def export_patients(bot, patient_ids, study, owner, out_file, progress_callback):
start_time = time.time()
count = 0
n_exported = 0
prop_names = bot.list_patient_class_properties()
writer = csv.writer(out_file)
writer.writerow(prop_names)
for patient_id in patient_ids:
progress_callback(count)
count += 1
if study != None:
patient_study = bot.get_study(patient_id)
if patient_study != study and not (study == '' and patient_study == None):
continue
if owner:
patient_owner = bot.get_owner(patient_id)
if PhenoTipsBot.qualify(patient_owner) != PhenoTipsBot.qualify(owner):
continue
patient = bot.get(patient_id)
patient['identifier'] = 'P' + patient['identifier'].zfill(7)
row = []
for prop_name in prop_names:
row.append(patient[prop_name])
writer.writerow(row)
n_exported += 1
return n_exported, timedelta(seconds=time.time() - start_time)
def get_clinvar_data(bot, patient_ids, study, owner, gene, progress_callback):
start_time = time.time()
count = 0
clinvar_data = OrderedDict()
for patient_id in patient_ids:
count += 1
progress_callback(count)
if study != None:
patient_study = bot.get_study(patient_id)
if study != patient_study.lower() and not (study == '' and patient_study == None):
continue
if owner:
patient_owner = bot.get_owner(patient_id)
if PhenoTipsBot.qualify(patient_owner) != PhenoTipsBot.qualify(owner):
continue
clinvar_variant_nums = bot.list_objects(patient_id, 'Main.ClinVarVariant')
if len(clinvar_variant_nums) == 0:
continue
patient_obj = bot.get(patient_id)
for clinvar_variant_num in clinvar_variant_nums:
clinvar_variant_obj = bot.get_object(patient_id, 'Main.ClinVarVariant', clinvar_variant_num)
gene_symbol = clinvar_variant_obj.get('gene_symbol')
if gene and (not gene_symbol or not gene in gene_symbol.upper().split(';')):
continue
#we aggregate all fields except for these
clinvar_data_key = (
clinvar_variant_obj['reference_sequence'] if 'reference_sequence' in clinvar_variant_obj else None,
clinvar_variant_obj['hgvs'] if 'hgvs' in clinvar_variant_obj else None,
clinvar_variant_obj['cis_or_trans'] if 'cis_or_trans' in clinvar_variant_obj else None,
clinvar_variant_obj['location'] if 'location' in clinvar_variant_obj else None,
patient_obj['omim_id'] if 'omim_id' in patient_obj else None,
clinvar_variant_obj['condition_category'] if 'condition_category' in clinvar_variant_obj else None,
clinvar_variant_obj['clinical_significance'] if 'clinical_significance' in clinvar_variant_obj else None,
clinvar_variant_obj['collection_method'] if 'collection_method' in clinvar_variant_obj else None,
clinvar_variant_obj['allele_origin'] if 'allele_origin' in clinvar_variant_obj else None,
clinvar_variant_obj['tissue'] if 'tissue' in clinvar_variant_obj else None,
patient_obj ['case_or_control'] if 'case_or_control' in patient_obj else None,
)
if not clinvar_data_key in clinvar_data:
clinvar_data[clinvar_data_key] = []
clinvar_data[clinvar_data_key].append((patient_obj, clinvar_variant_obj))
return clinvar_data, timedelta(seconds=time.time() - start_time)
base_url = 'http://' + base_url
base_url = base_url.rstrip('/')
if not username:
username = input('Input your username (blank for Admin): ')
if not username:
username = '******'
if not password:
password = getpass('Input your password (blank for admin): ')
if not password:
password = '******'
#log in
bot = PhenoTipsBot(base_url, username, password)
#parse PED file
#http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped
def get_id(external_id):
if external_id == '0':
return None
try:
return bot.get_id(external_id)
except HTTPError:
return None
print('Matching pedigree rows to the patient database...')
