class ProjectGrid(BootstrapGrid):
fields = [("Project id", "id"), ("User", "get_username"),
("Name", "project_name"),
("Samples", lambda obj: genshi.Markup(obj.samples_display)),
("Description", "description"), ("Date", "created"),
("Actions", lambda obj: genshi.Markup(
get_edit_link(obj.id) + get_delete_project(obj.id)))]
def pliki(self, obj):
import collections
if obj.filename:
if isinstance(obj.filename, collections.Iterable):
value= '<div><ol>'
for file in obj.filename:
value += '<li><a href="/files/{0}">{1}</a></li>'.format(file.filename, file.name)
value += '</ol></div>'
return value
else:
return genshi.Markup('<a href="/files/{0}">test_{0}</a>'.format(obj.filename.filename) )
else:
return genshi.Markup('<em>None</em>')
def redeemLicense(obj):
if obj.Assignemt.count_1 > 0:
return genshi.Markup(
'<a href="%s">Redeem</a>' %
url('/create_license', params=dict(id=obj.Computer.id)))
else:
return ''
def get_title(self):
cur_ordering = request.GET.get('ordercol')
if cur_ordering is not None:
cur_ordering = urllib2.unquote(cur_ordering.encode('utf8'))
args = re.findall('(\+|\-){1}(\w+)+', cur_ordering)
isin = False
for i in range(len(args)):
tmp = args[i]
sign = tmp[0]
word = tmp[1]
if word == self.name:
sign = sign == '+' and '-' or '+'
isin = True
args[i] = (sign, word)
if not isin:
args.append(('+', self.name))
else :
args = [('+', self.name)]
new_params = dict(request.GET)
new_params['ordercol'] = ''.join('%s%s' % (k, v) for k, v in args)
new_url = url(request.path_url, params=new_params)
return genshi.Markup('<a href=%s > %s </a>' % (new_url, self._title))
def to_json(self):
return {
'meas': {
'id':
self.meas.id,
'user':
self.get_name(),
'name':
self.get_meas_name(),
'description':
self.meas.description,
'created':
self.date.strftime(date_format),
'samples': [sample.to_json() for sample in self.samples],
'samples_display':
' ; '.join(['%s' % (sample.name) for sample in self.samples]),
'projects_display':
self.get_projects(),
'sample_type':
self.get_sample_type(),
'measurement_type':
self.get_measurement_type(),
'attributs_meas':
[a.to_json() for a in self.meas.attributs if not a.deprecated],
'attributs_samples':
self.get_attributs_samples_json(),
'scroll_info':
genshi.Markup(self.get_img_scroll()),
'get_extension':
self.get_extension
}
}
class MeasGrid(BootstrapGrid):
fields = [
("User", "get_username"),
("Sample", "samples_display"),
("Name", "name"),
('Attachment', lambda obj: genshi.Markup(obj.get_extension)),
("Description", "description"),
("Visibility", "get_status_type"),
("Raw", "get_type"),
("Date", "created"),
(
"Action",
lambda obj: genshi.Markup(
get_dl_link2(obj.id)
#+ get_UCSC_link(obj.id)
#+ get_GDV_link(obj.id)
+ get_edit_link(obj.id) + get_delete_link(obj.id)))
]
def make_tooltip(title, message):
return genshi.Markup('''
<div class='tooltip_gdv'>
<div class='tooltip_hider'></div>
<span class='tooltip_pane'>
<div class='tooltip_title'><h3>%s</h3></div>
<div class='tooltip_body'>%s</div>
</span>
</div>
''' % (title, message))
class SearchGridT(DataGrid):
# fields = [("User","get_username"),("Cell Type", lambda obj:genshi.Markup(obj.sample_cell_type)),
# ("Species",lambda obj:genshi.Markup(obj.sample_species)),
# ("Ab target", lambda obj:genshi.Markup(obj.sample_ab_target)),("Bio bg",lambda obj:genshi.Markup(obj.sample_bio_bg)),
# ("Type",lambda obj:genshi.Markup(obj.sample_type)),("DataType",lambda obj:genshi.Markup(obj.measurement_type)),
# ("Description",lambda obj:genshi.Markup(obj.description)),
# ("Action", lambda obj:genshi.Markup(
# get_info_link(obj.id,obj.description)
# +get_dl_link(obj.id)
# +get_UCSC_link(obj.id)
# +get_GDV_link(obj.id)
# +get_SPAN_id(obj.id)
# ))]
# ----------------------------- old version ---------------
# fields = [("User", "get_username"),
