def get_gene_list(direction, extraction_id):
"""Returns gene list in plain text file based on gene signature ID.
"""
gene_signature = database.get_gene_signature(extraction_id)
gene_list = _get_gene_list_by_direction(gene_signature, int(direction))
gene_list_str = file_manager.get_file_contents_as_string(gene_list)
response = Response(gene_list_str, mimetype='text/plain')
return response
def get_gene_list(direction, extraction_id):
"""Returns gene list in plain text file based on gene signature ID.
"""
gene_signature = database.get_gene_signature(extraction_id)
gene_list = _get_gene_list_by_direction(gene_signature, int(direction))
gene_list_str = file_manager.get_file_contents_as_string(gene_list)
response = Response(gene_list_str, mimetype='text/plain')
return response
def get_extraction(extraction_id):
"""Handles GET request based on extraction ID.
"""
gene_signature = database.get_gene_signature(extraction_id)
if gene_signature is None:
return jsonify(
{'error': 'No gene signatures with ID %s found' % extraction_id})
else:
return jsonify(gene_signature.serialize)
def perform_hierarchical_clustering(extraction_id):
"""Performs hierarchical clustering on a SOFT file.
"""
gene_signature = database.get_gene_signature(extraction_id)
link = clustergrammer.from_soft_file(gene_signature)
link = link + '&preview=true'
return render_template('pages/clustergrammer.html',
clustergrammer_link=link,
results_url=config.RESULTS_URL,
extraction_id=gene_signature.extraction_id)
def get_extraction(extraction_id):
"""Handles GET request based on extraction ID.
"""
gene_signature = database.get_gene_signature(extraction_id)
if gene_signature is None:
return jsonify({
'error': 'No gene signatures with ID %s found' % extraction_id
})
else:
return jsonify(gene_signature.serialize)
def perform_hierarchical_clustering(extraction_id):
"""Performs hierarchical clustering on a SOFT file.
"""
gene_signature = database.get_gene_signature(extraction_id)
link = clustergrammer.from_soft_file(gene_signature)
link = link + '&preview=true'
return render_template('pages/clustergrammer.html',
clustergrammer_link=link,
results_url=config.RESULTS_URL,
extraction_id=gene_signature.extraction_id)
def perform_soft_file_pca(extraction_id):
"""Performs PCA on a SOFT file, referenced by extraction_id.
"""
gene_signature = database.get_gene_signature(extraction_id)
if gene_signature:
pca_data = pca.from_soft_file(gene_signature.soft_file)
pca_json = json.dumps(pca_data)
return render_template('pages/pca.html',
pca_data=pca_json,
results_url=config.RESULTS_URL,
extraction_id=gene_signature.extraction_id)
def get_soft_file(extraction_id):
"""Returns SOFT file in plain text file based on gene signature ID.
"""
gene_signature = database.get_gene_signature(extraction_id)
soft_file = gene_signature.soft_file.actual_text_file
soft_file_str = ''
for line in soft_file:
print(line)
soft_file_str += line
response = Response(soft_file_str, mimetype='text/plain')
return response
def get_soft_file(extraction_id):
"""Returns SOFT file in plain text file based on gene signature ID.
"""
gene_signature = database.get_gene_signature(extraction_id)
soft_file = gene_signature.soft_file.actual_text_file
soft_file_str = ''
for line in soft_file:
print line
soft_file_str += line
response = Response(soft_file_str, mimetype='text/plain')
return response
def edit_result():
"""Edits gene signature, removing fields that are empty and adding new ones.
"""
extraction_id = request.form.get('extraction_id')
gene_signature = database.get_gene_signature(extraction_id)
for opt_meta in gene_signature.optional_metadata:
value = request.form.get(opt_meta.name)
if not value:
database.delete_object(opt_meta)
continue
opt_meta.value = value
database.update_object(opt_meta)
# Generate a new optional metadata field is requested.
new_meta_name = request.form.get('new_metadata_name')
new_meta_value = request.form.get('new_metadata_value')
if new_meta_name and new_meta_value:
new_opt_meta = OptionalMetadata(new_meta_name, new_meta_value)
gene_signature.optional_metadata.append(new_opt_meta)
database.update_object(gene_signature)
