def test_dump_index(self, api_paths):
myIo = IoAdapter(raiseExceptions=True)
containerList = myIo.readFile(
inputFilePath=str(api_paths['pathPdbxDictionary']))
dApi = DictionaryApi(containerList=containerList, consolidate=True)
print("Index = %r\n" % dApi.getItemNameList('pdbx_nmr_spectral_dim'))
print("Index = %r\n" %
dApi.getAttributeNameList('pdbx_nmr_spectral_dim'))
catIndex = dApi.getCategoryIndex()
print("Index = %r\n" % catIndex['pdbx_nmr_spectral_dim'])
assert catIndex['pdbx_nmr_spectral_dim'] is not None
def testDumpIndex(self):
"""Test case - dump methods for dictionary metadata"""
try:
myIo = IoAdapter(raiseExceptions=True)
self.__containerList = myIo.readFile(inputFilePath=self.__pathPdbxDictionary)
dApi = DictionaryApi(containerList=self.__containerList, consolidate=True, verbose=self.__verbose)
if self.__verbose:
dApi.dumpCategoryIndex(fh=self.__lfh)
logger.debug("Index = %r\n", dApi.getItemNameList("pdbx_nmr_spectral_dim"))
logger.debug("Index = %r\n", dApi.getAttributeNameList("pdbx_nmr_spectral_dim"))
catIndex = dApi.getCategoryIndex()
logger.debug("Index = %r\n", catIndex["pdbx_nmr_spectral_dim"])
self.assertIsNotNone(catIndex["pdbx_nmr_spectral_dim"])
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def test_markup_category_group(self, in_tmpdir, test_files, out_file_name,
groupSelectList):
oFile = out_file_name
rL = []
myIo = IoAdapter()
containerList = myIo.readFile(
str(test_files / "mmcif_pdbx_v5_next.dic"))
dApi = DictionaryApi(containerList=containerList, consolidate=True)
#
groupList = dApi.getCategoryGroups()
print('groupList %s\n' % groupList)
for groupName in groupList:
if groupSelectList and groupName not in groupSelectList:
continue
#
# Goup header details
#
rL.append("# Category Group %s" % groupName)
rL.append("")
rL.append("")
rL.append("%s" % dApi.getCategoryGroupDescription(groupName))
rL.append("")
rL.append("---")
rL.append("")
catNameList = dApi.getCategoryGroupCategories(groupName=groupName)
#
cList = self.__sortIgnoreCase(catNameList)
for catName in cList:
print('Group %s category %s\n' % (groupName, catName))
catDescription = dApi.getCategoryDescription(category=catName)
catExTupList = dApi.getCategoryExampleList(category=catName)
keyItemNameList = dApi.getCategoryKeyList(category=catName)
keyAttNameList = [
CifName.attributePart(k) for k in keyItemNameList
]
#
# Category header details
#
rL.append("## Category %s" % catName)
rL.append("")
rL.append("")
rL.append(" %s" % catDescription)
rL.append("")
rL.append("---")
rL.append("")
if catExTupList:
rL.extend(
self.__formatTupListInset(catExTupList, tab=' '))
#
# summary table
#
rL.append("")
rL.append("---")
rL.append("")
rL.append(
"| Attribute | Key | Required | Type | Units | Enumerated | Bounded |"
)
rL.append(
"| --------- | --- | -------- | ---- | ----- | ---------- | ------- |"
)
aList = self.__sortIgnoreCase(
dApi.getAttributeNameList(category=catName))
for attName in aList:
isKey = attName in keyAttNameList
attDescription = dApi.getDescription(category=catName,
attribute=attName)
attUnits = dApi.getUnits(category=catName,
attribute=attName)
attMandatory = dApi.getMandatoryCode(category=catName,
attribute=attName)
attTypeCode = dApi.getTypeCode(category=catName,
attribute=attName)
enumTupList = dApi.getEnumListWithDetail(category=catName,
attribute=attName)
if len(enumTupList) > 0:
isEnum = True
else:
isEnum = False
bL = dApi.getBoundaryList(category=catName,
attribute=attName)
if len(bL) > 0:
isBounded = True
else:
isBounded = False
rL.append(
'| %s | %s | %s | %s | %s | %s | %s |' %
(attName, self.__trB(isKey), attMandatory, attTypeCode,
attUnits, self.__trB(isEnum), self.__trB(isBounded)))
#
rL.append("")
rL.append("---")
rL.append("")
#
for attName in aList:
isKey = attName in keyAttNameList
attMandatory = dApi.getMandatoryCode(category=catName,
attribute=attName)
#
tN = '_' + catName + '.' + attName
if isKey:
tN = tN + ' (key)'
elif attMandatory.upper() in ['YES', 'Y']:
tN = tN + ' (required)'
#
rL.append("#### %s\n" % tN)
rL.append("")
attDescription = dApi.getDescription(category=catName,
attribute=attName)
rL.append(" %s\n" % attDescription)
rL.append("")
attUnits = dApi.getUnits(category=catName,
attribute=attName)
attTypeCode = dApi.getTypeCode(category=catName,
attribute=attName)
enumTupList = dApi.getEnumListWithDetail(category=catName,
attribute=attName)
if len(enumTupList) > 0:
rL.append("")
rL.append("---")
rL.append("")
rL.append("| Allowed Values | Detail |")
rL.append("| -------------- | ------ |")
for tup in enumTupList:
if tup[1] and len(tup[1]) > 0:
rL.append("| %s | %s |" % (tup[0], tup[1]))
else:
rL.append("| %s | %s |" % (tup[0], ' '))
rL.append("")
#
bL = dApi.getBoundaryList(category=catName,
attribute=attName)
btL = self.__processbounds(bL)
if len(btL) > 0:
tup = btL[0]
rL.append("")
rL.append("---")
rL.append("")
rL.append("| %s | %s |" % (tup[0], tup[1]))
#
rL.append("| ------------- | ------ |")
for tup in btL[1:]:
rL.append("| %s | %s |" % (tup[0], tup[1]))
rL.append("")
rL.append("")
with open(str(oFile), 'w') as ofh:
ofh.write('\n'.join(rL))
def __testScanRepo(self, contentType, scanType="full"):
"""Utility method to scan repo for data type and coverage content.
Using mock repos for tests.
"""
try:
containerList = self.__mU.doImport(self.__pathPdbxDictionary,
fmt="mmcif-dict")
dictApi = DictionaryApi(containerList=containerList,
consolidate=True,
verbose=True)
failedFilePath = os.path.join(
HERE, "test-output",
"%s-failed-list-%s.txt" % (contentType, scanType))
savedFilePath = os.path.join(
HERE, "test-output",
"%s-path-list-%s.txt" % (contentType, scanType))
scanDataFilePath = os.path.join(HERE, "test-output",
"%s-scan-data.pic" % (contentType))
dataCoverageFilePath = os.path.join(
HERE, "test-output",
"%s-scan-data-coverage-%s.json" % (contentType, scanType))
dataCoverageItemFilePath = os.path.join(
HERE, "test-output",
"%s-scan-data-item-coverage-%s.tdd" % (contentType, scanType))
dataTypeFilePath = os.path.join(
HERE, "test-output",
"%s-scan-data-type-%s.json" % (contentType, scanType))
#
###
categoryList = sorted(dictApi.getCategoryList())
dictSchema = {
catName: sorted(dictApi.getAttributeNameList(catName))
for catName in categoryList
}
attributeDataTypeD = OrderedDict()
for catName in categoryList:
aD = {}
for atName in dictSchema[catName]:
aD[atName] = dictApi.getTypeCode(catName, atName)
attributeDataTypeD[catName] = aD
###
#
sr = ScanRepoUtil(self.__cfgOb,
attributeDataTypeD=attributeDataTypeD,
numProc=self.__numProc,
chunkSize=self.__chunkSize,
fileLimit=self.__fileLimit,
workPath=self.__cachePath)
ok = sr.scanContentType(contentType,
scanType=scanType,
inputPathList=None,
scanDataFilePath=scanDataFilePath,
failedFilePath=failedFilePath,
saveInputFileListPath=savedFilePath)
self.assertTrue(ok)
ok = sr.evalScan(scanDataFilePath,
dataTypeFilePath,
evalType="data_type")
self.assertTrue(ok)
ok = sr.evalScan(scanDataFilePath,
dataCoverageFilePath,
evalType="data_coverage")
self.assertTrue(ok)
ok = sr.evalScanItem(scanDataFilePath, dataCoverageItemFilePath)
self.assertTrue(ok)
return ok
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def __testMarkupCategoryGroup(self, oFile, groupSelectList=None):
"""Test case - extract the content to be rendered -"""
startTime = time.time()
logger.debug("\nStarting at %s\n",
time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
try:
rL = []
myIo = IoAdapter()
containerList = myIo.readFile(self.__pathPdbxV50Dictionary)
dApi = DictionaryApi(containerList=containerList,