count = 0
class MainWindow(QMainWindow):
def __init__(self):
super(MainWindow, self).__init__()
uic.loadUi('mainwindow.ui', self)
self.statusLabel.setText("")
self.progressBar.setVisible(False)
self.previousButton.clicked.connect(self.previousButton_clicked)
self.nextButton.clicked.connect(self.nextButton_clicked)
self.siteSelector.lineEdit().returnPressed.connect(self.nextButton_clicked)
self.usernameTextbox.returnPressed.connect(self.nextButton_clicked)
self.passwordTextbox.returnPressed.connect(self.nextButton_clicked)
self.importCsvOption.clicked.connect(self.operationOption_clicked)
self.exportCsvOption.clicked.connect(self.operationOption_clicked)
self.exportClinVarOption.clicked.connect(self.operationOption_clicked)
self.browseButton.clicked.connect(self.browseButton_clicked)
def asyncAddGeneSelectorItem(self, item):
QMetaObject.invokeMethod(self, 'addGeneSelectorItem', Qt.QueuedConnection, Q_ARG(str, item))
def asyncAddOwnerSelectorItem(self, item):
QMetaObject.invokeMethod(self, 'addOwnerSelectorItem', Qt.QueuedConnection, Q_ARG(str, item))
def asyncAddStudySelectorItem(self, item):
QMetaObject.invokeMethod(self, 'addStudySelectorItem', Qt.QueuedConnection, Q_ARG(str, item))
def asyncClearOwnerSelector(self):
QMetaObject.invokeMethod(self.ownerSelector, 'clear', Qt.QueuedConnection)
def asyncClearStudySelector(self):
QMetaObject.invokeMethod(self.studySelector, 'clear', Qt.QueuedConnection)
def asyncHideGeneSelector(self):
QMetaObject.invokeMethod(self.geneLabel, 'setVisible', Qt.QueuedConnection, Q_ARG(bool, False))
QMetaObject.invokeMethod(self.geneSelector, 'setVisible', Qt.QueuedConnection, Q_ARG(bool, False))
def asyncLockUi(self, status, maxProgress = 0):
QMetaObject.invokeMethod(self, 'setEnabled', Qt.QueuedConnection, Q_ARG(bool, False))
self.asyncSetStatus(status, maxProgress)
QMetaObject.invokeMethod(self.progressBar, 'setVisible', Qt.QueuedConnection, Q_ARG(bool, True))
def asyncResetGeneSelector(self):
QMetaObject.invokeMethod(self.geneLabel, 'setVisible', Qt.QueuedConnection, Q_ARG(bool, True))
QMetaObject.invokeMethod(self.geneSelector, 'setVisible', Qt.QueuedConnection, Q_ARG(bool, True))
QMetaObject.invokeMethod(self.geneSelector, 'clear', Qt.QueuedConnection)
self.asyncAddGeneSelectorItem('All genes')
def asyncSetBrowseLabelText(self, text):
QMetaObject.invokeMethod(self.browseLabel, 'setText', Qt.QueuedConnection, Q_ARG(str, text))
def asyncSetConfirmation(self, confirmation):
QMetaObject.invokeMethod(self.confirmationLabel, 'setText', Qt.QueuedConnection, Q_ARG(str, confirmation))
def asyncSetOwnerLabelText(self, text):
QMetaObject.invokeMethod(self.ownerLabel, 'setText', Qt.QueuedConnection, Q_ARG(str, text))
def asyncSetOwnerSelectorText(self, text):
QMetaObject.invokeMethod(self.ownerSelector, 'setCurrentText', Qt.QueuedConnection, Q_ARG(str, text))
def asyncSetPage(self, index):
QMetaObject.invokeMethod(self.stackedWidget, 'setCurrentIndex', Qt.QueuedConnection, Q_ARG(int, index))
def asyncSetProgress(self, progress):
QMetaObject.invokeMethod(self.progressBar, 'setValue', Qt.QueuedConnection, Q_ARG(int, progress))
def asyncSetStatus(self, status, maxProgress = 0):
QMetaObject.invokeMethod(self.statusLabel, 'setText', Qt.QueuedConnection, Q_ARG(str, status))
QMetaObject.invokeMethod(self.progressBar, 'setMaximum', Qt.QueuedConnection, Q_ARG(int, maxProgress))
def asyncSetStudyLabelText(self, text):
QMetaObject.invokeMethod(self.studyLabel, 'setText', Qt.QueuedConnection, Q_ARG(str, text))
def asyncSetSummary(self, summary):
QMetaObject.invokeMethod(self.summaryLabel, 'setText', Qt.QueuedConnection, Q_ARG(str, summary))
def asyncUnlockUi(self, status = ''):
QMetaObject.invokeMethod(self, 'setEnabled', Qt.QueuedConnection, Q_ARG(bool, True))
QMetaObject.invokeMethod(self.progressBar, 'setVisible', Qt.QueuedConnection, Q_ARG(bool, False))
self.asyncSetStatus(status)
def turnToPage2(self):
self.asyncLockUi('Finding studies, users, and work groups...')
