def Import(self):
print "EOOO"
s_t = ''
c_t = 'lab'
bucket = {}
pc = getToolByName(self.context, 'portal_catalog')
bsc = getToolByName(self.context, 'bika_setup_catalog')
# collect up all values into the bucket
for row in self.get_rows(3):
c_t = row['Client_title'] if row['Client_title'] else 'lab'
if c_t not in bucket:
bucket[c_t] = {}
s_t = row['SampleType_title'] if row['SampleType_title'] else s_t
if s_t not in bucket[c_t]:
bucket[c_t][s_t] = []
service = bsc(portal_type='AnalysisService', title=row['service'])
if not service:
service = bsc(portal_type='AnalysisService',
getKeyword=row['service'])
try:
service = service[0].getObject()
bucket[c_t][s_t].append({
'keyword': service.getKeyword(),
'min': row.get('min','0'),
'max': row.get('max','0'),
'minpanic': row.get('minpanic','0'),
'maxpanic': row.get('maxpanic','0'),
'error': row.get('error','0'),
})
except IndexError:
warning = "Error with service name %s on sheet %s. Service not uploaded."
logger.warning(warning, row.get('service', ''), self.sheetname)
# write objects.
for c_t in bucket:
if c_t == 'lab':
folder = self.context.bika_setup.bika_analysisspecs
else:
folder = pc(portal_type='Client', title=c_t)
if (not folder or len(folder) != 1):
logger.warn("Client %s not found. Omiting client specifications." % c_t)
continue
folder = folder[0].getObject()
for s_t in bucket[c_t]:
resultsrange = bucket[c_t][s_t]
sampletype = bsc(portal_type='SampleType', title=s_t)[0]
_id = folder.invokeFactory('AnalysisSpec', id=tmpID())
obj = folder[_id]
obj.edit(
title=sampletype.Title,
ResultsRange=resultsrange)
obj.setSampleType(sampletype.UID)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def setup_health_catalogs(portal):
# an item should belong to only one catalog.
# that way looking it up means first looking up *the* catalog
# in which it is indexed, as well as making it cheaper to index.
def addIndex(cat, *args):
try:
cat.addIndex(*args)
except:
pass
def addColumn(cat, col):
try:
cat.addColumn(col)
except:
pass
logger.info("Setup catalogs ...")
# bika_catalog
bc = getToolByName(portal, 'bika_catalog', None)
if not bc:
logger.warning('Could not find the bika_catalog tool.')
return
addIndex(bc, 'getClientTitle', 'FieldIndex')
addIndex(bc, 'getPatientID', 'FieldIndex')
addIndex(bc, 'getPatientUID', 'FieldIndex')
addIndex(bc, 'getPatientTitle', 'FieldIndex')
addIndex(bc, 'getDoctorID', 'FieldIndex')
addIndex(bc, 'getDoctorUID', 'FieldIndex')
addIndex(bc, 'getDoctorTitle', 'FieldIndex')
addIndex(bc, 'getClientPatientID', 'FieldIndex')
addColumn(bc, 'getClientTitle')
addColumn(bc, 'getPatientID')
addColumn(bc, 'getPatientUID')
addColumn(bc, 'getPatientTitle')
addColumn(bc, 'getDoctorID')
addColumn(bc, 'getDoctorUID')
addColumn(bc, 'getDoctorTitle')
addColumn(bc, 'getClientPatientID')
# portal_catalog
pc = getToolByName(portal, 'portal_catalog', None)
if not pc:
logger.warning('Could not find the portal_catalog tool.')
return
addIndex(pc, 'getDoctorID', 'FieldIndex')
addIndex(pc, 'getDoctorUID', 'FieldIndex')
addIndex(pc, 'getPrimaryReferrerUID', 'FieldIndex')
addColumn(pc, 'getDoctorID')
addColumn(pc, 'getDoctorUID')
# bika_setup_catalog
bsc = getToolByName(portal, 'bika_setup_catalog', None)
if not bsc:
logger.warning('Could not find the bika_setup_catalog tool.')
