class EditMeas(twf.TableForm):
#fields
IDselected = twf.HiddenField(label_text="ID selected :")
name = twf.TextField(label_text="Name :",
placeholder="Measurement name...",
validator=twc.Required)
description = twf.TextArea(label_text="Description :")
samples = twf.MultipleSelectField(
label_text="Your samples : ",
help_text="You can add some of your existing data to this project.")
status_type = twf.CheckBox(
label_text="Privacy : ",
help_text=
"Check it if you want a public data (available for UCSC visualisation)"
)
type = twf.CheckBox(label_text="Raw data : ",
help_text="Check it is a raw data")
#parents management
parents = twf.MultipleSelectField(
label_text="Parents : ", help_text="Parent(s) of this measurement.")
uploaded = twf.LabelField(
help_text=
"is attached to this measurement. If you want to change, it's better to delete this measurement and create a new one."
)
url_path = twf.TextField(label_text="File's url",
placeholder="http://www....")
submit = twf.SubmitButton(value="Edit my measurement")
class EditProject(twf.TableForm):
pid = twf.HiddenField()
name = twf.TextField(label='Name : ',
validator=twc.Validator(required=True))
tracks = twf.MultipleSelectField(label='Tracks : ',
css_class='track_select')
submit = twf.SubmitButton(id="submit", value="Edit")
class child(twf.TableLayout):
hover_help = True
email_filter = twf.HiddenField()
id_filter = twf.HiddenField()
user_Id= twf.TextField(help_text='Enter a user id.', validator=twc.IntValidator(required=True))
licenses = twf.MultipleSelectField(help_text='Licenses to assign.', options=[], validator=twc.Required)
license_type = twf.SingleSelectField(help_text='Licenes Type.', value=0, options=[], validator=twc.Required)
count = twf.SingleSelectField(help_text='Number of licenses.', value=1, options=[(i, i) for i in range(1,6)], validator=twc.Required)
class NewTrackHub(twf.TableForm):
#fields
name = twf.TextField(label_text="Name : ", help_text="no space, use '_'")
assembly = twf.LabelField(
help_text=" is the assembly related to these files")
files = twf.MultipleSelectField(label_text="Files used : ")
extension = twf.LabelField(
help_text=" is your files extensions for this TrackHub")
submit = twf.SubmitButton(value="Visualise")
class NewProject(twf.TableForm):
# __omit_fields__ = ['id', 'user', 'date', 'created']
project_name = twf.TextField(label_text="Name :",
validator=twc.Validator(required=True))
description = twf.TextArea(label_text="Description :", )
samples = twf.MultipleSelectField(
label_text="Your samples : ",
help_text="You can add some of your existing samples to this project.")
submit = twf.SubmitButton(value="Create my project")
class EditProject(twf.TableForm):
# __omit_fields__ = ['user', 'date', 'created']
IDselected = twf.HiddenField(label_text="ID selected")
project_name = twf.TextField(label_text="Name :", validator=twc.Required)
description = twf.TextArea(label_text="Description :", )
samples = twf.MultipleSelectField(
label_text="Your samples : ",
help_text="You can add some of your existing samples to this project.")
selected_samples = twf.HiddenField(label_text="")
submit = twf.SubmitButton(id="submit", value="Edit my project")
class EditSample(twf.TableForm):
IDselected = twf.HiddenField(label_text="ID selected :")
project = twf.SingleSelectField(
label_text="Your projects : ",
help_text="the project which contains your sample is selected")
name = twf.TextField(label_text="Name :", validator=twc.Required)
type = twf.SingleSelectField(label_text="Type : ")
protocole = twf.TextArea(label_text="Protocole :")
measurements = twf.MultipleSelectField(
label_text="Attached measurement(s) : ")
submit = twf.SubmitButton(value="Edit my sample")
class ShareProject(twf.TableForm):
pid = twf.HiddenField()
circles = twf.MultipleSelectField(label='Circles : ',
css_class='circle_select')
submit = twf.SubmitButton(id="submit", value="Share")
def clone_form(user_lab, id_object):
'''
to clone dynamic measurement form
'''
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
#static list ]
list_static = [
twf.HiddenField(id="IDselected", label_text="ID selected :"),
twf.TextField(id="name",
label_text="Name :",
placeholder="Measurement name...",
validator=twc.Validator(required=True)),
twf.TextArea(id="description", label_text="Description :"),
twf.MultipleSelectField(
id="samples",
label_text="Your samples : ",
help_text="You can add some of your existing data to this project."
