but returning NA ...
elif (bLabel == "B"):
return ("NA")
else:
print " ERROR ??? <%s> <%s> --> returning NA " % (bLabel, usePrefix)
return ("NA")
rLen = len(str(curN))
if (len(bLabel) > rLen):
bLabel = bLabel[rLen:]
if (bLabel == "A"):
curN += 0.2
elif (bLabel == "B"):
curN += 0.4
elif (bLabel == "C"):
curN += 0.6
else:
print " left over in translateArabic <%s> <%s> <%s> " % (bLabel, aLabel, usePrefix)
return (curN)
else:
return ("NA") | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def translateRoman(aLabel, usePrefix):
romanList = ["VIII", "III", "VII", "IV", "IX", "II", "VI", "I", "V", "X"]
numbrList = [8, 3, 7, 4, 9, 2, 6, 1, 5, 10]
pLen = len(usePrefix)
bLabel = aLabel.upper()
if (bLabel.startswith(usePrefix)):
bLabel = bLabel[pLen:]
if (bLabel[0] == "_"):
bLabel = bLabel[1:]
found = 0
for kk in range(len(romanList)):
if (not found):
if (bLabel.startswith(romanList[kk])):
found = 1
curKK = kk
curN = numbrList[kk]
curR = romanList[kk]
if (not found):
if (bLabel == "X"):
return ("NA")
elif (bLabel == "TIS"):
return ("NA")
else:
print " ERROR ??? ", bLabel, usePrefix
sys.exit(-1)
rLen = len(curR)
if (len(bLabel) > rLen):
bLabel = bLabel[rLen:]
if (bLabel == "A"):
curN += 0.2
elif (bLabel == "B"):
curN += 0.4
elif (bLabel == "C"):
curN += 0.6
else:
print " left over in translateRoman <%s> <%s> <%s> " % (bLabel, aLabel, usePrefix)
return (curN)
else:
return ("NA") | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def checkRomanNumerals(labelList, usePrefix):
skipList = ["_"]
stripList = ["A", "B", "C", "X", "0"]
romanList = ["I", "V", "X"]
pLen = len(usePrefix)
yesR = 0
notR = 0
for aLabel in labelList:
bLabel = aLabel.upper()
if (bLabel.startswith(usePrefix)):
bLabel = bLabel[pLen:]
if (bLabel[-1] in stripList):
bLabel = bLabel[:-1]
for ii in range(len(bLabel)):
if (bLabel[ii] in romanList):
yesR += 1
else:
if (bLabel[ii] not in skipList):
notR += 1
# print " in checkRomanNumerals : ", yesR, notR
if (notR == 0):
return (1)
if (notR > yesR):
return (0)
if (yesR > 0):
print " ??? strange counts in checkRomanNumerals ??? "
return (1)
return (0) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def addNumericalFeatures(allClinDict):
print " "
print " "
print " in addNumericalFeatures ... "
keyList = allClinDict.keys()
keyList.sort()
# CAREFUL: add on things only at the end of this list ...
prefixList = ["T", "N", "M", "STAGE", "GRADE", "G", "PT"]
nPrefix = len(prefixList)
prefixBits = [0] * nPrefix
for aKey in keyList:
if (aKey == "bcr_patient_barcode"):
continue
(keyType, nCount, nNA, nCard, labelList,
labelCount) = miscClin.lookAtKey(allClinDict[aKey])
if (keyType == "NOMINAL"):
if (nCard > 2 and nCard < 15):
tmpKey = aKey.lower()
if (tmpKey.find("stage") >= 0 or tmpKey.find("grade") >= 0 or
tmpKey.find("pathologic_spread") >= 0):
print " considering this categorical feature ... ", aKey, keyType, nCard, labelList, labelCount
for iP in range(nPrefix):
aPrefix = prefixList[iP]
prefixBits[iP] = checkPrefix(labelList, aPrefix)
# if the 'GRADE' bit gets set, then unset the 'G' bit
if (prefixBits[4]):
prefixBits[5] = 0
# print prefixBits
usePrefix = ""
if (sum(prefixBits) == 1):
for iP in range(nPrefix):
if (prefixBits[iP]):
usePrefix = prefixList[iP]
elif (sum(prefixBits) > 1):
print " ERROR ??? how can it have multiple prefix bits ON ??? "
sys.exit(-1)
# print " usePrefix <%s> " % usePrefix
isRoman = checkRomanNumerals(labelList, usePrefix)
# print " isRoman = %d " % isRoman
if (aKey[1] == ":"):
tokenList = aKey.split(':')
newLabel = "N:" + \
tokenList[1] + ":" + tokenList[2] + "_derived"
for ii in range(3, len(tokenList)):
newLabel += ":" + tokenList[ii]
else:
newLabel = "N:CLIN:" + aKey + "_derived"
if (newLabel in allClinDict.keys()):
print " this feature label already exists ??? ", newLabel
sys.exit(-1)
curV = allClinDict[aKey]
numClin = len(curV)
tmpV = [0] * numClin
for kk in range(numClin):
if (curV[kk] == "NA"):
tmpV[kk] = "NA"
elif (isRoman):
tmpV[kk] = translateRoman(curV[kk], usePrefix)
else:
tmpV[kk] = translateArabic(curV[kk], usePrefix)
if (0):
if (tmpV[kk] == 0):
print " why is tmpV[kk] still ZERO ??? ", kk, numClin, curV[kk], usePrefix, tmpV[kk]
numNA = 0
notNA = 0
for kk in range(numClin):
if (tmpV[kk] == "NA"):
numNA += 1