return
at = getToolByName(portal, 'archetype_tool')
at.setCatalogsByType('Disease', [
'bika_setup_catalog',
])
at.setCatalogsByType('AetiologicAgent', [
'bika_setup_catalog',
])
at.setCatalogsByType('Treatment', ['bika_setup_catalog'])
at.setCatalogsByType('Symptom', ['bika_setup_catalog'])
at.setCatalogsByType('Drug', ['bika_setup_catalog'])
at.setCatalogsByType('DrugProhibition', ['bika_setup_catalog'])
at.setCatalogsByType('VaccinationCenter', [
'bika_setup_catalog',
])
at.setCatalogsByType('InsuranceCompany', [
'bika_setup_catalog',
])
at.setCatalogsByType('Immunization', [
'bika_setup_catalog',
])
at.setCatalogsByType('CaseStatus', [
'bika_setup_catalog',
])
at.setCatalogsByType('CaseOutcome', [
'bika_setup_catalog',
])
at.setCatalogsByType('IdentifierType', [
'bika_setup_catalog',
])
at.setCatalogsByType('CaseSyndromicClassification', ['bika_setup_catalog'])
at.setCatalogsByType('Ethnicity', [
'bika_setup_catalog',
])
addIndex(bsc, 'getGender', 'FieldIndex')
addColumn(bsc, 'getGender')
catalog_definitions_lims_health = getCatalogDefinitionsLIMS()
catalog_definitions_lims_health.update(getCatalogDefinitionsHealth())
# Updating health catalogs if there is any change in them
setup_catalogs(portal,
catalog_definitions_lims_health,
catalogs_extension=getCatalogExtensions())
logger.info("Setup catalogs [DONE]")
def setupHealthCatalogs(context):
# an item should belong to only one catalog.
# that way looking it up means first looking up *the* catalog
# in which it is indexed, as well as making it cheaper to index.
if context.readDataFile('bika.health.txt') is None:
return
portal = context.getSite()
def addIndex(cat, *args):
try:
cat.addIndex(*args)
except:
pass
def addColumn(cat, col):
try:
cat.addColumn(col)
except:
pass
# create lexicon
wordSplitter = Empty()
wordSplitter.group = 'Word Splitter'
wordSplitter.name = 'Unicode Whitespace splitter'
caseNormalizer = Empty()
caseNormalizer.group = 'Case Normalizer'
caseNormalizer.name = 'Unicode Case Normalizer'
stopWords = Empty()
stopWords.group = 'Stop Words'
stopWords.name = 'Remove listed and single char words'
elem = [wordSplitter, caseNormalizer, stopWords]
zc_extras = Empty()
zc_extras.index_type = 'Okapi BM25 Rank'
zc_extras.lexicon_id = 'Lexicon'
# bika_catalog
bc = getToolByName(portal, 'bika_catalog', None)
if bc == None:
logger.warning('Could not find the bika_catalog tool.')
return
addIndex(bc, 'getClientTitle', 'FieldIndex')
addIndex(bc, 'getPatientID', 'FieldIndex')
addIndex(bc, 'getPatientUID', 'FieldIndex')
addIndex(bc, 'getPatientTitle', 'FieldIndex')
addIndex(bc, 'getDoctorID', 'FieldIndex')
addIndex(bc, 'getDoctorUID', 'FieldIndex')
addIndex(bc, 'getDoctorTitle', 'FieldIndex')
addIndex(bc, 'getClientPatientID', 'FieldIndex')
addColumn(bc, 'getClientTitle')
addColumn(bc, 'getPatientID')
addColumn(bc, 'getPatientUID')
addColumn(bc, 'getPatientTitle')
addColumn(bc, 'getDoctorID')
addColumn(bc, 'getDoctorUID')
addColumn(bc, 'getDoctorTitle')
addColumn(bc, 'getClientPatientID')
# portal_catalog
pc = getToolByName(portal, 'portal_catalog', None)
if pc == None:
logger.warning('Could not find the portal_catalog tool.')
