def from_analysis(context, database_connection, analysis_connection, analysis_identifier,
reduction, derivatization, name):
database_connection = DatabaseBoundOperation(database_connection)
if name is not None:
name = validate_glycan_hypothesis_name(context, database_connection._original_connection, name)
click.secho("Building Glycan Hypothesis %s" % name, fg='cyan')
reduction = validate_reduction(context, reduction)
derivatization = validate_derivatization(context, derivatization)
analysis_connection = DatabaseBoundOperation(analysis_connection)
analysis = get_by_name_or_id(analysis_connection.session, Analysis, analysis_identifier)
if analysis.analysis_type == AnalysisTypeEnum.glycan_lc_ms:
job = GlycanAnalysisHypothesisSerializer(
analysis_connection._original_connection, analysis.id, name,
output_connection=database_connection._original_connection)
job.display_header()
job.start()
elif analysis.analysis_type == AnalysisTypeEnum.glycopeptide_lc_msms:
job = GlycopeptideAnalysisGlycanCompositionExtractionHypothesisSerializer(
analysis_connection._original_connection, analysis.id, name,
output_connection=database_connection._original_connection)
job.display_header()
job.start()
else:
click.secho("Analysis Type %r could not be converted" % (
analysis.analysis_type.name,), fg='red')
def from_analysis(context, database_connection, analysis_connection,
analysis_identifier, reduction, derivatization, name):
database_connection = DatabaseBoundOperation(database_connection)
if name is not None:
name = validate_glycan_hypothesis_name(
context, database_connection._original_connection, name)
click.secho("Building Glycan Hypothesis %s" % name, fg='cyan')
reduction = validate_reduction(context, reduction)
derivatization = validate_derivatization(context, derivatization)
analysis_connection = DatabaseBoundOperation(analysis_connection)
analysis = get_by_name_or_id(analysis_connection.session, Analysis,
analysis_identifier)
if analysis.analysis_type == AnalysisTypeEnum.glycan_lc_ms:
job = GlycanAnalysisHypothesisSerializer(
analysis_connection._original_connection,
analysis.id,
name,
output_connection=database_connection._original_connection)
job.display_header()
job.start()
elif analysis.analysis_type == AnalysisTypeEnum.glycopeptide_lc_msms:
job = GlycopeptideAnalysisGlycanCompositionExtractionHypothesisSerializer(
analysis_connection._original_connection,
analysis.id,
name,
output_connection=database_connection._original_connection)
job.display_header()
job.start()
else:
click.secho("Analysis Type %r could not be converted" %
(analysis.analysis_type.name, ),
fg='red')
def prebuilt_glycan(context, database_connection, recipe_name, name, reduction, derivatization):
database_connection = DatabaseBoundOperation(database_connection)
reduction = validate_reduction(context, reduction)
derivatization = validate_derivatization(context, derivatization)
if name is not None:
name = validate_glycan_hypothesis_name(
context, database_connection._original_connection, name)
recipe = prebuilt_hypothesis_register[recipe_name]()
recipe(database_connection._original_connection,
hypothesis_name=name, reduction=reduction,
derivatization=derivatization)
def glycan_combinatorial(context, rule_file, database_connection, reduction, derivatization, name):
if name is not None:
name = validate_glycan_hypothesis_name(context, database_connection, name)
click.secho("Building Glycan Hypothesis %s" % name, fg='cyan')
reduction = validate_reduction(context, reduction)
derivatization = validate_derivatization(context, derivatization)
builder = CombinatorialGlycanHypothesisSerializer(
rule_file, database_connection, reduction=reduction, derivatization=derivatization,
hypothesis_name=name)
builder.display_header()
builder.start()
def prebuilt_glycan(context, database_connection, recipe_name, name, reduction,
derivatization):
database_connection = DatabaseBoundOperation(database_connection)
reduction = validate_reduction(context, reduction)
derivatization = validate_derivatization(context, derivatization)
if name is not None:
name = validate_glycan_hypothesis_name(
context, database_connection._original_connection, name)
recipe = prebuilt_hypothesis_register[recipe_name]()