else:
notNA += 1
if (numNA > 10 * notNA):
print " --> NOT adding this new feature <%s> " % newLabel, list(set(tmpV)), numNA, notNA, usePrefix, isRoman
else:
print " --> ADDING new feature !!! <%s> " % newLabel, list(set(tmpV)), numNA, notNA, usePrefix, isRoman
allClinDict[newLabel] = tmpV
print " "
print " "
print " "
return (allClinDict) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def getMappingDict(featName, auxName):
mapDict = {}
if (featName[1] == ':'):
if (featName[6] == ':'):
tokenList = featName.split(':')
tmpFeatName = tokenList[2]
else:
tmpFeatName = featName
try:
mapFilename = "../" + auxName + "/" + tmpFeatName + ".map"
fh = file(mapFilename)
firstLine = 1
for aLine in fh:
aLine = aLine.strip()
## aLine = aLine.upper()
tokenList = aLine.split('\t')
if (firstLine):
if (tokenList[0].upper() == tmpFeatName.upper()):
numNew = len(tokenList) - 1
newNames = tokenList[1:]
print newNames
firstLine = 0
else:
print " ERROR ??? invalid mapping file ??? "
print mapFilename
print tokenList
print tmpFeatName
print " FAILING out of TRY "
sys.exit(-1)
else:
mapDict[str(tokenList[0])] = tokenList[1:]
fh.close()
print " mapping dictionary read from <%s> : " % mapFilename
print mapDict
print " "
return (mapDict, newNames)
except:
return (mapDict, []) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def getMapping ( mapDict, curV, ii ):
for k in mapDict.keys():
if ( k.lower() == curV.lower() ):
return ( mapDict[k][ii] )
print " FAILED TO GET MAPPING ??? ", curV, ii
print mapDict
sys.exit(-1) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def addDerivedFeatures(allClinDict, auxName):
print " "
print " "
print " in addDerivedFeatures ... "
keyList = allClinDict.keys()
keyList.sort()
for aKey in keyList:
if (aKey == "bcr_patient_barcode"):
continue
(keyType, nCount, nNA, nCard, labelList, labelCount) = miscClin.lookAtKey(allClinDict[aKey])
print " considering key <%s> " % (aKey), keyType, nCard
if (keyType == "NOMINAL"):
if (nCard > 2 and nCard < 25):
tmpKey = aKey.lower()
tmpList = []
for aLabel in labelList:
tmpL = str(aLabel)
if (tmpL not in tmpList):
tmpList += [tmpL]
labelList = tmpList
if (1):
print " considering this categorical feature ... ", aKey, keyType, nCard, labelList, labelCount
(mapDict, newNames) = getMappingDict(aKey, auxName)
# if there is no mapping file, then we won't be making any
# new features ...
if (len(newNames) == 0):
continue
# sanity check ...
if (0):
for bKey in mapDict.keys():
if ( stringInList_CaseInsens ( bKey, labelList ) ):
print " ERROR ??? mapping does not match this feature ??? "
print mapDict
print labelList
sys.exit(-1)
if (1):
for bLabel in labelList:
try:
if ( not stringInList_CaseInsens ( bLabel, mapDict.keys() ) ):
print " ************************************************** "
print " ERROR ??? feature value not in mapDict ??? ", bLabel
print " labelList : ", labelList
print " mapDict : ", mapDict
print " --> WILL NOT ADD ANY DERIVED FEATURES AT THIS TIME "
print " ************************************************** "
continue
# sys.exit(-1)
except:
doNothing = 1
# if there is no mapping file, then we won't be making any
# new features ...
if (len(newNames) == 0):
continue
# but if we do have one or more mappings, then we need
# to create those features ...
for ithName in range(len(newNames)):
aName = newNames[ithName]
print " looping over %d mappings ... " % len(newNames), ithName, aName
# the first thing we need to figure out is whether this is another
# categorical feature, or a numerical one ...
isNum = 1
uVec = []
for bKey in mapDict.keys():
curVal = mapDict[bKey][ithName]
if (curVal == "NA"):
continue
if ( stringInList_CaseInsens ( curVal, uVec ) ):
uVec += [curVal]
try:
fVal = float(curVal)
except:
isNum = 0
print " is numerical ??? ", isNum
if (len(uVec) == 1):
print " mapping to a constant ??? "
sys.exit(-1)
elif (len(uVec) == 2):
print " mapping is binary "
# if the mapping produces a binary feature, then
# over-ride the numerical feature
if (isNum):
print " over-riding the fact that the features LOOKS numerical ... "
isNum = 0
if (aName[1] == ":"):
if (aName[0] == "N"):
if (not isNum):
print " ERROR ??? new feature does not look to be numerical ???? "
print aName, uVec
sys.exit(-1)