return
addIndex(pc, 'getDoctorID', 'FieldIndex')
addIndex(pc, 'getDoctorUID', 'FieldIndex')
addColumn(pc, 'getDoctorID')
addColumn(pc, 'getDoctorUID')
# bika_setup_catalog
bsc = getToolByName(portal, 'bika_setup_catalog', None)
if bsc == None:
logger.warning('Could not find the bika_setup_catalog tool.')
return
at = getToolByName(portal, 'archetype_tool')
at.setCatalogsByType('Disease', ['bika_setup_catalog', ])
at.setCatalogsByType('AetiologicAgent', ['bika_setup_catalog', ])
at.setCatalogsByType('Treatment', ['bika_setup_catalog'])
at.setCatalogsByType('Symptom', ['bika_setup_catalog'])
at.setCatalogsByType('Drug', ['bika_setup_catalog'])
at.setCatalogsByType('DrugProhibition', ['bika_setup_catalog'])
at.setCatalogsByType('VaccinationCenter', ['bika_setup_catalog', ])
at.setCatalogsByType('InsuranceCompany', ['bika_setup_catalog', ])
at.setCatalogsByType('Immunization', ['bika_setup_catalog', ])
at.setCatalogsByType('CaseStatus', ['bika_setup_catalog', ])
at.setCatalogsByType('CaseOutcome', ['bika_setup_catalog', ])
at.setCatalogsByType('EpidemiologicalYear', ['bika_setup_catalog', ])
at.setCatalogsByType('IdentifierType', ['bika_setup_catalog', ])
at.setCatalogsByType('CaseSyndromicClassification', ['bika_setup_catalog', ])
at.setCatalogsByType('Ethnicity', ['bika_setup_catalog', ])
addIndex(bsc,'getGender', 'FieldIndex')
addColumn(bsc,'getGender')
# bika_patient_catalog
bpc = getToolByName(portal, 'bika_patient_catalog', None)
if bpc == None:
logger.warning('Could not find the bika_patient_catalog tool.')
return
bpc.manage_addProduct['ZCTextIndex'].manage_addLexicon('Lexicon', 'Lexicon', elem)
at = getToolByName(portal, 'archetype_tool')
at.setCatalogsByType('Patient', ['bika_patient_catalog'])
addIndex(bpc, 'path', 'ExtendedPathIndex', ('getPhysicalPath'))
addIndex(bpc, 'allowedRolesAndUsers', 'KeywordIndex')
addIndex(bpc, 'UID', 'FieldIndex')
addIndex(bpc, 'Title', 'ZCTextIndex', zc_extras)
addIndex(bpc, 'Description', 'ZCTextIndex', zc_extras)
addIndex(bpc, 'id', 'FieldIndex')
addIndex(bpc, 'getId', 'FieldIndex')
addIndex(bpc, 'Type', 'FieldIndex')
addIndex(bpc, 'portal_type', 'FieldIndex')
addIndex(bpc, 'created', 'DateIndex')
addIndex(bpc, 'Creator', 'FieldIndex')
addIndex(bpc, 'getObjPositionInParent', 'GopipIndex')
addIndex(bpc, 'sortable_title', 'FieldIndex')
addIndex(bpc, 'review_state', 'FieldIndex')
addIndex(bpc, 'getPatientID', 'FieldIndex')
addIndex(bpc, 'getClientPatientID', 'FieldIndex')
addIndex(bpc, 'getPrimaryReferrerUID', 'FieldIndex')
addIndex(bpc, 'getGender', 'FieldIndex')
addIndex(bpc, 'getAgeSplittedStr', 'FieldIndex')
addIndex(bpc, 'getPrimaryReferrerTitle', 'FieldIndex')
addIndex(bpc, 'getCitizenship', 'FieldIndex')
addIndex(bpc, 'getBirthDate', 'DateIndex')
addIndex(bpc, 'inactive_state', 'FieldIndex')
addColumn(bpc, 'id')
addColumn(bpc, 'UID')
addColumn(bpc, 'Title')
addColumn(bpc, 'Type')
addColumn(bpc, 'portal_type')
addColumn(bpc, 'sortable_title')
addColumn(bpc, 'Description')
addColumn(bpc, 'getPatientID')
addColumn(bpc, 'getClientPatientID')
addColumn(bpc, 'getPrimaryReferrerUID')
addColumn(bpc, 'review_state')
addColumn(bpc, 'inactive_state')
def setupHealthCatalogs(context):