# Update existing tags.
tag_names = request_utils.get_param_as_list(request.form, 'tags')
for tag in gene_signature.tags:
if tag.name not in tag_names:
database.delete_object(tag)
else:
tag_names.remove(tag.name)
database.update_object(gene_signature)
# Create any new tags. Note that any leftover tags are new ones.
if len(tag_names) > 0:
for tag_name in tag_names:
tag = Tag(tag_name)
gene_signature.tags.append(tag)
database.update_object(gene_signature)
return redirect(
url_for('results_page.view_result', extraction_id=extraction_id))
def edit_result():
"""Edits gene signature, removing fields that are empty and adding new ones.
"""
extraction_id = request.form.get('extraction_id')
gene_signature = database.get_gene_signature(extraction_id)
for opt_meta in gene_signature.optional_metadata:
value = request.form.get(opt_meta.name)
if not value:
database.delete_object(opt_meta)
continue
opt_meta.value = value
database.update_object(opt_meta)
# Generate a new optional metadata field is requested.
new_meta_name = request.form.get('new_metadata_name')
new_meta_value = request.form.get('new_metadata_value')
if new_meta_name and new_meta_value:
new_opt_meta = OptionalMetadata(new_meta_name, new_meta_value)
gene_signature.optional_metadata.append(new_opt_meta)
database.update_object(gene_signature)
# Update existing tags.
tag_names = request_utils.get_param_as_list(request.form, 'tags')
for tag in gene_signature.tags:
if tag.name not in tag_names:
database.delete_object(tag)
else:
tag_names.remove(tag.name)
database.update_object(gene_signature)
# Create any new tags. Note that any leftover tags are new ones.
if len(tag_names) > 0:
for tag_name in tag_names:
tag = Tag(tag_name)
gene_signature.tags.append(tag)
database.update_object(gene_signature)
return redirect(url_for('results_page.view_result',
extraction_id=extraction_id))
def view_result(extraction_id):
"""Renders extracted gene signature and associated metadata.
"""
gene_signature = database.get_gene_signature(extraction_id)
if gene_signature is None:
return render_template('pages/404.html')
gene_signature = _process_extraction_for_view(gene_signature)
use_crowdsourcing = False
for tag in gene_signature.tags:
if tag.name in CROWDSOURCING_TAGS:
use_crowdsourcing = True
if gene_signature.soft_file and gene_signature.soft_file.samples:
show_viz = True
else:
show_viz = False
if current_user.is_authenticated and current_user.name == 'admin':
show_admin_controls = True
tag_names = [t.name for t in gene_signature.tags]
else:
show_admin_controls = False
tag_names = None
if gene_signature.is_from_geo:
return render_template('pages/results.html',
show_admin_controls=show_admin_controls,
tag_names=json.dumps(tag_names),
gene_signature=gene_signature,
show_viz=show_viz,
use_crowdsourcing=use_crowdsourcing)
else:
return render_template('pages/results-not-from-geo.html',
show_admin_controls=show_admin_controls,
tag_names=json.dumps(tag_names),
gene_signature=gene_signature)
def view_result(extraction_id):
"""Renders extracted gene signature and associated metadata.
"""
gene_signature = database.get_gene_signature(extraction_id)
if gene_signature is None:
return render_template('pages/404.html')
gene_signature = _process_extraction_for_view(gene_signature)
use_crowdsourcing = False
for tag in gene_signature.tags:
if tag.name in CROWDSOURCING_TAGS:
use_crowdsourcing = True
if gene_signature.soft_file and gene_signature.soft_file.samples:
show_viz = True
else:
show_viz = False
if current_user.is_authenticated and current_user.name == 'admin':
show_admin_controls = True
tag_names = [t.name for t in gene_signature.tags]
else:
show_admin_controls = False
tag_names = None
if gene_signature.is_from_geo:
return render_template('pages/results.html',
show_admin_controls=show_admin_controls,
tag_names=json.dumps(tag_names),
gene_signature=gene_signature,
show_viz=show_viz,
use_crowdsourcing=use_crowdsourcing)
else:
return render_template('pages/results-not-from-geo.html',
show_admin_controls=show_admin_controls,
tag_names=json.dumps(tag_names),
gene_signature=gene_signature)