def establish_db_connection():
# Should be done during server startup or when calling a function to set or get data
o = Openbis(
os.environ['OPENBIS_SERVER'],
verify_certificates=False,
allow_http_but_do_not_use_this_in_production_and_only_within_safe_networks
=True)
o.login(os.environ['OPENBIS_USER'], os.environ['OPENBIS_PASSWORD'])
return o
def test_cached_token(openbis_instance):
openbis_instance.save_token()
assert openbis_instance.token_path is not None
assert openbis_instance.get_cached_token() is not None
another_instance = Openbis(openbis_instance.url)
assert another_instance.is_token_valid() is True
openbis_instance.delete_token()
assert openbis_instance.get_cached_token() is None
def log_in(
bisurl='openbis-empa-lab205.labnotebook.ch/openbis/webapp/eln-lims/',
bisuser='******',
bispasswd='openbisempa'
):
"""Function to login to openBIS."""
if Openbis(bisurl).is_token_valid():
session = Openbis(bisurl)
else:
Openbis(bisurl).login(bisuser, bispasswd, save_token=True)
session = Openbis(bisurl)
return session
def open_connection(username, url):
"creates connection to openbis and returns session object"
s = Openbis(url=url, verify_certificates=True)
if not username:
username = input("Enter OpenBis Username:"******"Enter password for {}: ".format(username))
s.login(username, password)
assert s.token is not None
assert s.is_token_valid() is True
return s
def on_login_clicked(self, *args):
"""Login button clicked button callback. Defines what should happen when the login button got clicked."""
obj = args[0]
try:
self.openbis = Openbis(url=self.openbis_login_ui.children[0].value,
verify_certificates=False)
self.openbis.login(
self.openbis_login_ui.children[1].children[0].value,
self.openbis_login_ui.children[1].children[1].value)
self.openbis_login_ui.children[1].value = '' # Security measure.
obj.button_style = 'success'
obj.description = 'Connected'
self.show_new_exp_ui()
except Exception as e:
self.openbis_login_ui.children[1].value = '' # Security measure.
obj.button_style = 'danger'
obj.description = 'Login failed. Retry.'
def openbis_instance():
instance = Openbis("http://localhost:20000")
print("\nLOGGING IN...")
instance.login('admin', 'anypassword')
yield instance
instance.logout()
print("LOGGED OUT...")
class UIDropfoot(object):
"""Constructs a UI object"""
output = widgets.Output()
def __init__(self, *args, **kwagrs):
"""Constructs a UI object"""
# Pass those as kwargs while object initialization
self.textform = Textfields()
self.wizard_page = 0
self.end_page = False
self.screen = GetSystemMetrics # 0 = width, 1 = height
self.init_study_metadata()
self.inc_crit = StudyCriteria(self.textform.including_criteria, 1,
self.screen)
self.ex_crit = StudyCriteria(self.textform.excluding_criteria, 2,
self.screen)
self.init_quest_orthese()
self.init_participant_info()
self.init_KlinUntersuch()
self.init_Sensibilitaet()
self.init_openbis_login()
self.init_new_experimental_step()
self.init_wizard_btn()
self.init_save_btn()
self.shoe_result = set()
if self.wizard_page == 0:
self.questshoe = dict()
def show_study_start(self):
"""Show the study start form to the user"""
display(Markdown("# " + self.textform.title[0]))
display(Markdown("## " + self.textform.title[1]))
display(self.meta.study_metadata)
display(Markdown(self.textform.declaration))
display(Markdown("---"))
self.show_wizard_btn()
def show_form(self):
"""
Show the rest of the study form to the user, depending on which page one is.