self.site = self.siteSelector.currentText().rstrip('/')
self.username = self.usernameTextbox.text()
self.password = self.passwordTextbox.text()
self.bot = PhenoTipsBot(self.site, self.username, self.password)
try:
self.studies = self.bot.list_studies()
self.users = self.bot.list_users()
self.groups = self.bot.list_groups()
self.gene_table = {}
if self.operation == EXPORT_CLINVAR:
self.asyncSetStatus('Getting patient list...')
patient_ids = self.bot.list()
self.asyncSetStatus('Getting gene list...', len(patient_ids))
count = 0
for patient_id in patient_ids:
for variant_num in self.bot.list_objects(patient_id, 'Main.ClinVarVariant'):
gene = self.bot.get_object(patient_id, 'Main.ClinVarVariant', variant_num).get('gene_symbol').upper()
if gene:
if gene not in self.gene_table:
self.gene_table[gene] = set()
self.gene_table[gene].add(patient_id)
count += 1
self.asyncSetProgress(count)
except Exception as err:
self.asyncUnlockUi(str(err))
return
if len(self.studies) or len(self.users) > 1 or len(self.groups):
self.asyncClearStudySelector()
self.asyncClearOwnerSelector()
if self.operation == IMPORT_CSV:
self.asyncSetStudyLabelText('Which study form should be used for the new patients?')
self.asyncSetOwnerLabelText('Who should own (have access to) the new patients?')
else:
self.asyncSetStudyLabelText('Which study do you want to export from?')
self.asyncAddStudySelectorItem('All studies')
self.asyncSetOwnerLabelText('Which user or group\'s patients do you want to export?')
self.asyncAddOwnerSelectorItem('All users')
self.asyncAddStudySelectorItem('Default study')
for study in self.studies:
self.asyncAddStudySelectorItem(study)
for user in self.users:
self.asyncAddOwnerSelectorItem(user)
for group in self.groups:
self.asyncAddOwnerSelectorItem('Groups.' + group)
if self.operation == IMPORT_CSV:
self.asyncSetOwnerSelectorText(self.username)
if self.operation == IMPORT_CSV:
self.asyncHideGeneSelector()
if len(self.users) > 1 or len(self.studies):
self.asyncSetPage(2)
else:
self.study = None
self.turnToPage3()
self.asyncUnlockUi()
elif self.operation == EXPORT_CSV:
self.asyncHideGeneSelector()
if len(self.studies) > 1:
self.asyncSetPage(2)
else:
self.study = None
self.turnToPage3()
self.asyncUnlockUi()
else:
if len(self.gene_table):
self.asyncResetGeneSelector()
for gene in self.gene_table:
self.asyncAddGeneSelectorItem(gene)
if len(self.studies) or len(self.gene_table) > 1:
self.asyncSetPage(2)
else:
self.study = None
self.owner = self.username
self.gene = None
self.asyncTurnToPage3()
self.asyncUnlockUi()
else:
self.asyncUnlockUi('There are no variants for ClinVar on this site.')
def turnToPage3(self):
if self.operation == IMPORT_CSV:
self.asyncSetBrowseLabelText('Please click Browse and open the file to import.')
elif self.operation == EXPORT_CSV:
self.asyncSetBrowseLabelText('Please click Browse and save the file to export.')
else:
self.asyncSetBrowseLabelText('Please click Browse and select the folder to save Variant.csv and CaseData.csv to.')
self.asyncSetPage(3)
def turnToPage4(self):
global confirmation
self.asyncLockUi('Parsing CSV file...')
