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 merge_glycan_hypotheses(context, database_connection, hypothesis_specification, name):
database_connection = DatabaseBoundOperation(database_connection)
hypothesis_ids = []
for connection, ident in hypothesis_specification:
hypothesis = get_by_name_or_id(DatabaseBoundOperation(connection), GlycanHypothesis, ident)
hypothesis_ids.append((connection, hypothesis.id))
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')
task = GlycanCompositionHypothesisMerger(
database_connection._original_connection, hypothesis_ids, name)
task.display_header()
task.start()
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 merge_glycan_hypotheses(context, database_connection,
hypothesis_specification, name):
database_connection = DatabaseBoundOperation(database_connection)
hypothesis_ids = []
for connection, ident in hypothesis_specification:
hypothesis = get_by_name_or_id(DatabaseBoundOperation(connection),
GlycanHypothesis, ident)
hypothesis_ids.append((connection, hypothesis.id))
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')
task = GlycanCompositionHypothesisMerger(
database_connection._original_connection, hypothesis_ids, name)
task.display_header()
task.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()