def post_to_l1000cds2(sig_id):
"""POST signature to L1000CDS2 API, then redirect to the result page.
"""
# get GeneSignature instance
gene_signature_fk = database.get(OptionalMetadata, sig_id,
'value').gene_signature_fk
gene_signature = database.get(GeneSignature, gene_signature_fk, 'id')
# retrieve up_genes, down_genes
up_genes = [rg.gene.name for rg in gene_signature.up_genes]
down_genes = [rg.gene.name for rg in gene_signature.down_genes]
# POST to L1000CDS2
cds2_url = 'http://amp.pharm.mssm.edu/L1000CDS2/query'
data = {'upGenes': up_genes, 'dnGenes': down_genes}
config = {
"aggravate": True,
"searchMethod": "geneSet",
"share": True,
"combination": False,
"db-version": "latest"
}
metadata = [{"key": "sig_id", "value": sig_id}]
payload = {"data": data, "config": config, "meta": metadata}
headers = {'content-type': 'application/json'}
resp = requests.post(cds2_url, data=json.dumps(payload), headers=headers)
if resp.status_code == 200:
resp = resp.json()
share_id = resp['shareId']
result_url = 'http://amp.pharm.mssm.edu/L1000CDS2/#/result/%s' % share_id
return redirect(result_url)
else:
abort(404)
def get_binary(sig_id):
"""Get up/down gene sets.
"""
# get GeneSignature instance
gene_signature_fk = database.get(OptionalMetadata, sig_id,
'value').gene_signature_fk
gene_signature = database.get(GeneSignature, gene_signature_fk, 'id')
# retrieve up_genes, down_genes
up_genes = [rg.gene.name for rg in gene_signature.up_genes]
down_genes = [rg.gene.name for rg in gene_signature.down_genes]
return json.dumps({
'up_genes': up_genes,
'down_genes': down_genes,
'sig_id': sig_id
})
def view_gene_signature(extraction_id):
"""Modal for gene signature.
"""
gene_signature = database.get(GeneSignature, extraction_id,
'extraction_id')
return render_template('pages/gene-signature.html',
gene_signature=gene_signature)
def view_custom_report(report_id, tag_name):
"""Views a custom report by report ID.
"""
tag = database.get(Tag, tag_name, 'name')
report = database.get(Report, report_id)
print(report.category)
print(report.gene_signatures)
if not tag or not report:
abort(404)
if report.pca_plot:
pca_json = report.pca_plot.data
else:
pca_json = None
return render_template('pages/report.html',
tag=tag,
report=report,
pca_json=pca_json)
def build_approved_report(tag_name):
"""Builds the an approved report for a tag.
"""
category = request.args.get('category')
tag = database.get(Tag, tag_name, 'name')
report_builder.build(tag, category=category)
return redirect(
url_for('report_pages.view_approved_report', tag_name=tag.name))
def reanalyze_approved_report(tag_name):
"""Reanalyze, i.e. requests new results from Enrichr and L1000CDS2, an
approved report for a tag.
"""
category = request.args.get('category')
tag = database.get(Tag, tag_name, 'name')
report_builder.build(tag, category=category, reanalyze=True)
return redirect(
url_for('report_pages.view_approved_report', tag_name=tag.name))
def view_custom_tag(report_id):
report = database.get(Report, report_id)
if report is None:
return abort(404)
else:
signatures = report.gene_signatures
# The signatures for a custom report are a subset of signatures for
# the main report. We show "tag-custom.html" because we do not want
# users to build custom reports from these subsets.
return render_template('pages/tag-custom.html', tag=report.tag,
report=report, gene_signatures=signatures)
def view_approved_tag(tag_name, extraction_id=None):
tag = database.get(Tag, tag_name, key='name')
if tag is None:
abort(404)
else:
signatures = tag.gene_signatures
metadata = _get_metadata_names_and_percentages(signatures)
return render_template('pages/tag.html', tag=tag,
gene_signatures=signatures,
extraction_id=extraction_id,
metadata=metadata)
def view_approved_report(tag_name):
"""Renders approved report page.