confirmation = ''
try:
def unrecognizedColumnHandler(column):
global confirmation
confirmation += 'WARNING: Ignoring unrecognized column "' + column + '"\n'
def unrecognizedValueHandler(value, field):
global confirmation
confirmation += 'WARNING: Ignoring unrecognized value "' + value + '" for "' + field + '"\n'
self.patients = parse_csv_file(self.path, unrecognizedColumnHandler, unrecognizedValueHandler)
self.asyncSetStatus('Checking ' + str(len(self.patients)) + ' external IDs...', len(self.patients))
self.patient_ids = get_patient_ids(self.bot, self.patients, self.asyncSetProgress)
self.n_to_import = str(len(self.patients) - len(self.patient_ids))
self.n_to_update = str(len(self.patient_ids))
except Exception as err:
self.asyncUnlockUi(str(err))
return
confirmation += '\nYou are about to import ' + self.n_to_import + ' new patients and update ' + self.n_to_update + ' existing patients.'
self.asyncSetConfirmation(confirmation.strip())
self.asyncSetPage(4)
self.asyncUnlockUi()
def turnToPage5(self):
if self.operation == IMPORT_CSV:
self.asyncLockUi('Importing/updating...', len(self.patients))
try:
elapsedTime = import_patients(self.bot, self.patients, self.patient_ids, self.study, self.owner, self.asyncSetProgress)
except Exception as err:
self.asyncUnlockUi(str(err))
return
self.asyncSetSummary(
'Imported ' + self.n_to_import + ' patients and updated ' + self.n_to_update + ' patients.\n' +
'Elapsed time ' + str(elapsedTime)
)
elif self.operation == EXPORT_CSV:
self.asyncLockUi('Getting patient list...')
try:
patient_ids = self.bot.list()
self.asyncSetStatus('Exporting...', len(patient_ids))
outFile = open(self.path, 'w')
n_exported, elapsedTime = export_patients(self.bot, patient_ids, self.study, self.owner, outFile, self.asyncSetProgress)
outFile.close()
except Exception as err:
self.asyncUnlockUi(str(err))
return
self.asyncSetSummary(
'Exported ' + str(n_exported) + ' patients.\n' +
'Elapsed time ' + str(elapsedTime))
else:
if self.gene:
patient_ids = self.gene_table[self.gene]
else:
patient_ids = set.intersection(*self.gene_table.values())
self.asyncLockUi('Exporting...', len(patient_ids))
try:
clinvar_data, elapsedTime1 = get_clinvar_data(self.bot, patient_ids, self.study, self.owner, self.gene, self.asyncSetProgress)
self.asyncSetStatus('Writing files Variant.csv and CaseData.csv...')
variantsFile = open(self.path + '/Variant.csv', 'w')
caseDataFile = open(self.path + '/CaseData.csv', 'w')
n_variants, n_cases, elapsedTime2 = write_clinvar_files(clinvar_data, variantsFile, caseDataFile)
variantsFile.close()
caseDataFile.close()
except Exception as err:
self.asyncUnlockUi(str(err))
return
self.asyncSetSummary(
'Exported ' + str(n_variants) + ' variants and ' + str(n_cases) + ' cases.\n' +
'Elapsed time ' + str(elapsedTime1 + elapsedTime2)
)
self.asyncSetPage(5)
self.asyncUnlockUi()
# slots #
@pyqtSlot(str)
def addGeneSelectorItem(self, item):
self.geneSelector.addItem(item)
@pyqtSlot(str)
def addStudySelectorItem(self, item):
self.studySelector.addItem(item)
@pyqtSlot(str)
def addOwnerSelectorItem(self, item):
self.ownerSelector.addItem(item)
def browseButton_clicked(self):
if self.operation == IMPORT_CSV:
path = QFileDialog.getOpenFileName(self, 'Import spreadsheet', '', '*.csv')[0]
elif self.operation == EXPORT_CSV:
path = QFileDialog.getSaveFileName(self, 'Export spreadsheet', '', '*.csv')[0]
else:
path = QFileDialog.getExistingDirectory(self, 'Export spreadsheets')
if path:
self.pathLabel.setText(path)
def nextButton_clicked(self):
if self.stackedWidget.currentIndex() == 0: #operation
self.importMode = self.importCsvOption.isChecked()
if self.importCsvOption.isChecked():
self.operation = IMPORT_CSV
