def __plate_setup_name_form(self, setup=None):
project_field = fl.project_field(setup.project.id if setup and setup.project else None, active_only=True, empty='')
author_field = fl.person_field(setup.author.id if setup and setup.author else None)
person_field = fl.person_field(setup.droplet_maker_id if setup and setup.droplet_maker_id else None)
return h.LiteralFormSelectPatch(
value = {'author_id': unicode(author_field['value']),
'project_id': unicode(project_field['value']),
'droplet_maker_id': unicode(person_field['value']),
'name': setup.name if setup else ''},
option = {'author_id': author_field['options'],
'project_id': project_field['options'],
'droplet_maker_id': person_field['options']}
)
def enzyme_conc_edit(self, id=None):
if id is None:
abort(404)
conc = Session.query(EnzymeConcentration).get(id)
if not conc:
abort(404)
c.conc = conc
enzyme_field = fl.enzyme_field(selected=unicode(conc.enzyme_id))
assay_field = fl.assay_field(blank=True, selected=unicode(conc.assay.id))
author_field = fl.person_field(selected=unicode(conc.author_id))
c.plate = None
c.form = h.LiteralFormSelectPatch(
value={
"enzyme_id": enzyme_field["value"],
"assay_id": assay_field["value"],
"author_id": author_field["value"],
"minimum_conc": conc.minimum_conc,
"maximum_conc": conc.maximum_conc,
"source_plate_id": conc.source_plate_id,
"notes": conc.notes,
},
option={
"enzyme_id": enzyme_field["options"],
"assay_id": assay_field["options"],
"author_id": author_field["options"],
},
)
return render("/assay/enzyme/edit.html")
def enzyme_conc_new(self):
enzyme_field = fl.enzyme_field()
assay_field = fl.assay_field(blank=True, empty="", selected=request.params.get("assay_id", None))
author_field = fl.person_field()
c.plate = None
if request.params.get("plate_id", None):
plate = Session.query(Plate).get(int(request.params.get("plate_id")))
if plate:
c.plate = plate
c.form = h.LiteralFormSelectPatch(
value={
"enzyme_id": enzyme_field["value"],
"assay_id": assay_field["value"],
"author_id": author_field["value"],
},
option={
"enzyme_id": enzyme_field["options"],
"assay_id": assay_field["options"],
"author_id": author_field["options"],
},
)
return render("/assay/enzyme/new.html")
def __setup_groove_fields(self):
c.droplet_makers = fl.person_field()
# TODO: limit?
c.plate_types = groove_plate_type_field()
c.droplet_types = droplet_type_field()
c.droplet_generators = groove_droplet_generator_field()
c.plate_layouts = groove_plate_layout_field()
def edit(self, id):
"""
Edits an assay.
"""
assay_q = Session.query(Assay)
assay = assay_q.filter_by(id=id).first()
dye_field = fl.assay_dye_field(assay.dye)
quencher_field = fl.assay_quencher_field(assay.quencher)
secondary_structure = fl.tertiary_field(assay.secondary_structure)
if assay is None:
abort(404)
else:
c.assay = assay
owner_field = fl.person_field(c.assay.owner_id)
c.form = h.LiteralFormSelectPatch(
value={
"dye": dye_field["value"],
"quencher": quencher_field["value"],
"owner_id": unicode(owner_field["value"]),
"secondary_structure": secondary_structure["value"],
},
option={
"chromosome": [("", "--")] + [(chr, chr) for chr in Chromosome.chrom_list],
"owner_id": owner_field["options"],
"dye": dye_field["options"],
"quencher": quencher_field["options"],
"secondary_structure": secondary_structure["options"],
},
)
values = {
"name": assay.name,
"gene": assay.gene,
"owner_id": unicode(assay.owner_id),
"primer_fwd": assay.primer_fwd,
"primer_rev": assay.primer_rev,
"chromosome": assay.chromosome,
"probe_pos": assay.probe_pos,
"probe_seq": assay.probe_seq,
"dye": assay.dye,
"quencher": assay.quencher,
"secondary_structure": secondary_structure["value"],
"amplicon_width": assay.amplicon_width,
"snp_rsid": assay.snp_rsid,
"notes": assay.notes,
"reference_source": assay.reference_source,
"optimal_anneal_temp": assay.optimal_anneal_temp,
}
if assay.assay_type == Assay.TYPE_LOCATION:
c.selectedTab = 1
elif assay.assay_type == Assay.TYPE_SNP:
c.selectedTab = 2
else:
c.selectedTab = 0
return htmlfill.render(render("/assay/edit.html"), values)
def __plate_list_query_form(self):
project_field = fl.project_field(c.project_id if hasattr(c, 'project_id') else None)
author_field = fl.person_field(c.author_id if hasattr(c, 'author_id') else None)
return h.LiteralFormSelectPatch(
value = {'project_id': unicode(project_field['value']),
'author_id': unicode(author_field['value'])},
option = {'project_id': project_field['options'],
'author_id': author_field['options']}
)
def reader_fix(self, id=None):
box2 = self.__setup_box2_context_by_code(id)
c.admin = True
reporter_field = fl.person_field()
c.form = h.LiteralForm(
option = {
'reporter_id': [('','--')] + reporter_field['options']
}
)
return render('/admin/reader_fix.html')
def reader_status(self, id=None):
box2 = self.__setup_box2_context_by_code(id)
c.admin = True
reporter_field = fl.person_field()
c.form = h.LiteralForm(
value = {'status': box2.status},
option = {
'status': [(0, 'Restricted/Off-line'),
(1, 'Caution'),
(2, 'OK')],
'reporter_id': [('','--')] + reporter_field['options']
}
)
return render('/admin/reader_status.html')
def new(self):
dye_field = fl.assay_dye_field()
quencher_field = fl.assay_quencher_field()
owner_field = fl.person_field()
secondary_structure = fl.tertiary_field()
c.form = h.LiteralFormSelectPatch(
value={
"dye": dye_field["value"],
"quencher": quencher_field["value"],
"owner_id": owner_field["value"],
"secondary_structure": secondary_structure["value"],
},
option={
"chromosome": [("", "--")] + [(chr, chr) for chr in Chromosome.chrom_list],
"owner_id": [("", "--")] + owner_field["options"],
"dye": dye_field["options"],
"quencher": quencher_field["options"],
"secondary_structure": secondary_structure["options"],
},
)
return render("/assay/new.html")
def _edit_base(self):
c.people = fl.person_field()
return render('/sequence/group_edit.html')
def __setup_batch_fields(self):
c.people = fl.person_field()
c.dg_method = dg_method_field()
c.plate_type = plate_type_field()