# an item should belong to only one catalog.
# that way looking it up means first looking up *the* catalog
# in which it is indexed, as well as making it cheaper to index.
if context.readDataFile('bika.health.txt') is None:
return
portal = context.getSite()
def addIndex(cat, *args):
try:
cat.addIndex(*args)
except:
pass
def addColumn(cat, col):
try:
cat.addColumn(col)
except:
pass
# create lexicon
wordSplitter = Empty()
wordSplitter.group = 'Word Splitter'
wordSplitter.name = 'Unicode Whitespace splitter'
caseNormalizer = Empty()
caseNormalizer.group = 'Case Normalizer'
caseNormalizer.name = 'Unicode Case Normalizer'
stopWords = Empty()
stopWords.group = 'Stop Words'
stopWords.name = 'Remove listed and single char words'
elem = [wordSplitter, caseNormalizer, stopWords]
zc_extras = Empty()
zc_extras.index_type = 'Okapi BM25 Rank'
zc_extras.lexicon_id = 'Lexicon'
# bika_catalog
bc = getToolByName(portal, 'bika_catalog', None)
if bc == None:
logger.warning('Could not find the bika_catalog tool.')
return
addIndex(bc, 'getClientTitle', 'FieldIndex')
addIndex(bc, 'getPatientID', 'FieldIndex')
addIndex(bc, 'getPatientUID', 'FieldIndex')
addIndex(bc, 'getPatientTitle', 'FieldIndex')
addIndex(bc, 'getDoctorID', 'FieldIndex')
addIndex(bc, 'getDoctorUID', 'FieldIndex')
addIndex(bc, 'getDoctorTitle', 'FieldIndex')
addIndex(bc, 'getClientPatientID', 'FieldIndex')
addColumn(bc, 'getClientTitle')
addColumn(bc, 'getPatientID')
addColumn(bc, 'getPatientUID')
addColumn(bc, 'getPatientTitle')
addColumn(bc, 'getDoctorID')
addColumn(bc, 'getDoctorUID')
addColumn(bc, 'getDoctorTitle')
addColumn(bc, 'getClientPatientID')
# portal_catalog
pc = getToolByName(portal, 'portal_catalog', None)
if pc == None:
logger.warning('Could not find the portal_catalog tool.')
return
addIndex(pc, 'getDoctorID', 'FieldIndex')
addIndex(pc, 'getDoctorUID', 'FieldIndex')
addColumn(pc, 'getDoctorID')
addColumn(pc, 'getDoctorUID')
# bika_setup_catalog
bsc = getToolByName(portal, 'bika_setup_catalog', None)
if bsc == None:
logger.warning('Could not find the bika_setup_catalog tool.')