# ("Samples", lambda obj:genshi.Markup(obj.samples_display)), ("Type", lambda obj:genshi.Markup(obj.sample_type)),
# ("Cell Type", lambda obj:genshi.Markup(obj.sample_cell_type)), ("Target", lambda obj:genshi.Markup(obj.sample_ab_target)),
# ("Bio bg", lambda obj:genshi.Markup(obj.sample_bio_bg)), ("Stage", lambda obj:genshi.Markup(obj.sample_stage)),
# ("Measurements", "name"), ("Assembly", "assembly"),
# ("DataType", lambda obj:genshi.Markup(obj.measurement_type)), ("Date", "created"), ("Final", lambda obj:genshi.Markup(obj.flag_final_type)),
# ("Description", lambda obj:genshi.Markup(obj.description)),
# ("Action", lambda obj:genshi.Markup(
# get_info_link(obj.id, obj.description)
# + get_dl_link(obj.id)
# + get_UCSC_link(obj.id)
# + get_GDV_link(obj.id)
# + get_SPAN_id(obj.id)
# ))]
fields = [
("User", "get_username"),
("Samples", lambda obj: genshi.Markup(obj.samples_display)),
("Type", lambda obj: genshi.Markup(obj.sample_type)),
("Measurements", "name"),
("DataType", lambda obj: genshi.Markup(obj.measurement_type)),
("Date", "created"),
("Action", lambda obj: genshi.Markup(
get_info_link(obj.id, obj.description) + get_dl_link(obj.id) +
get_UCSC_link(obj.id) + get_GDV_link(obj.id) + get_SPAN_id(obj.id))
)
]
def get_task_status(track=None):
'''
Get a output for the status of a task: a link to the traceback if the status is ``FAILURE``,
else the string representing the status.
@param track: the track to get the status from
'''
obj = track
if obj.status != constants.ERROR:
return obj.status
return genshi.Markup('<a href="%s">%s</a>' % (url('./traceback', params={'track_id': obj.id, 'tmp': obj.tmp}),
constants.ERROR
))
def track_grid_user(user, project=None):
return twf.DataGrid(fields=[
('Name', 'name'),
(hoover_action, lambda obj: hoover_actions(
helpers.export_link(obj.id, url('/tracks'), project=project) +
helpers.edit_link(obj.id, url('/tracks'), project=project) +
helpers.delete_link(obj.id, url('/tracks'), project=project))),
('Color', lambda obj: genshi.Markup(helpers.track_color(obj))),
('Owner', 'owner'),
('Created', 'created'),
('Assembly', 'sequence'),
('Type', 'vizu'),
(hidden_info, lambda obj: hide_info({
'tr_id': obj.id,
'tr_status': obj.status,
})),
])
def track_grid_permissions(user=None, rights=None, project=None):
# hidden info on the track
h_info = lambda obj: hide_info({
'tr_id': obj.id,
'tr_status': obj.status,
'tr_color': helpers.get_track_color(obj),
})
debug('Track grid permissions with %s' % rights)
return twf.DataGrid(fields=[
('Name', 'name'),
(hoover_action, lambda obj: get_actions(obj, user, rights, project)),
('Color', lambda obj: genshi.Markup(helpers.track_color(obj))),
('Owner', 'owner'),
('Created', 'created'),
('Assembly', 'sequence'),
('Type', 'vizu'),
(hidden_info, h_info),
])
def __init__(self, meas):
self.meas = meas
self.id = self.meas.id
self.user = self.get_name()
self.description = self.meas.description
self.date = self.meas.date
self.created = self.date.strftime(date_format)
self.samples = self.meas.samples
self.samples_display = ' ; '.join(
['%s' % (sample.name) for sample in self.samples])
self.projects_display = self.get_projects()
self.name = self.get_meas_name()
self.sample_type = self.get_sample_type()
self.measurement_type = self.get_measurement_type()
self.attributs_meas = [
a for a in self.meas.attributs if not a.deprecated
]
#self.searchable_attributs_meas = [a for a in self.attributs_meas if a.searchable]
self.attributs_samples = self.get_attributs_samples()
#self.searchable_attributs_samples = [a for a in self.attributs_samples if a.searchable]
self.scroll_info = genshi.Markup(self.get_img_scroll())
self.get_extension = self.get_extension()
def unlockComputer(obj):