consolidate=True,
verbose=self.__verbose)
#
groupList = dApi.getCategoryGroups()
logger.debug("groupList %s\n", groupList)
for groupName in groupList:
if groupSelectList and groupName not in groupSelectList:
continue
#
# Goup header details
#
rL.append("# Category Group %s" % groupName)
rL.append("")
rL.append("")
rL.append("%s" % dApi.getCategoryGroupDescription(groupName))
rL.append("")
rL.append("---")
rL.append("")
catNameList = dApi.getCategoryGroupCategories(
groupName=groupName)
#
cList = self.__sortIgnoreCase(catNameList)
for catName in cList:
logger.debug("Group %s category %s\n", groupName, catName)
catDescription = dApi.getCategoryDescription(
category=catName)
catExTupList = dApi.getCategoryExampleList(
category=catName)
keyItemNameList = dApi.getCategoryKeyList(category=catName)
keyAttNameList = [
CifName.attributePart(k) for k in keyItemNameList
]
#
# Category header details
#
rL.append("## Category %s" % catName)
rL.append("")
rL.append("")
rL.append(" %s" % catDescription)
rL.append("")
rL.append("---")
rL.append("")
if catExTupList:
rL.extend(
self.__formatTupListInset(catExTupList,
tab=" "))
#
# summary table
#
rL.append("")
rL.append("---")
rL.append("")
rL.append(
"| Attribute | Key | Required | Type | Units | Enumerated | Bounded |"
)
rL.append(
"| --------- | --- | -------- | ---- | ----- | ---------- | ------- |"
)
aList = self.__sortIgnoreCase(
dApi.getAttributeNameList(category=catName))
for attName in aList:
isKey = attName in keyAttNameList
attDescription = dApi.getDescription(category=catName,
attribute=attName)
attUnits = dApi.getUnits(category=catName,
attribute=attName)
attMandatory = dApi.getMandatoryCode(category=catName,
attribute=attName)
attTypeCode = dApi.getTypeCode(category=catName,
attribute=attName)
enumTupList = dApi.getEnumListWithDetail(
category=catName, attribute=attName)
if enumTupList:
isEnum = True
else:
isEnum = False
bL = dApi.getBoundaryList(category=catName,
attribute=attName)
if bL:
isBounded = True
else:
isBounded = False
rL.append("| %s | %s | %s | %s | %s | %s | %s |" %
(attName, self.__trB(isKey), attMandatory,
attTypeCode, attUnits, self.__trB(isEnum),
self.__trB(isBounded)))
#
rL.append("")
rL.append("---")
rL.append("")
#
for attName in aList:
isKey = attName in keyAttNameList
attMandatory = dApi.getMandatoryCode(category=catName,
attribute=attName)
#
tN = "_" + catName + "." + attName
if isKey:
tN = tN + " (key)"
elif attMandatory.upper() in ["YES", "Y"]:
tN = tN + " (required)"
#
rL.append("#### %s\n" % tN)
rL.append("")
attDescription = dApi.getDescription(category=catName,
attribute=attName)
rL.append(" %s\n" % attDescription)
rL.append("")
attUnits = dApi.getUnits(category=catName,
attribute=attName)
attTypeCode = dApi.getTypeCode(category=catName,
attribute=attName)
enumTupList = dApi.getEnumListWithDetail(
category=catName, attribute=attName)
if enumTupList:
rL.append("")
rL.append("---")
rL.append("")
rL.append("| Allowed Values | Detail |")
rL.append("| -------------- | ------ |")
for tup in enumTupList:
if tup[1]:
rL.append("| %s | %s |" % (tup[0], tup[1]))
else:
rL.append("| %s | %s |" % (tup[0], " "))
rL.append("")
#
bL = dApi.getBoundaryList(category=catName,
attribute=attName)
btL = self.__processbounds(bL)
if btL:
tup = btL[0]
rL.append("")
rL.append("---")
rL.append("")
rL.append("| %s | %s |" % (tup[0], tup[1]))
#
rL.append("| ------------- | ------ |")
for tup in btL[1:]:
rL.append("| %s | %s |" % (tup[0], tup[1]))
rL.append("")
rL.append("")
with open(oFile, "w") as ofh:
ofh.write("\n".join(rL))
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
endTime = time.time()
logger.debug("\nCompleted at %s (%.2f seconds)",
time.strftime("%Y %m %d %H:%M:%S", time.localtime()),
endTime - startTime)