def tearDown(self):
from qtools.model import Session
Session.delete(self.testUser)
Session.delete(self.testProject)
Session.delete(self.readQLP)
Session.delete(self.unreadQLP)
Session.commit()
def runs(self, id=None):
c.dg = Session.query(DropletGenerator).get(int(id))
if not c.dg:
abort(404)
reprocess_config_id = request.params.get('rp_id', None)
if reprocess_config_id:
reprocess_config_id = int(reprocess_config_id)
runs = Session.query(DropletGeneratorRun).filter(
and_(DropletGeneratorRun.droplet_generator_id == c.dg.id,
DropletGeneratorRun.run_number != None)).all()
run_dict = dict([(run.run_number, run) for run in runs])
wells = Session.query(WellMetric,
QLBWell.id,
QLBWell.sample_name,
QLBWell.dg_run_number,
QLBWell.consumable_channel_num)\
.join(QLBWell)\
.join(PlateMetric)\
.filter(and_(QLBWell.droplet_generator_id == id,
QLBWell.dg_run_number != None,
PlateMetric.reprocess_config_id == reprocess_config_id))\
.order_by(QLBWell.dg_run_number, QLBWell.consumable_channel_num).all()
sorted_runs = sorted(groupinto(wells, lambda tup: (tup[3])), key=operator.itemgetter(0))
c.runs = [(run_id, run_dict[run_id], sorted(info, key=operator.itemgetter(4))) for run_id, info in sorted_runs if run_dict.get(run_id, None)]
#raise Exception, c.runs
return render('/product/dg/runs.html')
def apply_setup_to_plate(qlplate, dbplate):
"""
Determine if a plate has an applicable template, either by
explicit setting or by implicit naming.
:param qlplate: The QLP file to read
:param dbplate: The DB plate to update
"""
if qlplate.plate_setup_id:
setup = Session.query(PlateSetup).get(int(qlplate.plate_setup_id))
if setup:
inherit_setup_attributes(dbplate, setup)
return True
dirname = dbplate.qlbplate.file.dirname
basename = dbplate.qlbplate.file.basename
complete_name = basename[:-4] # -- .qlp
setups = Session.query(PlateSetup).order_by('prefix desc').all()
for setup in setups:
if complete_name.startswith(setup.prefix):
inherit_setup_attributes(dbplate, setup)
return True
return False
def __vendor_enzymes(self, name):
vendor = Session.query(Vendor).filter_by(name=unicode(name)).first()
# this might be better off with a regular SQL statement
all_enzymes = Session.query(VendorEnzyme, Enzyme.name, Enzyme.cutseq, Enzyme.methylation_sensitivity,\
func.sum(VendorEnzyme.stock_units).label('total_stock_units')
).join(Enzyme).filter(VendorEnzyme.vendor_id == vendor.id).group_by(VendorEnzyme.enzyme_id).all()
return all_enzymes
def make_plate_name(plate, experiment_name=None):
"""
Given a plate and assigned project, operator
and experiment, generate a name that conforms
to the QTools naming standard.
Name will be project_operator_experiment.
:param plate:
:param experiment_name:
:return:
"""
# this is the hard way, before the relation is saved.
if plate.project_id:
project = Session.query(Project).get(plate.project_id)
if project:
if project.code:
project_code = project.code
else:
project_code = project.name
else:
project_code = ''
else:
project_code = ''
operator = Session.query(Person).get(plate.operator_id)
if operator:
user_code = operator.name_code
else:
user_code = ''
fields = [project_code, user_code, experiment_name]
return '_'.join([field for field in fields if field])
def apply_template_to_plate(qlplate, dbplate):
"""
Determine if a plate has an applicable template, either by
explicit setting or by implicit naming.