return genshi.Markup('<form method="POST" action="%s" class="button-to"><input type="hidden" name="_method" value="Unlock" /><input class="delete-button" onclick="return confirm(\'Are you sure you want to unlock this computer?\');" value="Unlock" type="submit" style="background-color:transparent; float:left; border:0; color: #286571; display:inline; margin:0; padding:0;"/></form>' % url('/unlock_computer', params=dict(id=obj.Computer.id)))
def redeemLicense(obj):
count = DBSession.query(model.Assignment).filter(model.Assignment.computer_id==obj.id, model.Assignment.user_id==obj.user_id).count()
if count > 0:
return genshi.Markup('<form method="POST" action="%s" class="button-to"><input type="hidden" name="_method" value="DELETE" /><input class="delete-button" onclick="return confirm(\'All assignments to this computer will be locked. Are you sure you want to redeem the assigned licenses?\');" value="Redeem" type="submit" style="background-color:transparent; float:left; border:0; color: #286571; display:inline; margin:0; padding:0;"/></form>' % url('/create_license', params=dict(id=obj.id)))
else:
return genshi.Markup('<a href="%s">Delete </a>' % url('/delete_computer', params=dict(id=obj.id)))
def removeAssignment(obj):
locked = DBSession.query(model.Assignment.locked).filter(model.Assignment.id==obj.Assignment.id, model.Assignment.user_id==obj.Assignment.user_id).first().locked
if locked == True:
return ''
else:
return genshi.Markup('<a href="%s">Delete</a>' % url('/delete_assignment', params=dict(id=obj.Assignment.id)))
def help_address(hurl, section, title):
return genshi.Markup('''
<a href="%s#%s" title="%s">
<img src="../images/question.png" width="16" height="16"/></a>
</a>
''' % (hurl, section, title))
def to_json_test(self):
static_fields = {
'Description':
self.meas.description,
'User':
self.get_name(),
'Measurements':
self.get_meas_name(),
'description':
self.meas.description,
'Created':
self.date.strftime(date_format),
'Samples':
' ; '.join(['%s' % (sample.name) for sample in self.samples]),
'Projects':
self.get_projects(),
'Type':
self.get_sample_type(),
'DataType':
self.get_measurement_type(),
'scroll_info':
genshi.Markup(self.get_img_scroll()),
'Attachment':
self.get_extension,
'Actions':
get_info_link(self.id) + get_dl_link(self.id) +
get_public_link(self.id) + get_UCSC_link(self.id) +
get_GViz_link(self.id) + get_SPAN_id(self.id)
}
#find None statics fields to change the display in datatables
for sf in static_fields.keys():
if static_fields[sf] is None or static_fields[sf] == "":
static_fields[sf] = None
dyn_in_searchgrid = session.get("search_grid_fields", [])
labo = session.get("current_lab")
for d in dyn_in_searchgrid:
new = d.replace("_", " ")
dyn_in_searchgrid.remove(d)
dyn_in_searchgrid.append(new)
meas_dynamic_fields = {}
samples_dynamic_fields = {}
attributs_meas = [
a.to_json() for a in self.meas.attributs if not a.deprecated
]
list_avalues_meas = self.meas.a_values
for avm in list_avalues_meas:
for am in attributs_meas:
key = am["key"].replace("_", " ")
if str(am["id"]) == str(avm.attribut_id):
if am["widget"] != "checkbox" and am[
"widget"] != "hiding_checkbox":
meas_dynamic_fields[key] = avm.value
else:
if check_boolean(avm.value):
meas_dynamic_fields[key] = key
else:
meas_dynamic_fields[key] = "NOT " + str(key)
attributs_samples = self.get_attributs_samples_json()
if len(self.samples) < 2:
for s in self.samples:
list_avalues_samples = s.a_values
for avs in list_avalues_samples:
for a_s in attributs_samples:
key = a_s["key"].replace("_", " ")
if str(a_s["id"]) == str(avs.attribut_id):
if a_s["widget"] != "checkbox" and a_s[
"widget"] != "hiding_checkbox":
samples_dynamic_fields[key] = avs.value
else:
if check_boolean(avs.value):
samples_dynamic_fields[key] = key
else:
samples_dynamic_fields[key] = "NOT " + str(
key)