),
twf.CheckBox(
id="status_type",
label_text="Privacy : ",
help_text=
"Check to have it available from outside EPFL (required for UCSC visualisation)"
),
twf.CheckBox(id="type",
label_text="Raw data : ",
help_text="Check if raw data"),
#twf.MultipleSelectField(id="parents", label_text="Parents : ", help_text="Parent(s) of this measurement."),
twd.HidingRadioButtonList(id="upload_way",
label_text='Upload my file via...',
options=('my computer', 'a Vital-IT path',
'a URL'),
mapping={
'my computer': ['upload'],
'a Vital-IT path': ['vitalit_path'],
'a URL': ['url_path', 'url_up'],
}),
twf.FileField(id="upload", help_text='Please provide a data'),
twf.TextField(id="vitalit_path",
label_text="Scratch path",
placeholder="/scratch/el/biorepo/dropbox/"),
twf.TextField(id="url_path",
label_text="File's url",
placeholder="http://www..."),
twf.CheckBox(id="url_up",
label_text="I want to upload the file from this URL : ",
help_text="tick it if you want to download it in BioRepo")
]
list_dynamic = []
if lab is None:
print "----- no dynamic fields detected ---------"
list_fields = [list_static, list_dynamic]
return list_fields
else:
to_clone = DBSession.query(Measurements).filter(
Measurements.id == int(id_object)).first()
tag = "measurements"
if to_clone is not None:
list_dynamic_attributes = to_clone.attributs
for att in list_dynamic_attributes:
if att.deprecated == False:
twf_type = convert_widget(att.widget)
twf_type.id = att.key
list_a_values = att.values
if att.widget == "textfield" or att.widget == "textarea" or att.widget == "hiding_textfield" or att.widget == "hiding_textarea":
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if to_clone in value_object:
twf_type.value = v.value
list_dynamic.append(twf_type)
elif att.widget == "checkbox" or att.widget == "hiding_checkbox":
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if to_clone in value_object:
#dynamic boolean are stored in varchar in the db, we have to cast them in boolean for the display
value_2_display = check_boolean(v.value)
twf_type.value = value_2_display
list_dynamic.append(twf_type)
elif att.widget == "multipleselectfield" or att.widget == "hiding_multipleselectfield":
list_possible_values = []
for v in list_a_values:
list_possible_values.append(v.value)
twf_type.options = list_possible_values
selected_values = []
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if to_clone in value_object:
selected_values.append(v.value)
twf_type.value = selected_values
list_dynamic.append(twf_type)
elif att.widget == "singleselectfield" or att.widget == "hiding_singleselectfield":
list_possible_values = []
for v in list_a_values:
if v.value not in list_possible_values:
list_possible_values.append(v.value)
twf_type.options = list_possible_values
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if to_clone in value_object:
twf_type.value = v.value
list_dynamic.append(twf_type)
else:
print "Your measurement was not found. ID problem. id :", id_object
raise
list_fields = [list_static, list_dynamic]
return list_fields
def edit_form(user_lab, owner, id_object):
'''
to edit dynamic form
'''
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
#static lists
list_static_samples = [
twf.HiddenField(id="IDselected", label_text="ID selected :"),
twf.SingleSelectField(
id="project",
label_text="Your projects : ",
help_text="the project which contains your sample is selected",
prompt_text=None),
twf.TextField(id="name", label_text="Name :", validator=twc.Required),
twf.SingleSelectField(id="type",
label_text="Type : ",
help_text="What technique do you use ?",
prompt_text=None),
twf.TextArea(
id="protocole",
label_text="Protocole :",
),
twf.MultipleSelectField(id="measurements",
label_text="Attached measurement(s) : ")
]
list_static_measurements = [
twf.HiddenField(id="IDselected", label_text="ID selected :"),
twf.TextField(id="name",
label_text="Name :",
placeholder="Measurement name...",
validator=twc.Required),
twf.TextArea(id="description", label_text="Description :"),
twf.MultipleSelectField(
id="samples",
label_text="Your samples : ",
help_text="You can add some of your existing data to this project."