# start setting up the new feature ...
newLabel = aName
if (newLabel in allClinDict.keys()):
print " this feature label already exists ??? ", newLabel
sys.exit(-1)
curV = allClinDict[aKey]
numClin = len(curV)
tmpV = [0] * numClin
for kk in range(numClin):
if (curV[kk].upper() == "NA"):
tmpV[kk] = "NA"
else:
try:
tmpV[kk] = getMapping ( mapDict, curV[kk], ithName )
## tmpV[kk] = mapDict[curV[kk]][ithName]
except:
print " ERROR ??? failed to map ??? setting to NA but MUST FIX !!! "
print kk, curV[kk], ithName
print mapDict
if (1):
tmpV[kk] = "NA"
else:
sys.exit(-1)
numNA = 0
notNA = 0
for kk in range(numClin):
if (tmpV[kk] == "NA"):
numNA += 1
else:
notNA += 1
if (numNA > 10 * notNA):
print " --> NOT adding this new feature <%s> " % newLabel, list(set(tmpV)), numNA, notNA
else:
print " --> ADDING new feature !!! <%s> " % newLabel, list(set(tmpV)), numNA, notNA
allClinDict[newLabel] = tmpV
print " "
print " "
print " "
print " RETURNING from addDerivedFeatures ... "
return (allClinDict) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def addIndicatorFeatures(allClinDict):
magicStrings = ["patient", "person", "vital", "surviv", "race", "ethnic",
"prior", "gender", "age_at", "ageat", "radiation", "chemo",
"therapy", "treat", "performance", "days_to_", "daysto",
"year_of", "yearof", "surgical", "recurrence", "pregnancies"]
keyList = allClinDict.keys()
keyList.sort()
for aKey in keyList:
if (aKey == "bcr_patient_barcode"):
continue
(keyType, nCount, nNA, nCard, labelList,
labelCount) = miscClin.lookAtKey(allClinDict[aKey])
if (keyType == "NOMINAL"):
if (nCard > 2 and nCard < 27):
print " "
print " "
print " in addIndicatorFeatures ... ", aKey, keyType, nCard, labelList, labelCount
for aLabel in labelList:
# sometimes even though we have a "categorical" feature, some of the
# categories appear to be integers or floating point values
# ...
if (type(aLabel) is float):
print " we seem to have a floating point value ??? ", aLabel
iVal = int(aLabel + 0.001)
xVal = float(aLabel) - iVal
print iVal, xVal
if (abs(xVal) < 0.001):
aLabel = "%d" % iVal
else:
aLabel = str(aLabel)
elif (type(aLabel) is int):
iVal = int(aLabel)
aLabel = "%d" % iVal
print " "
## print aKey, aLabel
try:
# 012345678901234567890123456789...
# C:CLIN:<label>
# C:CLIN:<label>:a:b:c:d:e
if (aKey[1] == ":" and aKey[6] == ":"):
# if this feature name already has a prefix (eg
# "C:CLIN:")
featType = aKey[2:7]
i1 = aKey[7:].find(':')
if (i1 < 0):
# if there are no further ':'
firstName = aKey[7:]
secondName = ":::::"
else:
# if there are ...
firstName = aKey[7:7 + i1]
secondName = aKey[7 + i1 + 1:]
print " (a) got to here ... ", featType, aLabel, firstName, secondName
newLabel = "B:" + featType + \
"I(" + aLabel + "|" + firstName + ")" + \
secondName
print " (b) got to here ... ", newLabel
if (newLabel.find("|):") > 0):
print " (a) BAILING !!!! ", newLabel
sys.exit(-1)
else:
# here we really need to have some way to guess whether this
# should be a CLIN or a SAMP feature ...
typeString = "UNK"
for aString in magicStrings:
if (aKey.find(aString) >= 0):
typeString = "CLIN"
if (typeString == "UNK"):
print " defaulting to type SAMP for this feature : <%s> " % (aKey)
typeString = "SAMP"
print " (c) got to here ... ", typeString, aLabel
newLabel = "B:" + typeString + ":" + \
"I(" + aLabel + "|" + aKey + ")"
except:
print " (b) BAILING !!! "
print " ERROR in addIndicatorFeatures ??? ", aLabel, aKey
sys.exit(-1)