recipe(database_connection._original_connection,
hypothesis_name=name,
reduction=reduction,
derivatization=derivatization)
def glycan_text(context, text_file, database_connection, reduction,
derivatization, name):
if name is not None:
name = validate_glycan_hypothesis_name(context, database_connection,
name)
click.secho("Building Glycan Hypothesis %s" % name, fg='cyan')
reduction = validate_reduction(context, reduction)
derivatization = validate_derivatization(context, derivatization)
builder = TextFileGlycanHypothesisSerializer(text_file,
database_connection,
reduction=reduction,
derivatization=derivatization,
hypothesis_name=name)
builder.display_header()
builder.start()
def glyspace_glycan_hypothesis(context, database_connection, motif_class, reduction, derivatization, name,
target_taxon=None, include_children=False, detatch_substituent=None):
database_connection = DatabaseBoundOperation(database_connection)
if name is not None:
name = validate_glycan_hypothesis_name(context, database_connection._original_connection, name)
click.secho("Building Glycan Hypothesis %s" % name, fg='cyan')
filter_funcs = []
if target_taxon is not None:
filter_funcs.append(TaxonomyFilter(target_taxon, include_children))
serializer_type = None
if motif_class == "n-linked":
serializer_type = NGlycanGlyspaceHypothesisSerializer
elif motif_class == "o-linked":
serializer_type = OGlycanGlyspaceHypothesisSerializer
reduction = validate_reduction(context, reduction)
derivatization = validate_derivatization(context, derivatization)
job = serializer_type(
database_connection._original_connection, name, reduction, derivatization, filter_funcs,
simplify=True, substituents_to_detatch=detatch_substituent)
job.display_header()
job.start()
def glyspace_glycan_hypothesis(context,
database_connection,
motif_class,
reduction,
derivatization,
name,
target_taxon=None,
include_children=False,
detatch_substituent=None):
database_connection = DatabaseBoundOperation(database_connection)
if name is not None:
name = validate_glycan_hypothesis_name(
context, database_connection._original_connection, name)
click.secho("Building Glycan Hypothesis %s" % name, fg='cyan')
filter_funcs = []
if target_taxon is not None:
filter_funcs.append(TaxonomyFilter(target_taxon, include_children))
serializer_type = None
if motif_class == "n-linked":
serializer_type = NGlycanGlyspaceHypothesisSerializer
elif motif_class == "o-linked":
serializer_type = OGlycanGlyspaceHypothesisSerializer
reduction = validate_reduction(context, reduction)
derivatization = validate_derivatization(context, derivatization)
job = serializer_type(database_connection._original_connection,
name,
reduction,
derivatization,
filter_funcs,
simplify=True,
substituents_to_detatch=detatch_substituent)
job.display_header()
job.start()
def build_glycan_search_space_process():
data = request.values
custom_reduction_type = data.get("custom-reduction-type")
custom_derivatization_type = data.get("custom-derivatization-type")
has_custom_reduction = custom_reduction_type != ""
has_custom_derivatization = custom_derivatization_type != ""
reduction_type = data.get("reduction-type")
derivatization_type = data.get("derivatization-type")
hypothesis_name = data.get("hypothesis-name")
hypothesis_name = g.manager.make_unique_hypothesis_name(hypothesis_name)
secure_name = secure_filename(hypothesis_name if hypothesis_name is not None else "glycan_database")
storage_path = g.manager.get_hypothesis_path(re.sub(r"[\s\(\)]", "_", secure_name)) + '_glycan_%s.database'
storage_path = make_unique_name(storage_path)
touch_file(storage_path)
if reduction_type in ("", "native"):
reduction_type = None
if derivatization_type in ("", "native"):
derivatization_type = None
try:
reduction_type = validate_reduction(None, reduction_type)
except Exception:
g.manager.add_message(Message("Could not validate reduction type %r" % reduction_type, 'update'))
return Response("Task Not Scheduled")
try:
derivatization_type = validate_derivatization(None, derivatization_type)
except Exception:
g.manager.add_message(Message("Could not validate derivatization type %r" % derivatization_type, 'update'))
return Response("Task Not Scheduled")
selected_method = data.get("selected-method", 'combinatorial')