),
twf.CheckBox(
id="status_type",
label_text="Privacy : ",
help_text=
"Check to have it available from outside EPFL (required for UCSC visualisation)"
),
twf.CheckBox(id="type",
label_text="Raw data : ",
help_text="Check if raw data"),
twf.MultipleSelectField(id="parents",
label_text="Parents : ",
help_text="Parent(s) of this measurement."),
twf.LabelField(
id="uploaded",
help_text=
"is attached to this measurement. If you want to change, it's better to delete this measurement and create a new one."
),
twf.TextField(
id="url_path",
help_text=
"If you want to add a new URL, your old URL will be stored into the description",
placeholder="http://www...")
#twf.CheckBox(id="url_up", label_text="I want to upload the file from this URL : ",
#help_text="tick it if you want to download it in BioRepo")
]
list_dynamic_samples = []
list_dynamic_measurements = []
if lab is None:
print "----- no dynamic fields detected ---------"
list_fields = [
list_static_samples, list_dynamic_samples,
list_static_measurements, list_dynamic_measurements
]
return list_fields
else:
if owner == "sample":
object_edited = DBSession.query(Samples).filter(
Samples.id == int(id_object)).first()
list_dynamic = list_dynamic_samples
tag = "samples"
elif owner == "meas":
object_edited = DBSession.query(Measurements).filter(
Measurements.id == int(id_object)).first()
list_dynamic = list_dynamic_measurements
tag = "measurements"
else:
print "----------------- owner error : ", owner, " <----owner --------------------"
raise
if object_edited is not None:
list_dynamic_attributes = object_edited.attributs
for att in list_dynamic_attributes:
if att.deprecated == False:
twf_type = convert_widget(att.widget)
twf_type.id = att.key
list_a_values = att.values
if att.widget == "textfield" or att.widget == "textarea" or att.widget == "hiding_textfield" or att.widget == "hiding_textarea":
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if object_edited in value_object:
twf_type.value = v.value
list_dynamic.append(twf_type)
elif att.widget == "checkbox" or att.widget == "hiding_checkbox":
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if object_edited in value_object:
#dynamic boolean are stored in varchar in the db, we have to cast them in boolean for the display
value_2_display = check_boolean(v.value)
twf_type.value = value_2_display
list_dynamic.append(twf_type)
elif att.widget == "multipleselectfield" or att.widget == "hiding_multipleselectfield":
list_possible_values = []
for v in list_a_values:
list_possible_values.append(v.value)
twf_type.options = list_possible_values
selected_values = []
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if object_edited in value_object:
selected_values.append(v.value)
twf_type.value = selected_values
list_dynamic.append(twf_type)
elif att.widget == "singleselectfield" or att.widget == "hiding_singleselectfield":
list_possible_values = []
for v in list_a_values:
if v.value not in list_possible_values:
list_possible_values.append(v.value)
twf_type.options = list_possible_values
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if object_edited in value_object:
twf_type.value = v.value
list_dynamic.append(twf_type)
else:
print "Your ", owner, " was not found. ID problem. id :", id_object
raise
list_fields = [
list_static_samples, list_dynamic_samples,
list_static_measurements, list_dynamic_measurements
]
return list_fields
def new_form_parents(user_lab):
'''for new form with parents'''
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
#static lists
list_static_samples = [
twf.SingleSelectField(id="project",
label_text="Your projects : ",
help_text="Select project for this sample",
prompt_text=None),
twf.TextField(id="name",
label_text="Name :",
validator=twc.Validator(required=True)),
twf.SingleSelectField(id="type",
label_text="Type : ",
help_text="Technique used",
prompt_text=None),
twf.TextArea(
id="protocole",
label_text="Protocole :",
)
]
list_static_measurements = [
twf.HiddenField(id="IDselected", label_text="ID selected :"),
twf.TextField(id="name",
label_text="Name :",
placeholder="Measurement name...",
validator=twc.Validator(required=True)),
twf.TextArea(id="description", label_text="Description :"),
twf.MultipleSelectField(
id="samples",
label_text="Your samples : ",
help_text="You can add some of your existing data to this project."