# make sure there are no blanks ...
newLabel = tsvIO.replaceBlanks(newLabel, "_")
if (newLabel in allClinDict.keys()):
print " this indicator variable already exists so I will not make a new one ... ", newLabel
continue
curV = allClinDict[aKey]
numClin = len(curV)
tmpV = [0] * numClin
print " ... looping over %d values ... default new value is zero " % (numClin)
for kk in range(numClin):
print kk, allClinDict[aKey][kk], aLabel, type(allClinDict[aKey][kk]), type(aLabel)
if (allClinDict[aKey][kk] == "NA"):
tmpV[kk] = "NA"
elif (str(allClinDict[aKey][kk]).lower() == str(aLabel).lower()):
tmpV[kk] = 1
print " adding new feature : ", newLabel
allClinDict[newLabel] = tmpV
return (allClinDict) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def addPairwiseIndicatorFeatures(allClinDict):
magicStrings = ["patient", "person", "vital", "surviv", "race", "ethnic",
"prior", "gender", "age_at", "ageat", "radiation", "chemo",
"therapy", "treat", "performance", "days_to_", "daysto",
"year_of", "yearof", "surgical", "recurrence", "pregnancies"]
print " "
print " "
keyList = allClinDict.keys()
keyList.sort()
for aKey in keyList:
if (aKey == "bcr_patient_barcode"):
continue
(keyType, nCount, nNA, nCard, labelList,
labelCount) = miscClin.lookAtKey(allClinDict[aKey])
if (keyType == "NOMINAL"):
# we do this only for categorical features with 3-9 categories
if (nCard > 2 and nCard < 10):
print " "
print " in addPairwiseIndicatorFeatures ... ", aKey, keyType, nCard, labelList, labelCount
for ak in range(len(labelList)):
aLabel = labelList[ak]
for bk in range(ak + 1, len(labelList)):
bLabel = labelList[bk]
print " aLabel=<%s> bLabel=<%s> " % (aLabel, bLabel)
try:
if (aKey[1] == ":" and aKey[6] == ":"):
i1 = aKey[7:].find(':')
if (i1 < 0):
i1 = len(aKey)
i2 = len(aKey)
else:
i1 = i1 + 7
i2 = aKey[(i1 + 1):].find(':')
if (i2 < 0):
i2 = len(aKey)
if (i2 > 0 and i2 < len(aKey)):
newLabel = "B:" + \
aKey[
2:7] + "I(" + aLabel + "," + bLabel + "|" + aKey[7:i1] + ")" + aKey[i2:]
else:
newLabel = "B:" + \
aKey[
2:7] + "I(" + aLabel + "," + bLabel + "|" + aKey[7:i1] + ")" + "::::"
else:
# here we really need to have some way to guess whether this
# should be a CLIN or a SAMP feature ...
typeString = "UNK"
for aString in magicStrings:
if (aKey.find(aString) >= 0):
typeString = "CLIN"
if (typeString == "UNK"):
print " defaulting to type SAMP for this feature : <%s> " % (aKey)
typeString = "SAMP"
newLabel = "B:" + typeString + ":" + \
"I(" + aLabel + "," + bLabel + "|" + aKey + ")" + \
"::::"
except:
print " NOT continuing in addPairwiseIndicatorFeatures !!! ", aLabel, bLabel, aKey
continue
# make sure there are no blanks ...
newLabel = tsvIO.replaceBlanks(newLabel, "_")
print " --> new label: <%s> " % newLabel
if (newLabel in allClinDict.keys()):
print " this indicator variable already exists so I will not make a new one ... ", newLabel
continue
curV = allClinDict[aKey]
numClin = len(curV)
tmpV = ["NA"] * numClin
for kk in range(numClin):
if (allClinDict[aKey][kk].lower() == aLabel.lower()):
tmpV[kk] = 1
elif (allClinDict[aKey][kk].lower() == bLabel.lower()):
tmpV[kk] = 0
print " adding new feature : ", newLabel
# print tmpV
allClinDict[newLabel] = tmpV
return (allClinDict) | cancerregulome/gidget | [
6,
3,
6,
11,
1383861509
] |
def __init__(self, client, config, serializer, deserializer):
self._client = client
self._serialize = serializer
self._deserialize = deserializer
self._config = config | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def begin_delete(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_long_running_output(pipeline_response):
if cls:
return cls(pipeline_response, None, {}) | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def _create_or_update_initial(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
parameters, # type: "_models.ApplicationGateway"
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def begin_create_or_update(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
parameters, # type: "_models.ApplicationGateway"
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_long_running_output(pipeline_response):
deserialized = self._deserialize('ApplicationGateway', pipeline_response)
if cls:
return cls(pipeline_response, deserialized, {})
return deserialized | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def _update_tags_initial(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
parameters, # type: "_models.TagsObject"
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def begin_update_tags(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
parameters, # type: "_models.TagsObject"
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_long_running_output(pipeline_response):
deserialized = self._deserialize('ApplicationGateway', pipeline_response)
if cls:
return cls(pipeline_response, deserialized, {})
return deserialized | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def list(
self,
resource_group_name, # type: str
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def prepare_request(next_link=None):
# Construct headers
header_parameters = {} # type: Dict[str, Any]
header_parameters['Accept'] = self._serialize.header("accept", accept, 'str')
if not next_link:
# Construct URL
url = self.list.metadata['url'] # type: ignore
path_format_arguments = {
'resourceGroupName': self._serialize.url("resource_group_name", resource_group_name, 'str'),
'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str'),
}
url = self._client.format_url(url, **path_format_arguments)
# Construct parameters
query_parameters = {} # type: Dict[str, Any]
query_parameters['api-version'] = self._serialize.query("api_version", api_version, 'str')
request = self._client.get(url, query_parameters, header_parameters)
else:
url = next_link
query_parameters = {} # type: Dict[str, Any]
request = self._client.get(url, query_parameters, header_parameters)
return request | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_next(next_link=None):
request = prepare_request(next_link)
pipeline_response = self._client._pipeline.run(request, stream=False, **kwargs)
response = pipeline_response.http_response
if response.status_code not in [200]:
map_error(status_code=response.status_code, response=response, error_map=error_map)
raise HttpResponseError(response=response, error_format=ARMErrorFormat)
return pipeline_response | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def list_all(
self,
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def prepare_request(next_link=None):
# Construct headers
header_parameters = {} # type: Dict[str, Any]
header_parameters['Accept'] = self._serialize.header("accept", accept, 'str')
if not next_link:
# Construct URL
url = self.list_all.metadata['url'] # type: ignore
path_format_arguments = {
'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str'),
}
url = self._client.format_url(url, **path_format_arguments)
# Construct parameters
query_parameters = {} # type: Dict[str, Any]
query_parameters['api-version'] = self._serialize.query("api_version", api_version, 'str')
request = self._client.get(url, query_parameters, header_parameters)
else:
url = next_link
query_parameters = {} # type: Dict[str, Any]
request = self._client.get(url, query_parameters, header_parameters)
return request | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_next(next_link=None):
request = prepare_request(next_link)
pipeline_response = self._client._pipeline.run(request, stream=False, **kwargs)
response = pipeline_response.http_response
if response.status_code not in [200]:
map_error(status_code=response.status_code, response=response, error_map=error_map)
raise HttpResponseError(response=response, error_format=ARMErrorFormat)
return pipeline_response | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def _start_initial(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def begin_start(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_long_running_output(pipeline_response):
if cls:
return cls(pipeline_response, None, {}) | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def _stop_initial(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def begin_stop(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_long_running_output(pipeline_response):
if cls:
return cls(pipeline_response, None, {}) | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def _backend_health_initial(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
expand=None, # type: Optional[str]
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def begin_backend_health(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
expand=None, # type: Optional[str]
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_long_running_output(pipeline_response):
deserialized = self._deserialize('ApplicationGatewayBackendHealth', pipeline_response)
if cls:
return cls(pipeline_response, deserialized, {})
return deserialized | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def _backend_health_on_demand_initial(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
probe_request, # type: "_models.ApplicationGatewayOnDemandProbe"
expand=None, # type: Optional[str]
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def begin_backend_health_on_demand(
self,
resource_group_name, # type: str
application_gateway_name, # type: str
probe_request, # type: "_models.ApplicationGatewayOnDemandProbe"
expand=None, # type: Optional[str]
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_long_running_output(pipeline_response):
deserialized = self._deserialize('ApplicationGatewayBackendHealthOnDemand', pipeline_response)
if cls:
return cls(pipeline_response, deserialized, {})
return deserialized | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def list_available_server_variables(
self,
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def list_available_request_headers(
self,
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def list_available_response_headers(
self,
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def list_available_waf_rule_sets(
self,
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def list_available_ssl_options(
self,
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def list_available_ssl_predefined_policies(
self,
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def prepare_request(next_link=None):
# Construct headers
header_parameters = {} # type: Dict[str, Any]
header_parameters['Accept'] = self._serialize.header("accept", accept, 'str')