else:
for s in self.samples:
list_avalues_samples = s.a_values
for avs in list_avalues_samples:
for a_s in attributs_samples:
key = a_s["key"].replace("_", " ")
if str(a_s["id"]) == str(avs.attribut_id):
if a_s["widget"] != "checkbox" and a_s[
"widget"] != "hiding_checkbox":
if key not in samples_dynamic_fields.keys():
samples_dynamic_fields[key] = [avs.value]
else:
if avs.value not in samples_dynamic_fields[
key]:
samples_dynamic_fields[key].append(
avs.value)
else:
if check_boolean(avs.value):
if key not in samples_dynamic_fields.keys(
):
samples_dynamic_fields[key] = [key]
else:
samples_dynamic_fields[key].append(key)
else:
if key not in samples_dynamic_fields.keys(
):
samples_dynamic_fields[key] = [
"NOT " + str(key)
]
else:
samples_dynamic_fields[key].append(
"NOT " + str(key))
for k in samples_dynamic_fields.keys():
samples_dynamic_fields[k] = " ; ".join(
samples_dynamic_fields[k])
#Sorting dynamic fields with conf file to display in searchgrid
dyn_fields = {}
for k in samples_dynamic_fields:
if k in dyn_in_searchgrid:
dyn_fields[k.capitalize()] = samples_dynamic_fields[k]
for key in meas_dynamic_fields:
if key in dyn_in_searchgrid:
dyn_fields[key.capitalize()] = meas_dynamic_fields[key]
#for the empty fields
for k in dyn_in_searchgrid:
if k.capitalize() not in dyn_fields.keys():
k_db = k.replace(" ", "_")
lab = DBSession.query(Labs).filter(Labs.name == labo).first()
lab_id = lab.id
k_obj = DBSession.query(Attributs).filter(
and_(Attributs.key == k_db,
Attributs.lab_id == lab_id)).first()
if k_obj.widget != "checkbox" and k_obj.widget != "hiding_checkbox":
dyn_fields[k.capitalize()] = None
else:
dyn_fields[k.capitalize()] = ["NOT " + str(k)]
final = dict(static_fields.items() + dyn_fields.items())
return final
def hoover_actions(actions):
return genshi.Markup("<div class='hoover_actions table_hidden'>%s</div>" %
actions)
from pygdv.lib import constants, helpers
import tw.forms as twf
import genshi
from tg import url
DEBUG_LEVEL = 0
def debug(s, t=0):
if DEBUG_LEVEL > 0:
print '[datagrid] %s%s' % ('\t' * t, s)
hidden_info = genshi.Markup("<span class='table_hidden'>hidden_info</span>")
hoover_action = genshi.Markup("<div class='table_hidden'>hidden_info</div>")
def hoover_actions(actions):
return genshi.Markup("<div class='hoover_actions table_hidden'>%s</div>" %
actions)
def hide_info(dict):
span = ''
for k, v in dict.iteritems():
span += "<span class='table_hidden %s'>%s</span>" % (k, v)
return genshi.Markup("<div class='hidden_info'>%s</div>" % span)
sequences_grid = twf.DataGrid(fields=[
def build_search_grid(measurements):
search_grid = BootstrapGrid()
#static end
end_fields = [('Attachment', lambda obj: genshi.Markup(obj.get_extension)),
('Description', "description"), ("Date", "created"),
("Action", lambda obj: genshi.Markup(
get_info_link(obj.id) + get_dl_link(obj.id) +
get_public_link(obj.id) + get_UCSC_link(obj.id) +
get_GViz_link(obj.id) + get_SPAN_id(obj.id)))]
#static and dynamic fields
fields = []
fields_static = [("", "scroll_info"), ("User", "user"), ("Projects", lambda obj:genshi.Markup(obj.projects_display)), ("Samples", lambda obj:genshi.Markup(
obj.samples_display)), ("Type", lambda obj:genshi.Markup(obj.sample_type)),\
("Measurements", lambda obj:genshi.Markup(obj.name)), ("DataType", lambda obj:genshi.Markup(obj.measurement_type))]
fields_dyn = []
list_searchable = []
positions_not_searchable = []
hidden_list = []
lab_id = None
if not isinstance(measurements, list):
measurements = [measurements]
if len(measurements) > 0:
meas = measurements[0]
#dyn meas
for att in meas.attributs:
#get the lab_id
lab_id = att.lab_id
vals = lambda obj, a=att: obj.get_values_from_attributs_meas(a)
fields_dyn.append((att.key, vals))
if att.searchable == True:
list_searchable.append(att.key)