),
twf.CheckBox(
id="status_type",
label_text="Privacy : ",
help_text=
"Check to have it available from outside EPFL (required for UCSC visualisation)"
),
twf.CheckBox(id="type",
label_text="Raw data : ",
help_text="Check if raw data"),
twf.MultipleSelectField(id="parents",
label_text="Parents : ",
help_text="Parent(s) of this measurement."),
twd.HidingRadioButtonList(id="upload_way",
label_text='Upload my file via...',
options=('my computer', 'a Vital-IT path',
'a URL'),
mapping={
'my computer': ['upload'],
'a Vital-IT path': ['vitalit_path'],
'a URL': ['url_path', 'url_up'],
}),
twf.FileField(id="upload", help_text='Please provide a data'),
twf.TextField(id="vitalit_path",
label_text="Scratch path",
placeholder="/scratch/el/biorepo/dropbox/"),
twf.TextField(id="url_path",
label_text="File's url",
placeholder="http://www..."),
twf.CheckBox(id="url_up",
label_text="I want to upload the file from this URL : ",
help_text="tick it if you want to download it in BioRepo")
]
list_dynamic_samples = []
list_hiding_samples = []
list_dynamic_measurements = []
list_hiding_meas = []
#catch the dynamic hiding fields
dic_hiding_meas = session.get("hiding_meas", {})
dic_hiding_samples = session.get("hiding_sample", {})
if lab is None:
print "----- no dynamic fields detected ---------"
list_fields = [
list_static_samples, list_dynamic_samples,
list_static_measurements, list_dynamic_measurements
]
return list_fields
else:
lab_id = lab.id
list_attributs = DBSession.query(Attributs).filter(
Attributs.lab_id == lab_id).all()
if len(list_attributs) > 0:
#lists_construction(list_attributs)
for a in list_attributs:
attribut_key = a.key
deprecated = a.deprecated
fixed_value = a.fixed_value
widget = a.widget
owner = a.owner
#############################
######### NEW SAMPLE ########
#############################
if owner == "sample":
#dynamic
if not deprecated and fixed_value:
twf_type = convert_widget(widget)
twf_type.id = attribut_key
if widget == "multipleselectfield" or widget == "singleselectfield":
list_values = []
list_attributes_values = DBSession.query(
Attributs_values).filter(
Attributs_values.attribut_id ==
a.id).all()
for av in list_attributes_values:
if not av.deprecated and av.value not in list_values:
list_values.append(av.value)
twf_type.options = list_values
list_dynamic_samples.append(twf_type)
elif widget == "checkbox":
list_dynamic_samples.append(twf_type)
elif widget == "hiding_singleselectfield":
list_values = []
list_attributes_values = DBSession.query(
Attributs_values).filter(
Attributs_values.attribut_id ==
a.id).all()
for av in list_attributes_values:
if not av.deprecated and av.value not in list_values:
list_values.append(av.value)
twf_type.options = list_values
list_hiding_samples.append(twf_type)
elif widget == "hiding_checkbox":
list_hiding_samples.append(twf_type)
else:
print widget, "-----ERROR----- ELSE, type samples widget in forms.py"
elif not deprecated and not fixed_value:
twf_type = convert_widget(widget)
twf_type.id = attribut_key
if widget == "textfield" or widget == "textarea":
twf_type.placeholder = "Write here..."