if not next_link:
# Construct URL
url = self.list_available_ssl_predefined_policies.metadata['url'] # type: ignore
path_format_arguments = {
'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str'),
}
url = self._client.format_url(url, **path_format_arguments)
# Construct parameters
query_parameters = {} # type: Dict[str, Any]
query_parameters['api-version'] = self._serialize.query("api_version", api_version, 'str')
request = self._client.get(url, query_parameters, header_parameters)
else:
url = next_link
query_parameters = {} # type: Dict[str, Any]
request = self._client.get(url, query_parameters, header_parameters)
return request | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_next(next_link=None):
request = prepare_request(next_link)
pipeline_response = self._client._pipeline.run(request, stream=False, **kwargs)
response = pipeline_response.http_response
if response.status_code not in [200]:
map_error(status_code=response.status_code, response=response, error_map=error_map)
raise HttpResponseError(response=response, error_format=ARMErrorFormat)
return pipeline_response | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_ssl_predefined_policy(
self,
predefined_policy_name, # type: str
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def __init__(self, client, config, serializer, deserializer) -> None:
self._client = client
self._serialize = serializer
self._deserialize = deserializer
self._config = config | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def prepare_request(next_link=None):
# Construct headers
header_parameters = {} # type: Dict[str, Any]
header_parameters['Accept'] = self._serialize.header("accept", accept, 'str')
if not next_link:
# Construct URL
url = self.list.metadata['url'] # type: ignore
path_format_arguments = {
'location': self._serialize.url("location", location, 'str'),
'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str'),
}
url = self._client.format_url(url, **path_format_arguments)
# Construct parameters
query_parameters = {} # type: Dict[str, Any]
query_parameters['api-version'] = self._serialize.query("api_version", api_version, 'str')
request = self._client.get(url, query_parameters, header_parameters)
else:
url = next_link
query_parameters = {} # type: Dict[str, Any]
request = self._client.get(url, query_parameters, header_parameters)
return request | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def load(cls, options):
"""Creates a project and loads it's configuration immediately"""
project = cls()
project.load_settings(options)
return project | ravenac95/virtstrap | [
7,
2,
7,
3,
1330379410
] |
def load_settings(self, options):
# Check if project directory is specified
project_dir = getattr(options, 'project_dir', None)
if not project_dir:
project_dir = self._find_project_dir()
project_dir = os.path.abspath(project_dir)
self._project_dir = project_dir
config_file = os.path.join(project_dir, options.config_file)
config = VirtstrapConfig.from_file(config_file,
profiles=options.profiles)
processor = ProjectNameProcessor(project_dir)
project_name = config.process_section('project_name', processor)
self._project_name = project_name
self._config = config
self._config_file = config_file
self._options = options | ravenac95/virtstrap | [
7,
2,
7,
3,
1330379410
] |
def name(self):
return self._project_name | ravenac95/virtstrap | [
7,
2,
7,
3,
1330379410
] |
def config_file(self):
if not os.path.isfile(self._config_file):
return None
return self._config_file | ravenac95/virtstrap | [
7,
2,
7,
3,
1330379410
] |
def path(self, *paths):
"""Create a path relative to the project"""
return os.path.join(self._project_dir, *paths) | ravenac95/virtstrap | [
7,
2,
7,
3,
1330379410
] |
def bin_path(self, *paths):
"""Create a path relative to the virtstrap-dir's bin directory"""
bin_py = 'bin'
if sys.platform == 'win32':
bin_py = 'Scripts'
return self.env_path(bin_py, *paths) | ravenac95/virtstrap | [
7,
2,
7,
3,
1330379410
] |
def config(self, section):
"""Grabs processed section data"""
return self._config.processed(section) | ravenac95/virtstrap | [
7,
2,
7,
3,
1330379410
] |
def find_project_dir(current_dir=None):
"""Finds the project directory for the current directory"""
current_dir = current_dir or os.path.abspath(os.curdir)
if VIRTSTRAP_DIR in os.listdir(current_dir):
vs_dir = os.path.join(current_dir, VIRTSTRAP_DIR)
if os.path.islink(vs_dir) or os.path.isdir(vs_dir):
return current_dir
parent_dir = os.path.abspath(os.path.join(current_dir, os.pardir))
if parent_dir == current_dir:
raise NoProjectFound('No project found')
return find_project_dir(parent_dir) | ravenac95/virtstrap | [
7,
2,
7,
3,
1330379410
] |
def __init__(self, project_dir):
self._project_dir = os.path.abspath(project_dir) | ravenac95/virtstrap | [
7,
2,
7,
3,
1330379410
] |
def __init__(self, client, config, serializer, deserializer):
self._client = client
self._serialize = serializer
self._deserialize = deserializer
self._config = config | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get(
self,
configuration_profile_preference_name, # type: str
resource_group_name, # type: str
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def delete(
self,
resource_group_name, # type: str