#dyn sample
if len(meas.samples) > 0:
sample = (meas.samples)[0]
for att in sample.attributs:
val = lambda obj, a=att: obj.get_values_from_attributs_sample(a
)
fields_dyn.append((att.key, val))
if att.searchable == True:
list_searchable.append(att.key)
############## CUSTOMIZE THE SEARCH GRID BY LAB #######################
#/!\ the grid begins at 0
#to customize hidden fields by lab
lab = DBSession.query(Labs).filter(Labs.id == lab_id).first()
movable_fields = fields_static + fields_dyn
if lab:
if lab.name == "ptbb":
pass
elif lab.name == "updub":
pass
elif lab.name == "lvg":
#move some field in the grid
for f in movable_fields:
if f[0] == "flag_final":
new_list = value_travel_into_da_list(
movable_fields, movable_fields.index(f),
len(movable_fields))
movable_fields = new_list
for f in movable_fields:
if f[0] == "quality":
new_list = value_travel_into_da_list(
movable_fields, movable_fields.index(f),
len(movable_fields))
movable_fields = new_list
#hide Samples name
for f in movable_fields:
if f[0] == "Samples":
i = movable_fields.index(f)
hidden_list.append(i)
for f in movable_fields:
if f[0] == "ab_source":
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "upnae":
fields_to_hide = ["replica_id", "drug_dose", "lane_id", "paired_end_id", "strand",\
"source", "machine", "starting_material", "treatment", "paired_end", "polya", "strand_specific",\
"viewpoint", "protein_bait", "technical_replica_id", "feeding_type", "light_condition"]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "stutz":
fields_to_hide = ["article_title", "strain", "time_point", "antibody", "treatment_time",\
"phase", "medium", "background"]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "shore":
fields_to_hide = [
"article_title", "year", "time_point", "sequencing_method",
"treatment_time", "phase"
]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
#addition with the 3 common end-fields
fields = movable_fields + end_fields
#build the list (positions_not_searchable) to send to the js for the searchable buttons
for f in fields:
search_grid.fields.append(f)
for i, item in enumerate(search_grid.fields):
if item[0] not in list_searchable:
positions_not_searchable.append(i)
for f in fields_static:
for i, item in enumerate(movable_fields):
#and i not in list_tmp
if f[0] == item[0] and f[
0] != '' and f in fields_static and i in positions_not_searchable:
positions_not_searchable.remove(i)
#build the list (ignored_list) for the ignored fields
total = len(search_grid.fields) - 1
hidden_list.append(total - 2)
#positions_not_searchable = delete the search button of the field
#hidden_list = the field does not appear anymore into the searchgrid and its search button disappears BUT it is still searchable !
return search_grid, hidden_list, positions_not_searchable
class TrackhubGrid(BootstrapGrid):
fields = [("Trackhub", "name"),
("Visualize - Edit Colors - Delete", lambda obj: genshi.Markup(
view_th(obj.url_th) + get_edit_th(obj.name) + get_delete_th(
obj.name)))]
def hide_info(dict):
span = ''
for k, v in dict.iteritems():
span += "<span class='table_hidden %s'>%s</span>" % (k, v)
return genshi.Markup("<div class='hidden_info'>%s</div>" % span)
class SampleGrid(BootstrapGrid):
fields = [("Sample id", "id"), ("User", "get_username"), ("Name", "name"),
("Type", "type"), ("Protocole", "protocole"),
("Date", "created"),
("Action", lambda obj: genshi.Markup(
get_edit_link(obj.id) + get_delete_link(obj.id)))]
def image(self, obj):
return genshi.Markup('<a class="thumbnail" href="#thumb"><img src="%s" width="120px" height="120px" border="0" /><span><img src="%s" /><br />[<b>%s</b>] %s</span></a>' %
(url("/l_images/" + "thumb" + str(obj.id) + ".png"), url("/l_images/" + str(obj.id) + ".png"), obj.id, obj.name)
)