"""
# Page 1
if self.wizard_page == 1:
# Formular Überprüfung Orthese
display(Markdown("# " + self.textform.pruef_orthese[0]))
display(self.orth.orthese)
display(Markdown(self.textform.pruef_orthese[5]))
# Participant information (Age, etc.)
display(
Markdown(
"# Teilnehmer spezifische Informationen / Anthropometrische Daten"
))
display(Markdown("---"))
self.parti.show_grid()
display(self.parti.erkrankung)
self.parti.show_grid_fersen()
display(self.parti.output)
# Reihenfolge der Messungen
display(Markdown("# Reihenfolge der Messungen"))
self.Messungen = widgets.VBox([
widgets.Text(value=self.textform.messkonditionen[0],
placeholder='',
description=str(1),
disabled=False,
layout=widgets.Layout(width='500px')),
widgets.Text(value=self.textform.messkonditionen[1],
placeholder='',
description=str(2),
disabled=False,
layout=widgets.Layout(width='500px')),
widgets.Text(value=self.textform.messkonditionen[2],
placeholder='',
description=str(3),
disabled=False,
layout=widgets.Layout(width='500px'))
])
display(self.Messungen)
# Page 2
elif self.wizard_page == 2:
display(Markdown("# Klinischer Untersuch"))
display(self.klin.klinunt1)
display(self.klin.klinunt2)
display(self.klin.klinunt3)
# Page 3
elif self.wizard_page == 3:
# In-/Exclusion criteria
self.stud_crit = DisplayStudyCriteria(self.textform, self.inc_crit,
self.ex_crit)
# Page 4
elif self.wizard_page == 4:
display(Markdown("# Sensibilitäts-Testung"))
image = mpimg.imread("Sensibilität.png")
plt.imshow(image)
plt.show()
display(Markdown(self.sens.sens1))
display(self.sens.sens2)
# Page 5
elif self.wizard_page == 5:
# Functional calibration
if hasattr(self, 'fc'):
self.fc = FunCalPage(self.textform, self.meta, self.screen,
self.fc)
else:
self.fc = FunCalPage(self.textform, self.meta, self.screen)
# Page 6
elif self.wizard_page == 6:
# Messung ohne Orthese
if hasattr(self, 'ohneOrth'):
self.ohneOrth = PageOhne(self.textform, self.meta, self.screen,
self.ohneOrth)
else:
self.ohneOrth = PageOhne(self.textform, self.meta, self.screen)
# Page 7
elif self.wizard_page == 7:
# Messung mit aktiver Fussorthese
if hasattr(self, 'aktiveOrth'):
self.aktiveOrth = PageAktive(self.textform, self.meta,
self.ohneOrth.TimeRange,
self.screen, self.aktiveOrth)
else:
self.aktiveOrth = PageAktive(self.textform, self.meta,
self.ohneOrth.TimeRange,
self.screen)
# Page 8
elif self.wizard_page == 8:
# Messung mit eigener Orthese
if hasattr(self, 'eigOrth'):
self.eigOrth = PageEigene(self.textform, self.meta,
self.ohneOrth.TimeRange, self.screen,
self.eigOrth)
else:
self.eigOrth = PageEigene(self.textform, self.meta,
self.ohneOrth.TimeRange, self.screen)
# Page 9
elif self.wizard_page == 9:
# Narrativer Report
if self.end_page:
display(self.questNarrative.narrative)
else:
self.init_FeedbackNarrative()
# Page 10
elif self.wizard_page == 10:
# Save form to html and to openBIS
self.end_page = True
self.upload_to_openbis()
display(Markdown("---"))
## -------------------------------------------------------------------------------- ##
## Initialization ##
def init_study_metadata(self):
""" Initialization of study metadata on date, participant id and investigator."""
self.meta = StudyMetadata()
def init_participant_info(self):
"""Initialization of participant information on age, height and weight."""
self.parti = ParticipantInfo(self.textform, self.screen)
def init_quest_orthese(self):
"""Initialization of participant information on age, height and weight."""
self.orth = QuestOrthese(self.textform, self.screen)
def init_KlinUntersuch(self):
"""Initialization of "Lauferfahrung" questionnaire"""
self.klin = QuestKlinUntersuch(self.screen)
def init_Sensibilitaet(self):
"""Initialization of "Lauferfahrung" questionnaire"""
self.sens = QuestSensibilitaet(self.screen)
def validate_subject(self):
"""Validation of the participant according to the inclusion and exclusion criteria for the study and the BMI."""
self.val_subject = ValidationSubject(self.inc_crit, self.ex_crit,
self.parti, self.wizard_page)
def validate_percent(self):
"""Validation of the participant according to the inclusion and exclusion criteria for the study and the BMI."""
self.val_perc = ValidatePercent(self.lauf)
def init_FeedbackNarrative(self, *args):
self.questNarrative = QuestNarrative(self.textform.messkonditionen[1],
self.screen)
## --------------------------------------------------------------------------- ##
## Button functions ##
def init_wizard_btn(self):
"""
Initialization of the form wizard buttons 'previous', 'next' and 'save'.