# Construct the argument set for a BuildCombinatorialGlycanHypothesis Task.
# This involves building a StringIO object buffer which contains the user's
# specified rules.
if selected_method == "combinatorial":
comb_monosaccharide_name = data.getlist('monosaccharide_name')[:-1]
comb_lower_bound = map(intify, data.getlist('monosaccharide_lower_bound')[:-1])
comb_upper_bound = map(intify, data.getlist('monosaccharide_upper_bound')[:-1])
comb_monosaccharide_name, comb_lower_bound, comb_upper_bound = remove_empty_rows(
comb_monosaccharide_name, comb_lower_bound, comb_upper_bound)
constraint_lhs = data.getlist("left_hand_side")[:-1]
constraint_op = data.getlist("operator")[:-1]
constraint_rhs = data.getlist("right_hand_side")[:-1]
constraints = zip(*remove_empty_rows(constraint_lhs, constraint_op, constraint_rhs))
rules = zip(comb_monosaccharide_name, comb_lower_bound, comb_upper_bound)
# File-like object to pass to the task in place of a path to a rules file
rules_buffer = _serialize_rules_to_buffer(rules, constraints, "generated")
task = BuildCombinatorialGlycanHypothesis(
rules_buffer, storage_path,
reduction=custom_reduction_type if has_custom_reduction else reduction_type,
derivatization=custom_derivatization_type if has_custom_derivatization else derivatization_type,
name=hypothesis_name,
callback=lambda: 0, user=g.user
)
g.add_task(task)
# Construct the argument set for a BuildTextFileGlycanHypothesis Task.
elif selected_method == "text-file":
glycan_list_file = request.files["glycan-list-file"]
secure_glycan_list_file = g.manager.get_temp_path(secure_filename(glycan_list_file.filename))
glycan_list_file.save(secure_glycan_list_file)
task = BuildTextFileGlycanHypothesis(
secure_glycan_list_file,
storage_path,
reduction=custom_reduction_type if has_custom_reduction else reduction_type,
derivatization=custom_derivatization_type if has_custom_derivatization else derivatization_type,
name=hypothesis_name,
callback=lambda: 0, user=g.user)
g.add_task(task)
elif selected_method == "pregenerated":
# include_human_n_glycan = data.get("glycomedb-human-n-glycan")
# include_human_o_glycan = data.get("glycomedb-human-o-glycan")
# include_mammalian_n_glycan = data.get("glycomedb-mammlian-n-glycan")
# include_mammalian_o_glycan = data.get("glycomedb-mammlian-o-glycan")
g.manager.add_message(Message("This method is not enabled at this time", 'update'))
return Response("Task Not Scheduled")
# Not yet implemented
elif selected_method == "merge-hypotheses":
id_1 = data.get("merged-hypothesis-1", 0)
id_2 = data.get("merged-hypothesis-2", 0)
if id_1 == 0 or id_2 == 0 or id_1 == id_2:
g.add_message(Message("Two different hypotheses must be selected to merge."))
return Response("Task Not Scheduled")
rec_1 = g.manager.hypothesis_manager.get(id_1)
rec_2 = g.manager.hypothesis_manager.get(id_2)
# g.add_message(Message("Not yet implemented."))
# return Response("Task Not Scheduled")
task = MergeGlycanHypotheses(
g.manager.connection_bridge, [(rec_1.path, rec_1.id), (rec_2.path, rec_2.id)], name=hypothesis_name,
callback=lambda: 0, user=g.user)
g.add_task(task)
else:
g.add_message(Message("This method is not recognized: \"%s\"" % (selected_method,), 'update'))
return Response("Task Not Scheduled")
return Response("Task Scheduled")