elif self.exportCsvOption.isChecked():
self.operation = EXPORT_CSV
else:
self.operation = EXPORT_CLINVAR
self.previousButton.setEnabled(True)
self.stackedWidget.setCurrentIndex(1) #login
elif self.stackedWidget.currentIndex() == 1: #login
Thread(target=self.turnToPage2).start() #study
elif self.stackedWidget.currentIndex() == 2: #study, owner, and gene
self.study = self.studySelector.currentText()
if self.study == 'All studies':
self.study = None
elif self.study == 'Default study':
if len(self.studies):
self.study = ''
else:
self.study = None
self.owner = self.ownerSelector.currentText()
if self.owner == 'All users':
self.owner = None
self.gene = self.geneSelector.currentText()
if self.gene == 'All genes':
self.gene = None
self.pathLabel.setText('')
Thread(target=self.turnToPage3).start() #file
elif self.stackedWidget.currentIndex() == 3: #file
self.path = self.pathLabel.text()
if self.path:
if self.operation == IMPORT_CSV:
Thread(target=self.turnToPage4).start() #confirmation
else:
Thread(target=self.turnToPage5).start() #summary
else:
self.browseButton_clicked()
elif self.stackedWidget.currentIndex() == 4: #confirmation
Thread(target=self.turnToPage5).start() #summary
elif self.stackedWidget.currentIndex() == 5: #summary
self.previousButton.setEnabled(False)
self.stackedWidget.setCurrentIndex(0) #operation
def operationOption_clicked(self):
self.nextButton.setEnabled(True)
def previousButton_clicked(self):
self.statusLabel.clear()
if self.stackedWidget.currentIndex() in [1, 5]: #login, summary
self.stackedWidget.setCurrentIndex(0) #operation
self.previousButton.setEnabled(False)
self.nextButton.setEnabled(True)
elif self.stackedWidget.currentIndex() == 2: #study
self.stackedWidget.setCurrentIndex(1) #login
self.previousButton.setEnabled(True)
self.nextButton.setEnabled(True)
elif self.stackedWidget.currentIndex() == 3: #file
if len(self.studies):
self.stackedWidget.setCurrentIndex(2) #study
else:
self.stackedWidget.setCurrentIndex(1) #login
self.nextButton.setEnabled(True)
elif self.stackedWidget.currentIndex() == 4: #confirmation
self.stackedWidget.setCurrentIndex(3) #file
def turnToPage2(self):
self.asyncLockUi('Finding studies, users, and work groups...')
self.site = self.siteSelector.currentText().rstrip('/')
self.username = self.usernameTextbox.text()
self.password = self.passwordTextbox.text()
self.bot = PhenoTipsBot(self.site, self.username, self.password)
try:
self.studies = self.bot.list_studies()
self.users = self.bot.list_users()
self.groups = self.bot.list_groups()
self.gene_table = {}
if self.operation == EXPORT_CLINVAR:
self.asyncSetStatus('Getting patient list...')
patient_ids = self.bot.list()
self.asyncSetStatus('Getting gene list...', len(patient_ids))
count = 0
for patient_id in patient_ids:
for variant_num in self.bot.list_objects(patient_id, 'Main.ClinVarVariant'):
gene = self.bot.get_object(patient_id, 'Main.ClinVarVariant', variant_num).get('gene_symbol').upper()
if gene:
if gene not in self.gene_table:
self.gene_table[gene] = set()
self.gene_table[gene].add(patient_id)
count += 1
self.asyncSetProgress(count)
except Exception as err:
self.asyncUnlockUi(str(err))
return
if len(self.studies) or len(self.users) > 1 or len(self.groups):
self.asyncClearStudySelector()
self.asyncClearOwnerSelector()
if self.operation == IMPORT_CSV:
self.asyncSetStudyLabelText('Which study form should be used for the new patients?')
self.asyncSetOwnerLabelText('Who should own (have access to) the new patients?')
else:
self.asyncSetStudyLabelText('Which study do you want to export from?')
self.asyncAddStudySelectorItem('All studies')
self.asyncSetOwnerLabelText('Which user or group\'s patients do you want to export?')