"""
previous_btn = widgets.Button(description='Previous',
tooltip='Previous')
previous_btn.on_click(self.on_previous_clicked)
next_btn = widgets.Button(description='Next', tooltip='Next')
next_btn.on_click(self.on_next_clicked)
save_btn = widgets.Button(description='Save', tooltip='Save')
save_btn.on_click(self.on_save_clicked)
funcal_btn = widgets.Button(description='Functional calibration',
tooltip='FunCal')
funcal_btn.on_click(self.on_funcal_clicked)
report_btn = widgets.Button(description='Narrative Report',
tooltip='Report')
report_btn.on_click(self.on_report_clicked)
self.wizard_btn = widgets.HBox(
[previous_btn, next_btn, save_btn, funcal_btn, report_btn])
def show_wizard_btn(self):
"""Show form wizard buttons to the user."""
display(self.wizard_btn)
@output.capture(clear_output=True)
def on_previous_clicked(self, *args):
"""Previous button clicked button callback. Defines what should happen when the previous button got clicked."""
if self.wizard_page > 1:
self.wizard_page -= 1
self.show_form()
self.show_wizard_btn()
else:
self.show_form()
self.show_wizard_btn()
@output.capture(clear_output=True)
def on_next_clicked(self, *args):
"""Next button clicked button callback. Defines what should happen when the next button got clicked."""
self.wizard_page += 1
if self.wizard_page != 4: # self.wizard_page != 2 and
self.show_form()
self.show_wizard_btn()
# Validate if subject fulfills in-/exclusion criteria
if self.wizard_page == 4:
self.validate_subject()
if self.val_subject.validator.value == True:
display(self.val_subject.validator)
self.show_form()
self.show_wizard_btn()
else:
display(self.val_subject.validator)
self.show_save_btn()
self.show_openbis_login()
@output.capture(clear_output=True)
def on_funcal_clicked(self, *args):
"""Previous button clicked button callback. Defines what should happen when the previous button got clicked."""
self.wizard_page = 5
self.show_form()
self.show_wizard_btn()
@output.capture(clear_output=True)
def on_report_clicked(self, *args):
"""Previous button clicked button callback. Defines what should happen when the previous button got clicked."""
self.wizard_page = 9
self.show_form()
self.show_wizard_btn()
@output.capture(clear_output=True)
def init_save_btn(self):
"""
Initialization of the save button.
"""
self.save_btn = widgets.Button(description='Save', tooltip='Save')
self.save_btn.on_click(self.on_save_clicked)
def show_save_btn(self):
"""
Show the save button to the user.
"""
display(self.save_btn)
@output.capture(clear_output=False)
## -------------------------------------------------------------------------------- ##
## Data Storage ##
def on_save_clicked(self, *args):
"""Save button clicked button callback. Defines what should happen when the save button got clicked."""