:param qlplate: The QLP file to read
:param dbplate: The DB plate to update
"""
# new-style: if plate file has plate_template_id in it,
# just bind
if qlplate.plate_template_id:
template = Session.query(PlateTemplate).get(int(qlplate.plate_template_id))
if template:
inherit_template_attributes(dbplate, template)
return True
# otherwise, check the name
dirname = dbplate.qlbplate.file.dirname
basename = dbplate.qlbplate.file.basename
complete_name = basename[:-4] # -- .qlp
# duplicate prefixes are possible; use most recent
templates = Session.query(PlateTemplate).order_by('prefix desc, id desc').all()
for template in templates:
if complete_name.startswith(template.prefix):
inherit_template_attributes(dbplate, template)
return True
return False
def by_well_tag(self):
well_tag_field = fl.well_tag_field(str(self.form_result['well_tag']))
c.group_by_plate = self.form_result['group_by_plate']
c.tag_id = self.form_result['well_tag']
c.tag_name = Session.query(WellTag).get(c.tag_id).name
c.form = h.LiteralFormSelectPatch(
value = {'well_tag': well_tag_field['value'],
'group_by_plate': [u'1' if c.group_by_plate else u'0']},
option = {'well_tag': [('--','--')]+well_tag_field['options'],
'group_by_plate': [(u'1', '')]}
)
well_tags = Session.query(WellTag).\
filter_by(id=c.tag_id).\
options(joinedload_all(WellTag.tag_wells, QLBWell.plate, QLBPlate.file, innerjoin=True),
joinedload_all(WellTag.tag_wells, QLBWell.plate, QLBPlate.plate, innerjoin=True)).\
all()
c.label_names = []
if not len(well_tags):
c.wells = []
c.well_groups = []
elif c.group_by_plate:
wells = sorted(well_tags[0].wells, key=lambda well: (well.plate_id, well.well_name))
well_groups = [(plate, list(wells)) for plate, wells in itertools.groupby(wells, lambda well: well.plate)]
c.well_groups = sorted(well_groups, key=lambda tup: tup[0].host_datetime)
c.well_groups.reverse()
else:
c.wells = sorted(well_tags[0].wells, key=lambda well: well.host_datetime)
c.wells.reverse()
return render('/box2/by_well_tag.html')
def reader_history(self, id=None, admin=True):
box2 = self.__setup_box2_context_by_code(id)
c.admin = admin != 'False'
logs = Session.query(Box2Log).filter_by(box2_id=box2.id)\
.order_by('time_effective desc')\
.options(joinedload_all(Box2Log.circuit))\
.all()
statuses = Session.query(DRStatusLog).filter_by(box2_id=box2.id)\
.order_by('time_effective desc')\
.options(joinedload_all(DRStatusLog.reporter))\
.all()
fixes = Session.query(DRFixLog).filter_by(box2_id=box2.id)\
.order_by('time_effective desc')\
.all()
log_pairs = [(logs[i].time_effective, [logs[i],(logs[i+1] if i < len(logs)-1 else None)]) for i in range(len(logs))]
for pair in log_pairs:
pair[1].append((sorted(box2log_mv.labeleditems(pair[1][0]).items()),
sorted(box2log_mv.labeleditems(pair[1][1]).items())))
status_pairs = [(status.time_effective, status) for status in statuses]
fix_pairs = [(fix.time_effective, fix) for fix in fixes]
changes = log_pairs + status_pairs + fix_pairs
c.changes = sorted(changes, key=operator.itemgetter(0))
c.changes.reverse()
return render('/admin/reader_history.html')
def command(self):
app = self.load_wsgi_app()
min_id = 0
if len(self.args) > 1:
min_id = self.args[0]
storage = QLStorageSource(app.config)
qlbplates = Session.query(QLBPlate).filter(QLBPlate.id > min_id).order_by('id').all()
for qlbplate in qlbplates:
try:
path = storage.qlbplate_path(qlbplate)
except Exception:
print "Could not find plate: %s (%s)" % (qlbplate.plate.name if qlbplate.plate else 'Name unknown', qlbplate.id)
continue
try:
qlplate = get_plate(path)
except Exception:
print "Could not read plate: %s (%s)" % (qlbplate.plate.name if qlbplate.plate else 'Name Unknown', qlbplate.id)
continue
if qlplate.is_fam_vic:
qlbplate.dyeset = QLBPlate.DYESET_FAM_VIC
elif qlplate.is_fam_hex:
qlbplate.dyeset = QLBPlate.DYESET_FAM_HEX
elif qlplate.is_eva_green:
qlbplate.dyeset = QLBPlate.DYESET_EVA
else:
qlbplate.dyeset = QLBPlate.DYESET_UNKNOWN
print "Assigned dye %s - %s (%s)" % (qlbplate.dyeset, qlbplate.plate.name if qlbplate.plate else 'Name Unknown', qlbplate.id)
Session.commit()
def register_algorithm(self):
storage = QSAlgorithmSource(config)
existing_folders = [tup[0] for tup in Session.query(ReprocessConfig.original_folder).all()]
errors = dict()
src_dir = self.form_result['src_dir']
if src_dir in existing_folders:
errors['src_dir'] = 'This algorithm has already been registered.'