list_dynamic_samples.append(twf_type)
elif widget == "checkbox":
list_dynamic_samples.append(twf_type)
elif widget == "hiding_textfield" or widget == "hiding_textarea":
twf_type.placeholder = "Write here..."
list_hiding_samples.append(twf_type)
elif widget == "hiding_checkbox":
list_hiding_samples.append(twf_type)
else:
print widget, "WIDGET SAMPLE NOT FOUND, add an elif please"
raise
elif deprecated:
pass
else:
print "WIDGET SAMPLES ERROR : widget type is not known --> ", widget
raise
################################
######## NEW MEASUREMENT #######
################################
elif owner == "measurement":
#dynamic
#for attributes with fixed values
if not deprecated and fixed_value:
twf_type = convert_widget(widget)
twf_type.id = attribut_key
if widget == "multipleselectfield" or widget == "singleselectfield":
list_values = []
list_attributes_values = DBSession.query(
Attributs_values).filter(
Attributs_values.attribut_id ==
a.id).all()
for av in list_attributes_values:
if not av.deprecated and av.value not in list_values:
list_values.append(av.value)
twf_type.options = list_values
list_dynamic_measurements.append(twf_type)
elif widget == "hiding_singleselectfield":
list_values = []
list_attributes_values = DBSession.query(
Attributs_values).filter(
Attributs_values.attribut_id ==
a.id).all()
for av in list_attributes_values:
if not av.deprecated and av.value not in list_values:
list_values.append(av.value)
twf_type.options = list_values
list_hiding_meas.append(twf_type)
#elif widget == "checkbox":
#list_dynamic_measurements.append(twf_type)
else:
print widget, "-----ERROR----- ELSE, type measurements widget in forms.py"
raise
#for others attributes
elif not deprecated and not fixed_value:
twf_type = convert_widget(widget)
twf_type.id = attribut_key
if widget == "textfield" or widget == "textarea":
twf_type.placeholder = "Write here..."
list_dynamic_measurements.append(twf_type)
elif widget == "checkbox":
list_dynamic_measurements.append(twf_type)
elif widget == "hiding_textfield" or widget == "hiding_textarea":
twf_type.placeholder = "Write here..."
list_hiding_meas.append(twf_type)
elif widget == "hiding_checkbox":
list_hiding_meas.append(twf_type)
else:
print widget, "WIGDET MEASUREMENT NOT FOUND, add an elif please"
raise
elif deprecated:
pass
#in bugs case
else:
print "WIDGET MEASUREMENTS ERROR : widget type is not known --> ", widget
raise
#TO TEST WITH SEVERAL TWD OBJECTS
#build dynamic dynamic fields
#samples
list_twd_s = []
for k in dic_hiding_samples:
twd_object = twd.HidingRadioButtonList()
twd_object.id = k
dico_mapping = dic_hiding_samples[k]
options = []
for key in dico_mapping.keys():
options.append(key)
twd_object.options = options
twd_object.mapping = dico_mapping
list_twd_s.append(twd_object)
list_dynamic_samples = list_dynamic_samples + list_twd_s + list_hiding_samples
#measurements
list_twd_m = []
for k in dic_hiding_meas:
twd_object = twd.HidingRadioButtonList()
twd_object.id = k
dico_mapping = dic_hiding_meas[k]
options = []
for key in dico_mapping.keys():
options.append(key)
twd_object.options = options
twd_object.mapping = dico_mapping
list_twd_m.append(twd_object)
list_dynamic_measurements = list_dynamic_measurements + list_twd_m + list_hiding_meas
list_fields = [
list_static_samples, list_dynamic_samples,
list_static_measurements, list_dynamic_measurements
]
return list_fields
else:
print "-----forms.py----- Houston, we have a problem : The lab ", lab.name, " doesn't get any attributes -----"
raise