try:
# Temporary data storage. Initialized empty. Some required fields needed
# for saving. Will be used to render html page (to_html, to_pdf, to_openbis)
date = self.meta.study_metadata.children[0].value
# Daten zu Messdatum & Probandendaten
for i in range(0, 3):
if self.parti.erkrankung.children[i].value:
if i < 2:
erkrankung = self.parti.erkrankung.children[
i].description
elif i == 2:
erkrankung = self.parti.erkrankung.children[i +
1].value
project_info = {
'title': self.textform.title[0],
'subtitle': self.textform.title[1],
'date': date.strftime('%d/%m/%Y'),
'investigator_name':
self.meta.study_metadata.children[2].value,
'invest_declaration': self.textform.declaration,
'subject_id': self.meta.study_metadata.children[1].value,
'subject_age': self.parti.participant0.value,
'subject_height': self.parti.participant1.value,
'subject_weight': self.parti.participant2.value,
'subject_shoesize': self.parti.participant3.value,
'subject_unfall': self.parti.participant4.value,
'subject_erkrankung': erkrankung
}
# Fersen-/Zehengang
for i in range(0, len(self.textform.participant_info_fersengang)):
ja_nein_f = getattr(self.parti, "fersengang%s" % (i))
if ja_nein_f.value == 1:
ja_nein_f.wert = True
elif ja_nein_f.value == 2:
ja_nein_f.wert = False
project_info["fersengang_jn%s" % (i)] = ja_nein_f.wert
# Überprüfung Orthese
for i in range(0, len(self.orth.orthese.children)):
project_info["orthese_text%s" %
(i)] = self.textform.pruef_orthese[i + 1]
if self.orth.orthese.children[i].value == 1:
ja_nein_o = True
elif self.orth.orthese.children[i].value == 2:
ja_nein_o = False
project_info["orthese_jn%s" % (i)] = ja_nein_o
# Messreihenfolge
for i, value in enumerate(self.textform.messkonditionen):
project_info["messungen%s" % (i)] = value
# Fragebogen Klinischer Untersuch
for i in range(0, len(self.klin.klinunt1.children)):
project_info["klinunt1text%s" %
(i)] = self.klin.klinunt1.children[i].description
project_info["klinunt1value%s" %
(i)] = self.klin.klinunt1.children[i].value
for i in range(0, len(self.klin.klinunt2.children)):
if self.klin.klinunt2.children[i].description == "Label":
project_info["klinunt2text%s" %
(i)] = self.klin.klinunt2.children[i].value
else:
project_info[
"klinunt2text%s" %
(i)] = self.klin.klinunt2.children[i].description
project_info["klinunt2value%s" %
(i)] = self.klin.klinunt2.children[i].value
for i in range(0, len(self.klin.klinunt3.children)):
project_info["klinunt3text%s" %
(i)] = self.klin.klinunt3.children[i].description
project_info["klinunt3value%s" %
(i)] = self.klin.klinunt3.children[i].value
# Einschlusskriterien
for i, value in enumerate(self.textform.including_criteria):
project_info["ethicsinc%s" % (i)] = value
ja_nein = getattr(self.inc_crit, "widget%s" % (i))
if ja_nein.value == 1:
ja_nein.wert = True
elif ja_nein.value == 2:
ja_nein.wert = False
project_info["ethicsinc_jn%s" % (i)] = ja_nein.wert
# Ausschlusskriterien
for i, value in enumerate(self.textform.excluding_criteria):
project_info["ethicsexc%s" % (i)] = value
ja_nein = getattr(self.ex_crit, "widget%s" % (i))
if ja_nein.value == 1:
ja_nein.wert = True
elif ja_nein.value == 2:
ja_nein.wert = False
project_info["ethicsexc_jn%s" % (i)] = ja_nein.wert
project_info["inc_exc_komm"] = self.stud_crit.komm_criteria.value
for i in range(0, len(self.sens.sens2.children)):
if self.sens.sens2.children[i].description == "Label":
project_info["senstext%s" %
(i)] = self.sens.sens2.children[i].value
else:
project_info["senstext%s" %
(i)] = self.sens.sens2.children[i].description
project_info["sensvalue%s" %
(i)] = self.sens.sens2.children[i].value
# FunCal
for i in range(0, len(self.textform.funcal_names)):
if i == 0:
project_info["funcalnames%s" %
(i)] = self.textform.funcal_names[i][2:]
elif i == 2 or i == 6 or i == 9:
project_info["funcalnames%s" %
(i)] = self.textform.funcal_names[i]
elif i == 3:
project_info["funcalnames%s" %
(i)] = self.textform.funcal_names[i][1:-1]
else:
project_info["funcalnames%s" %
(i)] = self.textform.funcal_names[i][3:]
project_info["funcal1"] = self.fc.FunCal1.get_object_state()
project_info["funcal2"] = self.fc.FunCal2.get_object_state()
project_info["funcal3"] = self.fc.FunCal3.get_object_state()
project_info["funcal4"] = self.fc.FunCal4.get_object_state()
project_info["funcal5"] = self.fc.FunCal5.get_object_state()
# Messung ohne Orthese
for i in range(0, len(self.textform.meas_text)):
if i == 0 or i == 4 or i == 7:
project_info["meastext%s" %
(i)] = self.textform.meas_text[i][3:]
elif i == 3 or i == 5 or i == 9:
project_info["meastext%s" %
(i)] = self.textform.meas_text[i][1:-1]
else:
project_info["meastext%s" %
(i)] = self.textform.meas_text[i]
project_info["ohneStat"] = self.ohneOrth.ohneStat.get_object_state(
)
project_info["ohneXW"] = self.ohneOrth.xxx_xw.get_object_state()
project_info["gewicht"] = self.ohneOrth.gewicht.value
project_info[
"lichtschranken0"] = self.ohneOrth.Lichtschranken.description
project_info[
"lichtschranken1"] = self.ohneOrth.Lichtschranken.value
project_info["timerange0"] = self.ohneOrth.TimeRange.children[
0].description
project_info["timerange1s1"] = self.ohneOrth.TimeRange.children[
0].value
project_info["timerange2"] = self.ohneOrth.TimeRange.children[
1].description
project_info["timerange3s1"] = self.ohneOrth.TimeRange.children[
1].value
# Bewertung des wahrgenommenen Druckes
for i, value in enumerate(self.ohneOrth.druck):
if i == 0:
project_info["druckname%s" % (i)] = value[1:]
else:
project_info["druckname%s" % (i)] = value
for i in range(0, len(self.ohneOrth.druck_num.children)):
project_info["drucknum%s" %
(i)] = self.ohneOrth.druck_num.children[i].value
# Bewertung der empfundenen Anstrengung
for i, value in enumerate(self.ohneOrth.anstrengung):
if i == 0:
project_info["anstrengungname%s" % (i)] = value[1:]
else:
project_info["anstrengungname%s" % (i)] = value
for i in range(0, len(self.ohneOrth.anstrengung_num.children)):
project_info[
"anstrengungnum%s" %
(i)] = self.ohneOrth.anstrengung_num.children[i].value
# Kommentar
project_info["komm_ohne"] = self.ohneOrth.komm_ohne.value
# Messung mit aktiver Fussorthese
project_info[
"aktivStat"] = self.aktiveOrth.aktivStat.get_object_state()
project_info["asc_xw"] = self.aktiveOrth.asc_xw.get_object_state()
project_info["asc_fw"] = self.aktiveOrth.asc_fw.get_object_state()
# Bewertung des wahrgenommenen Druckes
for i in range(0, len(self.aktiveOrth.druck_num.children)):
project_info["drucknumaktiv%s" %
(i)] = self.aktiveOrth.druck_num.children[i].value
# Bewertung der empfundenen Anstrengung
for i in range(0, len(self.aktiveOrth.anstrengung_num.children)):
project_info[
"anstrengungnumaktiv%s" %
(i)] = self.aktiveOrth.anstrengung_num.children[i].value
# System usability scale
t = 0
n = 0
for i in range(
0,
len(self.aktiveOrth.questUsabilityAktive.usability.children
)):
if len(self.aktiveOrth.questUsabilityAktive.usability.
children[i].description) > 1:
project_info["usabilitytext%s" % (
t
)] = self.aktiveOrth.questUsabilityAktive.usability.children[
i].description
t += 1
elif len(self.aktiveOrth.questUsabilityAktive.usability.
children[i].description) == 1:
if self.aktiveOrth.questUsabilityAktive.usability.children[
i].value:
project_info["usabilitynum%s" % (
n
)] = self.aktiveOrth.questUsabilityAktive.usability.children[
i].description
n += 1
elif len(self.aktiveOrth.questUsabilityAktive.usability.