return
at = getToolByName(portal, 'archetype_tool')
at.setCatalogsByType('Disease', [
'bika_setup_catalog',
])
at.setCatalogsByType('AetiologicAgent', [
'bika_setup_catalog',
])
at.setCatalogsByType('Treatment', ['bika_setup_catalog'])
at.setCatalogsByType('Symptom', ['bika_setup_catalog'])
at.setCatalogsByType('Drug', ['bika_setup_catalog'])
at.setCatalogsByType('DrugProhibition', ['bika_setup_catalog'])
at.setCatalogsByType('VaccinationCenter', [
'bika_setup_catalog',
])
at.setCatalogsByType('InsuranceCompany', [
'bika_setup_catalog',
])
at.setCatalogsByType('Immunization', [
'bika_setup_catalog',
])
at.setCatalogsByType('CaseStatus', [
'bika_setup_catalog',
])
at.setCatalogsByType('CaseOutcome', [
'bika_setup_catalog',
])
at.setCatalogsByType('EpidemiologicalYear', [
'bika_setup_catalog',
])
at.setCatalogsByType('IdentifierType', [
'bika_setup_catalog',
])
at.setCatalogsByType('CaseSyndromicClassification', [
'bika_setup_catalog',
])
at.setCatalogsByType('Ethnicity', [
'bika_setup_catalog',
])
addIndex(bsc, 'getGender', 'FieldIndex')
addColumn(bsc, 'getGender')
catalog_definitions_lims_health = getCatalogDefinitionsLIMS()
catalog_definitions_lims_health.update(getCatalogDefinitionsHealth())
# Updating health catalogs if there is any change in them
setup_catalogs(portal,
catalog_definitions_lims_health,
catalogs_extension=getCatalogExtensions())
def setupHealthCatalogs(context):
# an item should belong to only one catalog.
# that way looking it up means first looking up *the* catalog
# in which it is indexed, as well as making it cheaper to index.
if context.readDataFile('bika.health.txt') is None:
return
portal = context.getSite()
def addIndex(cat, *args):
try:
cat.addIndex(*args)
except:
pass
def addColumn(cat, col):
try:
cat.addColumn(col)
except:
pass
# create lexicon
wordSplitter = Empty()
wordSplitter.group = 'Word Splitter'
wordSplitter.name = 'Unicode Whitespace splitter'
caseNormalizer = Empty()
caseNormalizer.group = 'Case Normalizer'
caseNormalizer.name = 'Unicode Case Normalizer'
stopWords = Empty()
stopWords.group = 'Stop Words'
stopWords.name = 'Remove listed and single char words'
elem = [wordSplitter, caseNormalizer, stopWords]
zc_extras = Empty()
zc_extras.index_type = 'Okapi BM25 Rank'
zc_extras.lexicon_id = 'Lexicon'
# bika_catalog
bc = getToolByName(portal, 'bika_catalog', None)
if bc == None:
logger.warning('Could not find the bika_catalog tool.')
return
addIndex(bc, 'getClientTitle', 'FieldIndex')
addIndex(bc, 'getPatientID', 'FieldIndex')
addIndex(bc, 'getPatientUID', 'FieldIndex')
addIndex(bc, 'getPatientTitle', 'FieldIndex')
addIndex(bc, 'getDoctorID', 'FieldIndex')
addIndex(bc, 'getDoctorUID', 'FieldIndex')
addIndex(bc, 'getDoctorTitle', 'FieldIndex')
addIndex(bc, 'getClientPatientID', 'FieldIndex')
addColumn(bc, 'getClientTitle')
addColumn(bc, 'getPatientID')
addColumn(bc, 'getPatientUID')
addColumn(bc, 'getPatientTitle')
addColumn(bc, 'getDoctorID')
addColumn(bc, 'getDoctorUID')
addColumn(bc, 'getDoctorTitle')
addColumn(bc, 'getClientPatientID')
# portal_catalog
pc = getToolByName(portal, 'portal_catalog', None)
if pc == None:
logger.warning('Could not find the portal_catalog tool.')
return
addIndex(pc, 'getDoctorID', 'FieldIndex')
addIndex(pc, 'getDoctorUID', 'FieldIndex')
addColumn(pc, 'getDoctorID')
addColumn(pc, 'getDoctorUID')
# bika_setup_catalog
bsc = getToolByName(portal, 'bika_setup_catalog', None)
if bsc == None:
logger.warning('Could not find the bika_setup_catalog tool.')