"""
tag = database.get(Tag, tag_name, 'name')
drug = database.get(Drug, tag_name, 'pert_id')
if not tag:
# abort(404)
return render_template('pages/report-empty.html', drug=drug)
else:
report = tag.approved_report
print tag.name
print report.id
if not report.complete(Config.SUPPORTED_ENRICHR_LIBRARIES):
print 'Report for %s is not complete, building...' % tag.name
print len(report.heat_maps)
print len(report.enrichr_heat_maps)
report_builder.rebuild(tag, category='cell')
return render_template('pages/report.html',
tag=tag,
drug=drug,
report=report)
def build_custom_report_from_all_signatures(tag_name):
"""Builds a custom report from all signatures.
"""
tag = database.get(Tag, tag_name, 'name')
if not tag:
abort(404)
report_name = tag.name
category = None
report_id = report_builder.build_custom(tag, tag.gene_signatures,
report_name, category)
new_url = '%s/%s/%s' % (Config.REPORT_URL, report_id, tag.name)
return redirect(new_url)
def download_gene_list(extraction_id, direction):
"""Generate txt file for gene lists in gene signatures.
direction should be attr name in one of ('combined_genes', 'up_genes', 'down_genes')
"""
gene_signature = database.get(GeneSignature, extraction_id,
'extraction_id')
gene_list = map(lambda x: x.gene.name, getattr(gene_signature, direction))
# Make a file on-the-fly
gene_list = '\n'.join(gene_list)
filename = '%s-%s.txt' % (extraction_id, direction)
response = make_response(gene_list)
response.headers[
"Content-Disposition"] = "attachment; filename=%s" % filename
return response
def build_custom_report(tag_name):
"""Builds a custom report.
"""
tag = database.get(Tag, tag_name, 'name')
if not tag:
abort(404)
category = request.json.get('category')
report_name = request.json.get('report_name')
extraction_ids = _get_extraction_ids(request)
gene_signatures = database.get_signatures_by_ids(extraction_ids)
report_id = report_builder.build_custom(tag, gene_signatures, report_name,
category)
# This endpoint is hit via an AJAX request. JavaScript must perform the
# redirect.
new_url = '%s/%s/%s' % (Config.REPORT_URL, report_id, tag.name)
return jsonify({'new_url': new_url})
def create(type_, Session=None, **kwargs):
"""Returns link to hierarchical clustering.
"""
category_name = kwargs.get('category')
TYPES = ['genes', 'enrichr', 'l1000cds2']
if type_ not in TYPES:
raise ValueError('Invalid type_ argument. Must be in %s' % str(TYPES))
if 'extraction_ids' in kwargs:
signatures = []
for extraction_id in kwargs.get('extraction_ids', []):
signature = database.get(GeneSignature, extraction_id,
'extraction_id')
signatures.append(signature)
else:
signatures = kwargs.get('signatures')
diff_exp_method = kwargs.get('diff_exp_method')
payload = {}
if type_ == 'enrichr':
library = kwargs.get('library')
payload['is_up_down'] = True
payload['columns'] = prepare_enriched_terms(Session, signatures,
category_name, library)
elif type_ == 'l1000cds2':
payload['columns'] = prepare_perturbations(Session, signatures,
category_name)
payload['is_up_down'] = True
elif type_ == 'genes':
payload['columns'] = prepare_ranked_genes(diff_exp_method, signatures,
category_name)
payload['is_up_down'] = False
net = Network()
net.load_vect_post_to_net(payload)
net.make_clust()
result = net.export_net_json()
return result
def test(tag_name):
"""Returns a zipped directory with one plain text file for each signature.
"""
tag = database.get(Tag, tag_name, 'name')
# Write the contents of the signatures to file and get the filenames.
filenames = _get_signature_files(tag)
# Folder name in ZIP archive which contains the above files
zip_subdir = tag.name
zip_filename = '%s.zip' % zip_subdir
# Open StringIO to grab in-memory ZIP contents
s = StringIO.StringIO()
# The zip compressor
zf = zipfile.ZipFile(s, 'w')
for fpath in filenames:
# Calculate path for file in zip
fdir, fname = os.path.split(fpath)
zip_path = os.path.join(zip_subdir, fname)
# Add file, at correct path
zf.write(fpath, zip_path)
zf.close()
# Grab ZIP file from in-memory, make response with correct MIME-type
resp = Response(s.getvalue(), mimetype='application/x-zip-compressed')
resp.headers[
'Content-Disposition'] = 'attachment; filename=%s' % zip_filename
# Remove files from disc
for f in filenames:
os.remove(f)
return resp