elif not storage.source_path_exists(src_dir):
errors['src_dir'] = 'This algorithm is not accessible in the file system.'
if self.form_result['peak_detection_version'] == (0,0):
# this is arbitrary
peak_detection_version = (0, QUANTASOFT_DIR_VERSION_RE.search(src_dir).group(1).split('_')[-1])
else:
peak_detection_version = self.form_result['peak_detection_version']
if self.form_result['peak_quantitation_version'] == (0,0):
peak_quantitation_version = (0, QUANTASOFT_DIR_VERSION_RE.search(src_dir).group(1).split('_')[-1])
else:
peak_quantitation_version = self.form_result['peak_quantitation_version']
if errors:
resp = self._algorithms_base()
defaults = AlgorithmRegisterForm.from_python(self.form_result)
return h.render_bootstrap_form(resp,
defaults=defaults,
errors=errors,
error_formatters=h.tw_bootstrap_error_formatters)
try:
rp = ReprocessConfig(name=src_dir.split(os.path.sep)[0],
code=self.form_result['code'],
peak_detection_major=peak_detection_version[0],
peak_detection_minor=peak_detection_version[1],
peak_quant_major=peak_quantitation_version[0],
peak_quant_minor=peak_quantitation_version[1],
trigger_fixed_width=100,
active=True,
cluster_mode=ReprocessConfig.CLUSTER_MODE_CLUSTER,
original_folder=src_dir)
storage.add_reprocessor(src_dir, self.form_result['code'])
Session.add(rp)
Session.commit()
session['flash'] = 'New algorithm reprocessor created.'
session.save()
return redirect(url(controller='product', action='algorithms'))
except shutil.Error:
session['flash'] = 'Could not copy source algorithm to destination.'
session['flash_class'] = 'error'
session.save()
return redirect(url(controller='product', action='algorithms'))
except IOError:
session['flash'] = "Could not access the algorithm's file system."
session['flash_class'] = 'error'
session.save()
return redirect(url(controller='product', action='algorithms'))
def batch_plate_template_download(self, id=None):
plate = self.__load_batch_plate(id)
box2 = Session.query(Box2).get(self.form_result['box2_id'])
if not plate or not box2:
abort(404)
code = plate.batch.plate_type.code
if self.form_result['qc_plate']:
plate.qc_plate = self.form_result['qc_plate']
Session.commit()
# TODO FIXFIX or incorporate into model
if plate.qc_plate:
serial = 'QC'
else:
serial = box2.name.split(' ')[-1]
# only mfgco supported right now
if code == 'mfgco':
qlt_file = "%s/carryover.qlt" % config['qlb.setup_template_store']
elif code == 'fvtitr':
qlt_file = "%s/fvbatch_QC.qlt" % config['qlb.setup_template_store']
else:
abort(404)
response.headers['Content-Type'] = 'application/quantalife-template'
h.set_download_response_header(request, response, "%s_%s.qlt" % (serial, plate.name))
response.headers['Pragma'] = 'no-cache'
response.headers['Cache-Control'] = 'no-cache'
return forward(FileApp(qlt_file, response.headerlist))
def batch_csfv_unhook(self):
plate = self.__load_batch_plate(self.form_result['batch_plate_id'])
plate.plate_id = None
Session.commit()
session['flash'] = 'CSFV QC plate discarded.'
