def _copy_analysis_across_file_boundaries(database_connection, source, hypothesis_name,
identifier=None):
source_handle = DatabaseBoundOperation(source)
source_analysis_id = None
source_analysis_name = None
try:
hypothesis_id = int(identifier)
inst = source_handle.query(Analysis).get(hypothesis_id)
if inst is not None:
source_analysis_id = hypothesis_id
source_analysis_name = inst.name
except TypeError:
hypothesis_name = identifier
inst = source_handle.query(Analysis).filter(
Analysis.name == hypothesis_name).first()
if inst is not None:
source_analysis_id = inst.id
source_analysis_name = inst.name
if hypothesis_name is None:
hypothesis_name = source_analysis_name
mover = GlycanAnalysisHypothesisSerializer(
source, source_analysis_id, hypothesis_name,
database_connection)
mover.run()
return mover.hypothesis_id
class HypothesisGlycanSourceValidator(GlycanSourceValidatorBase):
def __init__(self,
database_connection,
source,
source_type,
source_identifier=None):
super(HypothesisGlycanSourceValidator,
self).__init__(database_connection, source, source_type,
source_identifier)
self.handle = DatabaseBoundOperation(source)
def validate(self):
if self.source_identifier is None:
click.secho("No value passed through --glycan-source-identifier.",
fg='magenta')
return False
try:
hypothesis_id = int(self.source_identifier)
inst = self.handle.query(GlycanHypothesis).get(hypothesis_id)
return inst is not None
except TypeError:
hypothesis_name = self.source
inst = self.handle.query(GlycanHypothesis).filter(
GlycanHypothesis.name == hypothesis_name).first()
return inst is not None
def mass_search_dispatch(uuid):
try:
arguments, state = request_arguments_and_context()
record = _locate_hypothesis(uuid)
handle = DatabaseBoundOperation(record.path)
hypothesis = handle.query(GlycanHypothesis).filter(
GlycanHypothesis.uuid == record.uuid).first()
if hypothesis is not None:
return search_glycan_hypothesis(hypothesis.uuid, arguments['mass'],
arguments['tolerance'])
hypothesis = handle.query(GlycopeptideHypothesis).filter(
GlycopeptideHypothesis.uuid == record.uuid).first()
if hypothesis is not None:
return search_glycopeptide_hypothesis(hypothesis.uuid,
arguments['mass'],
arguments['tolerance'])
return jsonify(*[])
except Exception, e:
logging.exception("An exception occurred for %r",
request.get_json(),
exc_info=e)
return jsonify(*[])
def _copy_hypothesis_across_file_boundaries(database_connection,
source,
hypothesis_name,
identifier=None):
source_handle = DatabaseBoundOperation(source)
source_hypothesis_id = None
source_hypothesis_name = None
try:
hypothesis_id = int(identifier)
inst = source_handle.query(GlycanHypothesis).get(hypothesis_id)
if inst is not None:
source_hypothesis_id = hypothesis_id
source_hypothesis_name = inst.name
except TypeError:
hypothesis_name = identifier
inst = source_handle.query(GlycanHypothesis).filter(
GlycanHypothesis.name == hypothesis_name).first()
if inst is not None:
source_hypothesis_id = inst.id
source_hypothesis_name = inst.name
if source == database_connection:
return source_hypothesis_id
mover = GlycanHypothesisCopier(database_connection,
[(source, source_hypothesis_id)],
hypothesis_name=source_hypothesis_name)
mover.run()
return mover.hypothesis_id
def _copy_hypothesis_across_file_boundaries(database_connection, source, hypothesis_name,
identifier=None):
source_handle = DatabaseBoundOperation(source)
source_hypothesis_id = None
source_hypothesis_name = None
try:
hypothesis_id = int(identifier)
inst = source_handle.query(GlycanHypothesis).get(hypothesis_id)
if inst is not None:
source_hypothesis_id = hypothesis_id
source_hypothesis_name = inst.name
except TypeError:
hypothesis_name = identifier
inst = source_handle.query(GlycanHypothesis).filter(
GlycanHypothesis.name == hypothesis_name).first()
if inst is not None:
source_hypothesis_id = inst.id
source_hypothesis_name = inst.name
if source == database_connection:
return source_hypothesis_id
mover = GlycanHypothesisCopier(
database_connection, [(source, source_hypothesis_id)],
hypothesis_name=source_hypothesis_name)
mover.run()
return mover.hypothesis_id
def _copy_analysis_across_file_boundaries(database_connection,
source,
hypothesis_name,
identifier=None):
source_handle = DatabaseBoundOperation(source)
source_analysis_id = None
source_analysis_name = None
try:
hypothesis_id = int(identifier)
inst = source_handle.query(Analysis).get(hypothesis_id)
if inst is not None:
source_analysis_id = hypothesis_id
source_analysis_name = inst.name
except TypeError:
hypothesis_name = identifier
inst = source_handle.query(Analysis).filter(
Analysis.name == hypothesis_name).first()
if inst is not None:
source_analysis_id = inst.id
source_analysis_name = inst.name
if hypothesis_name is None:
hypothesis_name = source_analysis_name
mover = GlycanAnalysisHypothesisSerializer(source, source_analysis_id,
hypothesis_name,
database_connection)
mover.run()
return mover.hypothesis_id
def validate_unique_name(context, database_connection, name, klass):
handle = DatabaseBoundOperation(database_connection)
obj = handle.query(klass).filter(klass.name == name).first()
if obj is not None:
return klass.make_unique_name(handle.session, name)
else:
return name
def validate_unique_name(context, database_connection, name, klass):
handle = DatabaseBoundOperation(database_connection)
obj = handle.query(klass).filter(
klass.name == name).first()
if obj is not None:
return klass.make_unique_name(handle.session, name)
else:
return name
class HypothesisGlycanSourceValidator(GlycanSourceValidatorBase):
def __init__(self, database_connection, source, source_type, source_identifier=None):
super(HypothesisGlycanSourceValidator, self).__init__(
database_connection, source, source_type, source_identifier)
self.handle = DatabaseBoundOperation(source)
def validate(self):
if self.source_identifier is None:
click.secho("No value passed through --glycan-source-identifier.", fg='magenta')
return False
try:
hypothesis_id = int(self.source_identifier)
inst = self.handle.query(GlycanHypothesis).get(hypothesis_id)
return inst is not None
except TypeError:
hypothesis_name = self.source
inst = self.handle.query(GlycanHypothesis).filter(GlycanHypothesis.name == hypothesis_name).first()
return inst is not None
def view_hypothesis_dispatch(uuid):
try:
arguments, state = request_arguments_and_context()
record = _locate_hypothesis(uuid)
handle = DatabaseBoundOperation(record.path)
hypothesis = handle.query(GlycanHypothesis).filter(
GlycanHypothesis.uuid == record.uuid).first()
if hypothesis is not None:
return handle_glycan_hypothesis(hypothesis)
hypothesis = handle.query(GlycopeptideHypothesis).filter(
GlycopeptideHypothesis.uuid == record.uuid).first()
if hypothesis is not None:
return handle_glycopeptide_hypothesis(hypothesis)
return Response("<h2>%s</h2>" % record.name)
except Exception as e:
logging.exception("An exception occurred for %r",
request.get_json(), exc_info=e)
return Response("<h2>No display method is implemented for %s </h2>" % request.get_json())
class GlycopeptideAnalysisGlycanCompositionExtractionHypothesisSerializer(
GlycanHypothesisSerializerBase):
def __init__(self,
input_connection,
analysis_id,
hypothesis_name,
output_connection=None):
if output_connection is None:
output_connection = input_connection
self.input_connection = DatabaseBoundOperation(input_connection)
self.output_connection = DatabaseBoundOperation(output_connection)
GlycanHypothesisSerializerBase.__init__(self, output_connection,
hypothesis_name)
self.analysis_id = analysis_id
self.seen_cache = set()
def get_all_compositions(self):
return self.input_connection.query(DBGlycanComposition).join(
GlycanCombinationGlycanComposition).join(
Glycopeptide,
GlycanCombinationGlycanComposition.c.combination_id ==
Glycopeptide.glycan_combination_id).join(
IdentifiedGlycopeptide, IdentifiedGlycopeptide.structure_id
== Glycopeptide.id).filter(
IdentifiedGlycopeptide.analysis_id == self.analysis_id)
def extract_composition(self, db_obj):
composition = GlycanComposition.parse(db_obj.composition)
if str(composition) in self.seen_cache:
return
self.seen_cache.add(str(composition))
mass = composition.mass()
composition_string = composition.serialize()
formula_string = formula(composition.total_composition())
inst = DBGlycanComposition(calculated_mass=mass,
formula=formula_string,
composition=composition_string,
hypothesis_id=self.hypothesis_id)
self.output_connection.session.add(inst)
self.output_connection.session.flush()
for sc in db_obj.structure_classes:
self.output_connection.session.execute(
GlycanCompositionToClass.insert(),
dict(glycan_id=inst.id, class_id=sc.id))
self.output_connection.session.flush()
def run(self):
q = self.get_all_compositions()
for gc in q:
self.extract_composition(gc)
self.output_connection.session.commit()
class GlycopeptideAnalysisGlycanCompositionExtractionHypothesisSerializer(GlycanHypothesisSerializerBase):
def __init__(self, input_connection, analysis_id, hypothesis_name, output_connection=None):
if output_connection is None:
output_connection = input_connection
self.input_connection = DatabaseBoundOperation(input_connection)
self.output_connection = DatabaseBoundOperation(output_connection)
GlycanHypothesisSerializerBase.__init__(self, output_connection, hypothesis_name)
self.analysis_id = analysis_id
self.seen_cache = set()
def get_all_compositions(self):
return self.input_connection.query(DBGlycanComposition).join(GlycanCombinationGlycanComposition).join(
Glycopeptide,
GlycanCombinationGlycanComposition.c.combination_id == Glycopeptide.glycan_combination_id).join(
IdentifiedGlycopeptide, IdentifiedGlycopeptide.structure_id == Glycopeptide.id).filter(
IdentifiedGlycopeptide.analysis_id == self.analysis_id)
def extract_composition(self, db_obj):
composition = GlycanComposition.parse(db_obj.composition)
if str(composition) in self.seen_cache:
return
self.seen_cache.add(str(composition))
mass = composition.mass()
composition_string = composition.serialize()
formula_string = formula(composition.total_composition())
inst = DBGlycanComposition(
calculated_mass=mass, formula=formula_string,
composition=composition_string,
hypothesis_id=self.hypothesis_id)
self.output_connection.session.add(inst)
self.output_connection.session.flush()
for sc in db_obj.structure_classes:
self.output_connection.session.execute(
GlycanCompositionToClass.insert(), dict(glycan_id=inst.id, class_id=sc.id))
self.output_connection.session.flush()
def run(self):
q = self.get_all_compositions()
for gc in q:
self.extract_composition(gc)
self.output_connection.session.commit()
def get_glycopeptide_hypothesis(uuid):
record = g.manager.hypothesis_manager.get(uuid)
handle = DatabaseBoundOperation(record.path)
hypothesis = handle.query(GlycopeptideHypothesis).filter(
GlycopeptideHypothesis.uuid == record.uuid).first()
return hypothesis