def _get_paea_link(ranked_genes, description):
"""Wrapper for paea module's get_link function.
"""
paea_genes = _apply_cutoff(ranked_genes, PAEA_CUTOFF)
link = paea.get_link(paea_genes, description)
target_app = get_or_create(TargetApp, name='paea')
return TargetAppLink(target_app, link)
def _get_crowdsourcing_link(ranked_genes, optional_metadata, soft_file, tags):
"""Wrapper for crowdsourcing module's get_link function.
"""
link = crowdsourcing.get_link(ranked_genes, optional_metadata, soft_file,
tags)
target_app = get_or_create(TargetApp, name='crowdsourcing')
return TargetAppLink(target_app, link)
def _get_paea_link(ranked_genes, description):
"""Wrapper for paea module's get_link function.
"""
paea_genes = _apply_cutoff(ranked_genes, PAEA_CUTOFF)
link = paea.get_link(paea_genes, description)
target_app = get_or_create(TargetApp, name='paea')
return TargetAppLink(target_app, link)
def _get_l1000cds2_link(ranked_genes, required_metadata):
"""Wrapper for l1000cds2 module's get_link function.
"""
# This is a hard cutoff and is also independent of user selection.
l1000cds2_genes = _apply_cutoff(ranked_genes, L1000CDS2_CUTOFF)
link = l1000cds2.get_link(l1000cds2_genes, required_metadata)
target_app = get_or_create(TargetApp, name='l1000cds2')
return TargetAppLink(target_app, link)
def _get_enrichr_link(ranked_genes, required_metadata, description):
"""Wrapper for enrichr module's get_link function.
"""
enrichr_cutoff = _get_cutoff(required_metadata)
enrichr_genes = _apply_cutoff(ranked_genes, enrichr_cutoff)
link = enrichr.get_link(enrichr_genes, description)
target_app = get_or_create(TargetApp, name='enrichr')
return TargetAppLink(target_app, link)
def _get_l1000cds2_link(ranked_genes, required_metadata):
"""Wrapper for l1000cds2 module's get_link function.
"""
# This is a hard cutoff and is also independent of user selection.
l1000cds2_genes = _apply_cutoff(ranked_genes, L1000CDS2_CUTOFF)
link = l1000cds2.get_link(l1000cds2_genes, required_metadata)
target_app = get_or_create(TargetApp, name='l1000cds2')
return TargetAppLink(target_app, link)
def _get_enrichr_link(ranked_genes, required_metadata, description):
"""Wrapper for enrichr module's get_link function.
"""
enrichr_cutoff = _get_cutoff(required_metadata)
enrichr_genes = _apply_cutoff(ranked_genes, enrichr_cutoff)
link = enrichr.get_link(enrichr_genes, description)
target_app = get_or_create(TargetApp, name='enrichr')
return TargetAppLink(target_app, link)
def from_http_request(args):
"""Returns list of Tag instances.
"""
tag_names = get_param_as_list(args, 'tags')
tags = []
for name in tag_names:
# If the name is not an empty string or just whitespace.
if bool(name.strip()):
tags.append(get_or_create(Tag, name=name))
return tags
def do(a_vals, b_vals, genes, metadata):
"""Delegates to the correct helper function based on client or default
configuration.
"""
if metadata.diff_exp_method == 'ttest':
genes, values = ttest(a_vals, b_vals, genes,
metadata.ttest_correction_method,
metadata.threshold)
else:
genes, values = chdir(a_vals, b_vals, genes)
# TODO: We should do this *after* the potential cutoff.
genes = [get_or_create(Gene, name=name) for name in genes]
ranked_genes = [
RankedGene(pair[0], pair[1]) for pair in zip(genes, values)
]
return ranked_genes
def do(a_vals, b_vals, genes, metadata):
"""Delegates to the correct helper function based on client or default
configuration.
"""
if metadata.diff_exp_method == 'ttest':
genes, values = ttest(
a_vals, b_vals, genes,
metadata.ttest_correction_method,
metadata.threshold
)
else:
genes, values = chdir(a_vals, b_vals, genes)
# TODO: We should do this *after* the potential cutoff.
genes = [get_or_create(Gene, name=name) for name in genes]
ranked_genes = [RankedGene(pair[0], pair[1]) for pair in zip(genes, values)]
return ranked_genes
def _get_crowdsourcing_link(ranked_genes, optional_metadata, soft_file, tags):
"""Wrapper for crowdsourcing module's get_link function.
"""
link = crowdsourcing.get_link(ranked_genes, optional_metadata, soft_file, tags)
target_app = get_or_create(TargetApp, name='crowdsourcing')
return TargetAppLink(target_app, link)