configuration_profile_preference_name, # type: str
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def update(
self,
configuration_profile_preference_name, # type: str
resource_group_name, # type: str
parameters, # type: "models.ConfigurationProfilePreferenceUpdate"
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def list_by_resource_group(
self,
resource_group_name, # type: str
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def prepare_request(next_link=None):
# Construct headers
header_parameters = {} # type: Dict[str, Any]
header_parameters['Accept'] = 'application/json'
if not next_link:
# Construct URL
url = self.list_by_resource_group.metadata['url'] # type: ignore
path_format_arguments = {
'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str', min_length=1),
'resourceGroupName': self._serialize.url("resource_group_name", resource_group_name, 'str', max_length=90, min_length=1, pattern=r'^[-\w\._\(\)]+$'),
}
url = self._client.format_url(url, **path_format_arguments)
# Construct parameters
query_parameters = {} # type: Dict[str, Any]
query_parameters['api-version'] = self._serialize.query("api_version", api_version, 'str')
request = self._client.get(url, query_parameters, header_parameters)
else:
url = next_link
query_parameters = {} # type: Dict[str, Any]
request = self._client.get(url, query_parameters, header_parameters)
return request | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_next(next_link=None):
request = prepare_request(next_link)
pipeline_response = self._client._pipeline.run(request, stream=False, **kwargs)
response = pipeline_response.http_response
if response.status_code not in [200]:
error = self._deserialize(models.ErrorResponse, response)
map_error(status_code=response.status_code, response=response, error_map=error_map)
raise HttpResponseError(response=response, model=error, error_format=ARMErrorFormat)
return pipeline_response | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def list_by_subscription(
self,
**kwargs # type: Any | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def prepare_request(next_link=None):
# Construct headers
header_parameters = {} # type: Dict[str, Any]
header_parameters['Accept'] = 'application/json'
if not next_link:
# Construct URL
url = self.list_by_subscription.metadata['url'] # type: ignore
path_format_arguments = {
'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str', min_length=1),
}
url = self._client.format_url(url, **path_format_arguments)
# Construct parameters
query_parameters = {} # type: Dict[str, Any]
query_parameters['api-version'] = self._serialize.query("api_version", api_version, 'str')
request = self._client.get(url, query_parameters, header_parameters)
else:
url = next_link
query_parameters = {} # type: Dict[str, Any]
request = self._client.get(url, query_parameters, header_parameters)
return request | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def get_next(next_link=None):
request = prepare_request(next_link)
pipeline_response = self._client._pipeline.run(request, stream=False, **kwargs)
response = pipeline_response.http_response
if response.status_code not in [200]:
error = self._deserialize(models.ErrorResponse, response)
map_error(status_code=response.status_code, response=response, error_map=error_map)
raise HttpResponseError(response=response, model=error, error_format=ARMErrorFormat)
return pipeline_response | Azure/azure-sdk-for-python | [
3526,
2256,
3526,
986,
1335285972
] |
def set_test_params(self):
self.setup_clean_chain = True
self.num_nodes = 1
self.supports_cli = False | syscoin/syscoin2 | [
164,
70,
164,
5,
1456717652
] |
def mine_chain(self):
self.log.info('Create some old blocks')
address = self.nodes[0].get_deterministic_priv_key().address
for t in range(TIME_GENESIS_BLOCK, TIME_GENESIS_BLOCK + 200 * 600, 600):
# ten-minute steps from genesis block time
self.nodes[0].setmocktime(t)
self.nodes[0].generatetoaddress(1, address)
assert_equal(self.nodes[0].getblockchaininfo()['blocks'], 200) | syscoin/syscoin2 | [
164,
70,
164,
5,
1456717652
] |
def _test_getchaintxstats(self):
self.log.info("Test getchaintxstats")
# Test `getchaintxstats` invalid extra parameters
assert_raises_rpc_error(-1, 'getchaintxstats', self.nodes[0].getchaintxstats, 0, '', 0)
# Test `getchaintxstats` invalid `nblocks`
assert_raises_rpc_error(-1, "JSON value is not an integer as expected", self.nodes[0].getchaintxstats, '')
assert_raises_rpc_error(-8, "Invalid block count: should be between 0 and the block's height - 1", self.nodes[0].getchaintxstats, -1)
assert_raises_rpc_error(-8, "Invalid block count: should be between 0 and the block's height - 1", self.nodes[0].getchaintxstats, self.nodes[0].getblockcount())
# Test `getchaintxstats` invalid `blockhash`
assert_raises_rpc_error(-1, "JSON value is not a string as expected", self.nodes[0].getchaintxstats, blockhash=0)
assert_raises_rpc_error(-8, "blockhash must be of length 64 (not 1, for '0')", self.nodes[0].getchaintxstats, blockhash='0')
assert_raises_rpc_error(-8, "blockhash must be hexadecimal string (not 'ZZZ0000000000000000000000000000000000000000000000000000000000000')", self.nodes[0].getchaintxstats, blockhash='ZZZ0000000000000000000000000000000000000000000000000000000000000')