session.save()
return redirect(url(controller='product', action='batch_plates', id=plate.mfg_batch_id))
def __update_batch_plate_record(self, record):
record.dg_method = self.form_result['dg_method']
record.qc_plate = self.form_result['qc_plate'] and True or False
record.plate_notes = self.form_result['plate_notes']
record.thermal_cycler_id = self.form_result['thermal_cycler_id']
Session.add(record)
Session.commit()
def plate_query():
# writing it this way because the .join seems to muck up
# filter_by statements downstream
box2s = [tup[0] for tup in Session.query(Box2.id).all()]
query = Session.query(Plate).filter(Plate.box2_id.in_(box2s))
return query
def sensitivity(self):
enz = Session.query(Enzyme).get(self.form_result['enzyme'])
if not self.form_result['sensitivity']:
enz.methylation_sensitivity = None
else:
enz.methylation_sensitivity = self.form_result['sensitivity']
Session.commit()
return "OK"
def save(self):
if self.form_result['plate_setup_id']:
ps = Session.query(PlateSetup).get(self.form_result['plate_setup_id'])
prefix = ps.prefix
elif self.form_result['plate_template_id']:
pt = Session.query(PlateTemplate).get(self.form_result['plate_template_id'])
prefix = pt.prefix
else:
prefix = 'output'
response.headers['Content-Type'] = 'application/quantalife-template'
h.set_download_response_header(request, response, "%s.qlt" % prefix)
response.headers['Pragma'] = 'no-cache'
# build a plate
# TODO: add default fields
plate = ExperimentMetadataQLPlate(channel_names=['FAM','VIC'],
host_datetime=datetime.now(),
host_machine='QTools',
host_user='******',
plate_template_id=self.form_result['plate_template_id'],
plate_setup_id=self.form_result['plate_setup_id'])
for cell in sorted(self.form_result['cells'], key=lambda c: c['cell_name']):
well = ExperimentMetadataQLWell(name=cell['cell_name'],
num_channels=2,
sample=cell['sample'],
experiment_comment=cell['experiment_comment'],
experiment_name=cell['experiment_name'],
experiment_type=cell['experiment_type'],
temperature=cell['temperature'],
enzyme=cell['enzyme'],
enzyme_conc=cell['enzyme_conc'],
additive=cell['additive'],
additive_conc=cell['additive_conc'],
expected_cpd=cell['expected_cpd'],
expected_cpul=cell['expected_cpul'],
target_copy_num=cell['target_copy_num'],
ref_copy_num=cell['ref_copy_num'],
dg_cartridge=cell['cartridge'],
supermix=cell['supermix'])
well.channels[0].target = cell['fam_target']
well.channels[0].type = cell['fam_type']
well.channels[1].target = cell['vic_target']
well.channels[1].type = cell['vic_type']
plate.wells[str(cell['cell_name'])] = well
# generate QLT
# TODO: rowcol order
writer = QLTWriter(rowcol_order=self.form_result['rowcol_order'],
fgcolorfunc=self.__qlt_fgcolorfunc,
bgcolorfunc=self.__qlt_bgcolorfunc)
qlt = writer.getbytes(plate)
return qlt
def instock(self):
enz = Session.query(VendorEnzyme).get(self.form_result['vendor_enzyme_id'])
if self.form_result['in_stock']:
enz.stock_units = 1
else:
enz.stock_units = 0
Session.commit()
return 'OK'
def _list_base(self):
groove_test = Session.query(Project).filter_by(name="GrooveTest").first()
query = Session.query(PlateSetup).filter_by(project_id=groove_test.id).order_by("time_updated desc, name")
c.paginator = paginate.Page(query, page=int(request.params.get("page", 1)), items_per_page=20)
c.pager_kwargs = {}
c.plate_type_field = groove_plate_type_field()
return render("/product/groove/list.html")
def enzyme_conc_create(self):
conc = EnzymeConcentration()
for k, v in self.form_result.items():
setattr(conc, k, v)
Session.add(conc)
Session.commit()
redirect(url(controller="assay", action="view", id=self.form_result["assay_id"]))
def save_reagents(self, id=None):
self.__load_context()
setup, struct = self.__load_setup(id)
if not setup:
abort(404)