children[i].value) > 1:
project_info["usabilitytext%s" % (
t
)] = self.aktiveOrth.questUsabilityAktive.usability.children[
i].value
t += 1
# Kommentar
project_info["komm_aktive"] = self.aktiveOrth.komm_aktive.value
# Messung mit eigener Orthese
project_info[
"eigenStat"] = self.eigOrth.eigenStat.get_object_state()
project_info["esc_xw"] = self.eigOrth.esc_xw.get_object_state()
project_info["esc_fw"] = self.eigOrth.esc_fw.get_object_state()
# Bewertung des wahrgenommenen Druckes
for i in range(0, len(self.eigOrth.druck_num.children)):
project_info["drucknumeigen%s" %
(i)] = self.eigOrth.druck_num.children[i].value
# Bewertung der empfundenen Anstrengung
for i in range(0, len(self.eigOrth.anstrengung_num.children)):
project_info[
"anstrengungnumeigen%s" %
(i)] = self.eigOrth.anstrengung_num.children[i].value
# Kommentar
project_info["komm_eigene"] = self.eigOrth.komm_eigene.value
# Narrative Report
for i in range(0, len(self.questNarrative.narrative.children)):
project_info["narrative%s" % (
i)] = self.questNarrative.narrative.children[i].description
project_info[
"narrativevalue%s" %
(i)] = self.questNarrative.narrative.children[i].value
# root property as identification i.e case or participant id.
root = os.path.abspath(
"C:\\Users\\paui\\Documents\\Anaconda\\Jupyter_Beispiele\\CRF_Dropfoot"
)
templates_dir = os.path.join(root, 'templates_Dropfoot')
env = Environment(loader=FileSystemLoader(templates_dir))
template = env.get_template('report_template.html')
filename_report = os.path.join(root, 'output_Dropfoot',
'final_report.html')
with open(filename_report, 'w') as fh:
fh.write(template.render(project_info))
# fh.append(template.render(participant_info))
filename_data = os.path.join(root, 'output_Dropfoot',
'final_report.json')
with open(filename_data, 'w') as json_file:
json.dump(project_info, json_file)
self.save_btn.button_style = 'success'
self.save_btn.description = 'Successfully saved results!'
self.save_btn.layout = widgets.Layout(width='200px')
except Exception as e:
self.save_btn.button_style = 'danger'
self.save_btn.description = 'Saving failed!'
print(e)
## --------------------------------------------------------------------------------- ##
## Connection to openBIS ##
def init_openbis_login(self):
"""
Initialization ot the openbis login button.
"""
# Create login ui
login_btn = widgets.Button(description='Login to openBIS',
tooltip='Login to openBIS')
login_btn.on_click(self.on_login_clicked)
openbis_instance = widgets.Text(
description='openBIS URL:',
value=
'https://openbis-zhaw-gtf.labnotebook.ch/openbis/webapp/eln-lims/?'
)
user = widgets.Text(description='Username:'******'Password:'******'Upload', tooltip='Upload')
upload_btn.on_click(self.on_upload_clicked)
exp_step_name = widgets.Text(description='New participant name:',
placeholder='PROJECT_SUBJECT',
style={'description_width': 'initial'})
exp_name = widgets.Text(description='Experiment:',
placeholder='EXPERIMENT',
style={'description_width': 'initial'})
project = widgets.Text(description='Project:', placeholder='PROJECT')
space = widgets.Text(description='Space:', placeholder='SPACE')
self.new_exp_ui = widgets.VBox(
[exp_step_name, exp_name, project, space, upload_btn])
def show_new_exp_ui(self):
"""Show the new openbis experiment form to the user."""
display(self.new_exp_ui)
def upload_to_openbis(self):
"""Show the openbis login form to the user."""
self.show_openbis_login()
@output.capture(clear_output=False)
def on_login_clicked(self, *args):
"""Login button clicked button callback. Defines what should happen when the login button got clicked."""
obj = args[0]
try:
self.openbis = Openbis(url=self.openbis_login_ui.children[0].value,
verify_certificates=False)
self.openbis.login(
self.openbis_login_ui.children[1].children[0].value,
self.openbis_login_ui.children[1].children[1].value)
self.openbis_login_ui.children[1].value = '' # Security measure.
obj.button_style = 'success'
obj.description = 'Connected'
self.show_new_exp_ui()
except Exception as e:
self.openbis_login_ui.children[1].value = '' # Security measure.
obj.button_style = 'danger'
obj.description = 'Login failed. Retry.'