assert_raises_rpc_error(-5, "Block not found", self.nodes[0].getchaintxstats, blockhash='0000000000000000000000000000000000000000000000000000000000000000')
blockhash = self.nodes[0].getblockhash(200)
self.nodes[0].invalidateblock(blockhash)
assert_raises_rpc_error(-8, "Block is not in main chain", self.nodes[0].getchaintxstats, blockhash=blockhash)
self.nodes[0].reconsiderblock(blockhash)
chaintxstats = self.nodes[0].getchaintxstats(nblocks=1)
# 200 txs plus genesis tx
assert_equal(chaintxstats['txcount'], 201)
# tx rate should be 1 per 10 minutes, or 1/600
# we have to round because of binary math
assert_equal(round(chaintxstats['txrate'] * 600, 10), Decimal(1))
b1_hash = self.nodes[0].getblockhash(1)
b1 = self.nodes[0].getblock(b1_hash)
b200_hash = self.nodes[0].getblockhash(200)
b200 = self.nodes[0].getblock(b200_hash)
time_diff = b200['mediantime'] - b1['mediantime']
chaintxstats = self.nodes[0].getchaintxstats()
assert_equal(chaintxstats['time'], b200['time'])
assert_equal(chaintxstats['txcount'], 201)
assert_equal(chaintxstats['window_final_block_hash'], b200_hash)
assert_equal(chaintxstats['window_final_block_height'], 200)
assert_equal(chaintxstats['window_block_count'], 199)
assert_equal(chaintxstats['window_tx_count'], 199)
assert_equal(chaintxstats['window_interval'], time_diff)
assert_equal(round(chaintxstats['txrate'] * time_diff, 10), Decimal(199))
chaintxstats = self.nodes[0].getchaintxstats(blockhash=b1_hash)
assert_equal(chaintxstats['time'], b1['time'])
assert_equal(chaintxstats['txcount'], 2)
assert_equal(chaintxstats['window_final_block_hash'], b1_hash)
assert_equal(chaintxstats['window_final_block_height'], 1)
assert_equal(chaintxstats['window_block_count'], 0)
assert 'window_tx_count' not in chaintxstats
assert 'window_interval' not in chaintxstats
assert 'txrate' not in chaintxstats | syscoin/syscoin2 | [
164,
70,
164,
5,
1456717652
] |
def _test_getblockheader(self):
node = self.nodes[0]
assert_raises_rpc_error(-8, "hash must be of length 64 (not 8, for 'nonsense')", node.getblockheader, "nonsense")
assert_raises_rpc_error(-8, "hash must be hexadecimal string (not 'ZZZ7bb8b1697ea987f3b223ba7819250cae33efacb068d23dc24859824a77844')", node.getblockheader, "ZZZ7bb8b1697ea987f3b223ba7819250cae33efacb068d23dc24859824a77844")
assert_raises_rpc_error(-5, "Block not found", node.getblockheader, "0cf7bb8b1697ea987f3b223ba7819250cae33efacb068d23dc24859824a77844")
besthash = node.getbestblockhash()
secondbesthash = node.getblockhash(199)
header = node.getblockheader(blockhash=besthash)
assert_equal(header['hash'], besthash)
assert_equal(header['height'], 200)
assert_equal(header['confirmations'], 1)
assert_equal(header['previousblockhash'], secondbesthash)
assert_is_hex_string(header['chainwork'])
assert_equal(header['nTx'], 1)
assert_is_hash_string(header['hash'])
assert_is_hash_string(header['previousblockhash'])
assert_is_hash_string(header['merkleroot'])
assert_is_hash_string(header['bits'], length=None)
assert isinstance(header['time'], int)
assert isinstance(header['mediantime'], int)
assert isinstance(header['nonce'], int)
assert isinstance(header['version'], int)
assert isinstance(int(header['versionHex'], 16), int)
assert isinstance(header['difficulty'], Decimal) | syscoin/syscoin2 | [
164,
70,
164,
5,
1456717652
] |
def _test_getnetworkhashps(self):
hashes_per_second = self.nodes[0].getnetworkhashps()
# This should be 2 hashes every 10 minutes or 1/300
assert abs(hashes_per_second * 300 - 1) < 0.0001 | syscoin/syscoin2 | [
164,
70,
164,
5,
1456717652
] |
def _test_waitforblockheight(self):
self.log.info("Test waitforblockheight")
node = self.nodes[0]
node.add_p2p_connection(P2PInterface())
current_height = node.getblock(node.getbestblockhash())['height']
# Create a fork somewhere below our current height, invalidate the tip
# of that fork, and then ensure that waitforblockheight still
# works as expected.
#
# (Previously this was broken based on setting
# `rpc/blockchain.cpp:latestblock` incorrectly.)
#
b20hash = node.getblockhash(20)
b20 = node.getblock(b20hash)
def solve_and_send_block(prevhash, height, time):
b = create_block(prevhash, create_coinbase(height), time)
b.solve()
node.p2p.send_message(msg_block(b))
node.p2p.sync_with_ping()
return b
b21f = solve_and_send_block(int(b20hash, 16), 21, b20['time'] + 1)
b22f = solve_and_send_block(b21f.sha256, 22, b21f.nTime + 1)
node.invalidateblock(b22f.hash)
def assert_waitforheight(height, timeout=2):
assert_equal(
node.waitforblockheight(height=height, timeout=timeout)['height'],
current_height)
assert_waitforheight(0)
assert_waitforheight(current_height - 1)
assert_waitforheight(current_height)
assert_waitforheight(current_height + 1) | syscoin/syscoin2 | [
164,
70,
164,
5,
1456717652
] |
def model_name(table_name):
if table_name in [
'vtm',
'vpi',
'vmp',
'vmpp',
'amp',
'ampp',
'gtin',
]:
return table_name.upper()
else:
return ''.join(tok.title() for tok in table_name.split('_')) | annapowellsmith/openpresc | [
91,
25,
91,
305,
1441229895
] |
def mock_get_coi_returning_coindex_around_coords(self, params_dict):
return json.loads(COINDEX_JSON) | csparpa/pyowm | [
746,
159,
746,
16,
1378111431
] |
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