self.asyncAddOwnerSelectorItem('All users')
self.asyncAddStudySelectorItem('Default study')
for study in self.studies:
self.asyncAddStudySelectorItem(study)
for user in self.users:
self.asyncAddOwnerSelectorItem(user)
for group in self.groups:
self.asyncAddOwnerSelectorItem('Groups.' + group)
if self.operation == IMPORT_CSV:
self.asyncSetOwnerSelectorText(self.username)
if self.operation == IMPORT_CSV:
self.asyncHideGeneSelector()
if len(self.users) > 1 or len(self.studies):
self.asyncSetPage(2)
else:
self.study = None
self.turnToPage3()
self.asyncUnlockUi()
elif self.operation == EXPORT_CSV:
self.asyncHideGeneSelector()
if len(self.studies) > 1:
self.asyncSetPage(2)
else:
self.study = None
self.turnToPage3()
self.asyncUnlockUi()
else:
if len(self.gene_table):
self.asyncResetGeneSelector()
for gene in self.gene_table:
self.asyncAddGeneSelectorItem(gene)
if len(self.studies) or len(self.gene_table) > 1:
self.asyncSetPage(2)
else:
self.study = None
self.owner = self.username
self.gene = None
self.asyncTurnToPage3()
self.asyncUnlockUi()
else:
self.asyncUnlockUi('There are no variants for ClinVar on this site.')
base_url = 'http://localhost:8080'
if not base_url.startswith('http://') and not base_url.startswith('https://'):
base_url = 'http://' + base_url
base_url = base_url.rstrip('/')
if not username:
username = input('Input your username (blank for Admin): ')
if not username:
username = '******'
if not password:
password = getpass('Input your password (blank for admin): ')
if not password:
password = '******'
bot = PhenoTipsBot(base_url, username, password)
patient_ids = bot.list()
stderr.write('Looking through ' + str(len(patient_ids)) + ' patient records...\n')
stderr.write('\n')
count = 0
patient_total = 0
positive_phenotype_total = 0
negative_phenotype_total = 0
owners = set()
studies = set()
fields_used = set()
for patient_id in patient_ids:
stderr.write(str(count) + '\r')
if not base_url.startswith('http://') and not base_url.startswith('https://'):
base_url = 'http://' + base_url
base_url = base_url.rstrip('/')
if not username:
sys.stderr.write('Input your username (blank for Admin): ')
username = input()
if not username:
username = '******'
if not password:
password = getpass('Input your password (blank for admin): ', sys.stderr)
if not password:
password = '******'
bot = PhenoTipsBot(base_url, username, password)
if study == None:
studies = bot.list_studies()
if len(studies):
print('Available studies:')
print('* ' + '\n* '.join(studies))
sys.stderr.write('Are you exporting from a particular study (blank for no)? ')
study = input()
if study and study[0] == 'y':
sys.stderr.write('Input the study to export from (blank for default): ')
study = input()
else:
study = None
elif study == 'None':
study = None
base_url = 'http://localhost:8080'
if not base_url.startswith('http://') and not base_url.startswith('https://'):
base_url = 'http://' + base_url
base_url = base_url.rstrip('/')
if not username:
username = input('Input your username (blank for Admin): ')
if not username:
username = '******'
if not password:
password = getpass('Input your password (blank for admin): ')
if not password:
password = '******'
bot = PhenoTipsBot(base_url, username, password)
if study == None and len(bot.list_studies()):
study = input('Are you submitting on a particular study (blank for no)? ')
if study and study[0] == 'y':
study = input('Input the study to submit on (blank for default): ').lower()
else:
study = None
elif study == 'None':
study = None
if owner == None:
users = bot.list_users()
groups = bot.list_groups()
if len(users) > 1:
print('Available users:')
base_url = 'http://localhost:8080'
if not base_url.startswith('http://') and not base_url.startswith('https://'):
base_url = 'http://' + base_url
base_url = base_url.rstrip('/')
if not username:
username = input('Input your username (blank for Admin): ')
if not username:
username = '******'
if not password:
password = getpass('Input your password (blank for admin): ')
if not password:
password = '******'
bot = PhenoTipsBot(base_url, username, password)
#parse CSV file
patients = parse_csv_file(
bot,
args[0],
lambda column: print('WARNING: Ignoring unrecognized column "' + column + '"'),
lambda value, field: print('WARNING: Ignoring unrecognized value "' + value + '" for "' + field + '"'),
lambda: print('WARNING: Ignoring identifier column; all existing patients must be identified using the external_id column and all new patients must receive new PhenoTips IDs.')