@output.capture(clear_output=True)
def on_upload_clicked(self, *args):
"""Upload button clicked button callback. Defines what should happen when the upload button got clicked."""
obj = args[0]
date = self.meta.study_metadata.children[0].value
try:
# Create new properties for new subject
pt = self.openbis.new_property_type(
code='GEWICHT_KINETIK',
label='Gewichtsmessung für Kinetik [kg]',
description='Gewichtsmessung für Kinetik [kg]',
dataType='REAL')
# Create new subject in openBIS
exp_step = self.openbis.new_sample(
code=self.new_exp_ui.children[0].value,
type='EXPERIMENTAL_STEP',
space=self.new_exp_ui.children[3].value,
experiment='/' + self.new_exp_ui.children[3].value + '/' +
self.new_exp_ui.children[2].value + '/' +
self.new_exp_ui.children[1].value,
props={
"id": str(self.meta.study_metadata.children[1].value),
"date": date.strftime('%Y-%m-%d %H:%M'),
"investigator": self.meta.study_metadata.children[2].value,
"gewicht_kinetik": self.ohneOrth.gewicht.value
})
exp_step.save()
print(os.getcwd())
# Upload data files to new subject
ds_new = self.openbis.new_dataset(
type='ANALYZED_DATA',
experiment='/' + self.new_exp_ui.children[3].value + '/' +
self.new_exp_ui.children[2].value + '/' +
self.new_exp_ui.children[1].value,
sample='/' + self.new_exp_ui.children[3].value + '/' +
self.new_exp_ui.children[2].value + '/' +
self.new_exp_ui.children[1].value + '/' +
self.new_exp_ui.children[0].value,
files=[
'output_Dropfoot\\final_report.html',
'output_Dropfoot\\final_report.json'
])
ds_new.save()
obj.button_style = 'success'
obj.description = 'Upload successfull'
except Exception as e:
obj.button_style = 'danger'
obj.description = 'Upload failed. Retry.'
print(e)
self.show_new_exp_ui()
level=logging.INFO,
format=
'%(levelname)s %(asctime)s: %(funcName)s() %(lineno)d: \t%(message)s',
datefmt='%Y/%m/%d %H:%M:%S')
logger = logging.getLogger()
tqdm_out = TqdmToLogger(logger, level=logging.INFO)
# Add the log message handler to the logger
handler = logging.handlers.RotatingFileHandler(LOG_FILENAME,
maxBytes=1E7,
backupCount=5)
logger.addHandler(handler)
# open the session first
o = Openbis('https://s3itdata.uzh.ch', verify_certificates=True)
if not o.is_session_active():
o = Openbis('https://s3itdata.uzh.ch', verify_certificates=False)
config = configparser.ConfigParser()
config.read(os.path.expanduser('~/.pybis/cred.ini'))
username = config['credentials']['username']
password = config['credentials']['password']
o.login(username, password, save_token=True)
logging.info('-----------Mapping session starting------------')
for pro in [
'antibodies', 'resistance', 'metagenomics', 'plasmids', 'other',
'retroseq', 'consensus'
]:
general_mapping(pro)
logging.info('-----------Mapping session finished------------')
def test_token(openbis_instance):
assert openbis_instance.hostname is not None
new_instance = Openbis(openbis_instance.url)
new_instance.login('admin', 'any_test_password')
assert new_instance.token is not None
assert new_instance.is_token_valid() is True
new_instance.logout()
assert new_instance.is_token_valid() is False
invalid_connection = Openbis(openbis_instance.url)
with pytest.raises(Exception):
invalid_connection.login('invalid_username', 'invalid_password')
assert invalid_connection.token is None
assert invalid_connection.is_token_valid() is False
def establish_db_connection():
# Should be done during server startup or when calling a function to set or get data
o = Openbis(os.environ['OPENBIS_SERVER'], verify_certificates=False)
o.login(os.environ['OPENBIS_USER'], os.environ['OPENBIS_PASSWORD'])
return o