for k, v in self.form_result.items():
setattr(setup, k, v)
Session.commit()
redirect(url(controller='setup', action='dg', id=id, beta=c.beta))
def _algcommand_base(self):
ags = Session.query(AnalysisGroup).filter_by(active=True).order_by(AnalysisGroup.name).all()
rps = Session.query(ReprocessConfig).filter_by(active=True).order_by(ReprocessConfig.name).all()
c.analysis_groups = {'value': '',
'options': [(ag.id, ag.name) for ag in ags]}
c.reprocess_configs = {'value': '',
'options': [(rp.id, rp.name) for rp in rps]}
return render('/product/algorithms/select.html')
def update_reader(self):
log_entry = self.__make_box2_log_entry(self.form_result)
Session.add(log_entry)
Session.commit()
box2 = Session.query(Box2).get(self.form_result['box2_id'])
session['flash'] = 'Configuration for %s updated.' % box2.name
session.save()
redirect(url(controller='admin', action='reader_history', id=box2.code))
def __form_to_model(self, form, model=None):
if not model:
model = SequenceGroupTag()
Session.add(model)
model.name = form['name']
model.notes = form['notes']
model.owner_id = form['owner_id']
Session.merge(model)
return model
def update(self, id=None):
batch = self.__batch(id)
batch.manufacturer = self.form_result["manufacturer"]
batch.insert = self.form_result["insert"]
batch.consumable_molding_style_id = self.form_result["molding_style"]
batch.consumable_bonding_style_id = self.form_result["bonding_style"]
batch.manufacturing_date = self.form_result["manufacture_date"]
batch.bside = self.form_result["bside"]
Session.commit()
session.flash = "Updated batch %s" % batch.lot_num
return redirect(url(controller="consumable", action="details", id=batch.id))
def donotrun(self, id=None):
c.beta = True
setup, struct = self.__load_setup(id)
if not setup:
abort(404)
setup.donotrun = True
Session.commit()
session['flash'] = "Marked %s as skipped." % setup.name
session.save()
redirect(url(controller='setup', action='list', beta=c.beta))
def __save_setup(self, setup, key, block):
setup_obj = json.loads(setup.setup or '{}')
# Hack.
if type(block) == type(dict()) and block.get('notes', None) is not None:
notes = block.pop('notes')
setup.notes = notes
setup_obj[key] = block
setup.setup = json.dumps(setup_obj)
if key == 'progress':
setup.completed = (self.__check_progress(setup_obj) == 'Done')
Session.commit()
def create(self):
self.__load_context()
plate_setup = PlateSetup()
plate_setup.project_id = self.form_result['project_id']
plate_setup.author_id = self.form_result['author_id']
plate_setup.name = self.form_result['name']
plate_setup.prefix = make_setup_name(plate_setup)
Session.add(plate_setup)
Session.commit()
redirect(url(controller='setup', action='consumable', id=plate_setup.id, beta=c.beta))
def delete_file(self, id=None):
self.__setup_box2_code_context(id)
thefile = self.__file_id_query(c.box2.id, self.form_result['file_id'])
if not thefile:
abort(404)
Session.delete(thefile)
Session.commit()
session['flash'] = 'File deleted.'
session.save()
return redirect(url(controller='metrics', action='certification', id=c.box2.code))
def save_name(self, id=None):
self.__load_context()
setup, struct = self.__load_setup(id)
if not setup:
abort(404)
for k, v in self.form_result.items():
setattr(setup, k, v)
setup.prefix = make_setup_name(setup)
Session.commit()
redirect(url(controller='setup', action='consumable', id=id, beta=c.beta))
def command(self):
self.load_wsgi_app()
qlbplates = Session.query(QLBPlate).\
filter(and_(QLBPlate.file_id != None, QLBPlate.plate_id != None)).\
order_by(desc(QLBPlate.id)).\
options(joinedload_all(QLBPlate.plate, innerjoin=True))
for qlbplate in qlbplates:
qlbplate.plate.score = Plate.compute_score(qlbplate.plate)
print "%s: %s points" % (qlbplate.plate.id, qlbplate.plate.score)
Session.commit()