return
at = getToolByName(portal, 'archetype_tool')
at.setCatalogsByType('Disease', [
'bika_setup_catalog',
])
at.setCatalogsByType('AetiologicAgent', [
'bika_setup_catalog',
])
at.setCatalogsByType('Treatment', ['bika_setup_catalog'])
at.setCatalogsByType('Symptom', ['bika_setup_catalog'])
at.setCatalogsByType('Drug', ['bika_setup_catalog'])
at.setCatalogsByType('DrugProhibition', ['bika_setup_catalog'])
at.setCatalogsByType('VaccinationCenter', [
'bika_setup_catalog',
])
at.setCatalogsByType('InsuranceCompany', [
'bika_setup_catalog',
])
at.setCatalogsByType('Immunization', [
'bika_setup_catalog',
])
at.setCatalogsByType('CaseStatus', [
'bika_setup_catalog',
])
at.setCatalogsByType('CaseOutcome', [
'bika_setup_catalog',
])
at.setCatalogsByType('EpidemiologicalYear', [
'bika_setup_catalog',
])
at.setCatalogsByType('IdentifierType', [
'bika_setup_catalog',
])
at.setCatalogsByType('CaseSyndromicClassification', [
'bika_setup_catalog',
])
at.setCatalogsByType('Ethnicity', [
'bika_setup_catalog',
])
addIndex(bsc, 'getGender', 'FieldIndex')
addColumn(bsc, 'getGender')
# bika_patient_catalog
bpc = getToolByName(portal, 'bika_patient_catalog', None)
if bpc == None:
logger.warning('Could not find the bika_patient_catalog tool.')
return
bpc.manage_addProduct['ZCTextIndex'].manage_addLexicon(
'Lexicon', 'Lexicon', elem)
at = getToolByName(portal, 'archetype_tool')
at.setCatalogsByType('Patient', ['bika_patient_catalog'])
addIndex(bpc, 'path', 'ExtendedPathIndex', ('getPhysicalPath'))
addIndex(bpc, 'allowedRolesAndUsers', 'KeywordIndex')
addIndex(bpc, 'UID', 'FieldIndex')
addIndex(bpc, 'Title', 'ZCTextIndex', zc_extras)
addIndex(bpc, 'Description', 'ZCTextIndex', zc_extras)
addIndex(bpc, 'id', 'FieldIndex')
addIndex(bpc, 'getId', 'FieldIndex')
addIndex(bpc, 'Type', 'FieldIndex')
addIndex(bpc, 'portal_type', 'FieldIndex')
addIndex(bpc, 'created', 'DateIndex')
addIndex(bpc, 'Creator', 'FieldIndex')
addIndex(bpc, 'getObjPositionInParent', 'GopipIndex')
addIndex(bpc, 'sortable_title', 'FieldIndex')
addIndex(bpc, 'review_state', 'FieldIndex')
addIndex(bpc, 'getPatientID', 'FieldIndex')
addIndex(bpc, 'getClientPatientID', 'FieldIndex')
addIndex(bpc, 'getPrimaryReferrerUID', 'FieldIndex')
addIndex(bpc, 'getGender', 'FieldIndex')
addIndex(bpc, 'getAgeSplittedStr', 'FieldIndex')
addIndex(bpc, 'getPrimaryReferrerTitle', 'FieldIndex')
addIndex(bpc, 'getCitizenship', 'FieldIndex')
addIndex(bpc, 'getBirthDate', 'DateIndex')
addIndex(bpc, 'inactive_state', 'FieldIndex')
addColumn(bpc, 'id')
addColumn(bpc, 'UID')
addColumn(bpc, 'Title')
addColumn(bpc, 'Type')
addColumn(bpc, 'portal_type')
addColumn(bpc, 'sortable_title')
addColumn(bpc, 'Description')
addColumn(bpc, 'getPatientID')
addColumn(bpc, 'getClientPatientID')
addColumn(bpc, 'getPrimaryReferrerUID')
addColumn(bpc, 'review_state')
addColumn(bpc, 'inactive_state')
