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 from_soft_file(gene_signature):
"""Performs hierarchical clustering on SOFT file.
"""
target_app_link = __get_clustergrammer_link(gene_signature)
# Only create the link from Clustergrammer once.
# TODO: Move into targetapp module. API should not know about this.
if not target_app_link:
link = __from_soft_file(gene_signature)
link = '{0}?preview=true'.format(link)
target_app = database.get_or_create(TargetApp, name='clustergrammer')
target_app_link = TargetAppLink(target_app, link)
gene_signature.gene_lists[2].target_app_links.append(target_app_link)
database.save_gene_signature(gene_signature)
return target_app_link.link