)
#get the rest of the missing arguments
if study == None:
studies = bot.list_studies()
base_url = 'http://localhost:8080'
if not base_url.startswith('http://') and not base_url.startswith('https://'):
base_url = 'http://' + base_url
base_url = base_url.rstrip('/')
if not username:
username = input('Input your username (blank for Admin): ')
if not username:
username = '******'
if not password:
password = getpass('Input your password (blank for admin): ')
if not password:
password = '******'
bot = PhenoTipsBot(base_url, username, password)
if study == None:
studies = bot.list_studies()
if len(studies):
print('Available study forms:')
print('* ' + '\n* '.join(studies))
study = input('Input the study form to use (blank for default): ')
elif study == 'None':
study = None
#begin import
if yes or input('You are about to import ' + str(len(patients)) + ' patients. Type y to continue: ')[0] == 'y':
count = 0
start_time = time.time()
if not base_url.startswith('http://') and not base_url.startswith('https://'):
base_url = 'http://' + base_url
base_url = base_url.rstrip('/')
if not username:
sys.stderr.write('Input your username (blank for Admin): ')
username = input()
if not username:
username = '******'
if not password:
password = getpass('Input your password (blank for admin): ', sys.stderr)
if not password:
password = '******'
bot = PhenoTipsBot(base_url, username, password)
if study == None:
studies = bot.list_studies()
if len(studies):
sys.stderr.write('Are you exporting from a particular study (blank for no)? ')
study = input()
if study and study[0] == 'y':
print('Available studies:')
print('* ' + '\n* '.join(studies))
sys.stderr.write('Input the study to export from (blank for default): ')
study = input()
else:
study = None
elif study == 'None':
study = None
if not base_url.startswith('http://') and not base_url.startswith('https://'):
base_url = 'http://' + base_url
base_url = base_url.rstrip('/')
if not username:
sys.stderr.write('Input your username (blank for Admin): ')
username = input()
if not username:
username = '******'
if not password:
password = getpass('Input your password (blank for admin): ', sys.stderr)
if not password:
password = '******'
bot = PhenoTipsBot(base_url, username, password)
if study == None:
studies = bot.list_studies()
if len(studies):
print('Available studies:')
print('* ' + '\n* '.join(studies))
sys.stderr.write('Are you exporting from a particular study (blank for no)? ')
study = input()
if study and study[0] == 'y':
sys.stderr.write('Input the study to export from (blank for default): ')
study = input()
else:
study = None
elif study == 'None':
study = None
base_url = 'http://localhost:8080'
if not base_url.startswith('http://') and not base_url.startswith('https://'):
base_url = 'http://' + base_url
base_url = base_url.rstrip('/')
if not username:
username = input('Input your username (blank for Admin): ')
if not username:
username = '******'
if not password:
password = getpass('Input your password (blank for admin): ')
if not password:
password = '******'
bot = PhenoTipsBot(base_url, username, password)
if study == None and len(bot.list_studies()):
study = input('Are you submitting on a particular study (blank for no)? ')
if study and study[0] == 'y':
study = input('Input the study to submit on (blank for default): ').lower()
else:
study = None
elif study == 'None':
study = None
if owner == None:
users = bot.list_users()
groups = bot.list_groups()
if len(users) > 1:
print('Available users:')
base_url = 'http://localhost:8080'
if not base_url.startswith('http://') and not base_url.startswith('https://'):
base_url = 'http://' + base_url
base_url = base_url.rstrip('/')
if not username:
username = input('Input your username (blank for Admin): ')
if not username:
username = '******'
if not password:
password = getpass('Input your password (blank for admin): ')
if not password:
password = '******'
bot = PhenoTipsBot(base_url, username, password)
patient_ids = bot.list()
stderr.write('Looking through ' + str(len(patient_ids)) + ' patient records...\n')
stderr.write('\n')
count = 0
patient_total = 0
positive_phenotype_total = 0
negative_phenotype_total = 0
fields_used = set()
for patient_id in patient_ids:
stderr.write(str(count) + '\r')
count += 1
