def _case_created(self, case, **kwargs): if hasattr(self, "projects") and self.projects is not None: upload_files(self.log, case.name, case.storages, self.projects) config = GlobalConfig( case.project.get_conf(platform_name=DEFAULT_PLATFORM_NAME), dict(user_id=self.user_id, workspace=self.workspace)) self.results_path = PathsConfig(config).results_path()
def run(type):
if type not in [COHORT_ANALYSIS, SINGLE_TUMOR_ANALYSIS]:
abort(400)
if request.method == "GET":
form = dict(
ofm_genes_threshold=ONCODRIVEFM_GENES_THRESHOLD,
ofm_pathways_threshold=ONCODRIVEFM_PATHWAYS_THRESHOLD,
oclust_genes_threshold=ONCODRIVECLUST_MUTATIONS_THRESHOLD)
return render_template("analysis.html", type=type, form=form)
if current_app.wok.cases_count(current_user) >= current_app.config.get("LIMIT_NUM_CASES", 100):
flash("""There is a limit on the number of simultaneous analysis that can be managed.
You must remove finished analysis before running new ones.""", "error")
return redirect(url_for("cases.index"))
mutations_file = request.files['mutations_file']
file_name = os.path.basename(mutations_file.filename)
project_id = request.form['project_name']
if len(project_id) == 0:
project_id = os.path.splitext(file_name)[0]
project_id = unique_project_id(normalize_id(project_id))
'''
if not current_user.validated:
flash("""You can not run an analysis with your data until you are completely registered.
Please check your email and follow the instructions to validate this account.""", "error")
flash("Meanwhile you can play with the included examples.")
return redirect(url_for("examples"))
'''
cb = ConfigBuilder()
cb.add_value("user_id", current_user.nick)
cb.add_value("workspace", DEFAULT_WORKSPACE)
cb.add_value("project.id", project_id)
#case_name = "-".join([current_user.nick, project_id])
#cb.add_value("wok.instance.name", case_name)
results_path, project_path, project_temp_path = get_paths(project_id)
if not current_user.is_anonymous():
cb.add_value("website.user_id", current_user.nick)
if type == SINGLE_TUMOR_ANALYSIS: #request.form.get("variants_only") == "1":
cb.add_value("variants_only", True)
cb.add_value("skip_oncodrivefm", True)
cb.add_value("skip_oncodriveclust", True)
try:
threshold = request.form["ofm_genes_threshold"]
if re.match(r"^[1-9]\d*%?$", threshold):
cb.add_value(ONCODRIVEFM_GENES_THRESHOLD_KEY, threshold)
except:
if type == COHORT_ANALYSIS:
current_app.logger.warn("[{}] Wrong form input: {}={}".format(
current_user.nick, "ofm_genes_threshold", request.form.get("ofm_genes_threshold")))
try:
threshold = request.form["ofm_pathways_threshold"]
if re.match(r"^[1-9]\d*%?$", threshold):
cb.add_value(ONCODRIVEFM_PATHWAYS_THRESHOLD_KEY, threshold)
except:
if type == COHORT_ANALYSIS:
current_app.logger.warn("[{}] Wrong form input: {}={}".format(
current_user.nick, "ofm_pathways_threshold", reuqest.form.get("ofm_pathways_threshold")))
try:
threshold = int(request.form["oclust_genes_threshold"])
if threshold >= 1:
cb.add_value(ONCODRIVECLUST_GENES_THRESHOLD_KEY, threshold)
except:
if type == COHORT_ANALYSIS:
current_app.logger.warn("[{}] Wrong form input: {}={}".format(
current_user.nick, "oclust_genes_threshold", request.form.get("oclust_genes_threshold")))
genes_filter_enabled = request.form.get('genes_filter_enabled') == "1"
cb.add_value(ONCODRIVEFM_FILTER_ENABLED_KEY, genes_filter_enabled)
cb.add_value(ONCODRIVECLUST_FILTER_ENABLED_KEY, genes_filter_enabled)
if genes_filter_enabled:
try:
genes_filter_file = request.files['genes_filter_file']
genes_filter_file_path = os.path.join(project_temp_path, "genes-filter.txt")
genes_filter_file.save(genes_filter_file_path)
if os.path.getsize(genes_filter_file_path) != 0:
cb.add_value(ONCODRIVEFM_GENES_FILTER_KEY, genes_filter_file_path)
cb.add_value(ONCODRIVECLUST_GENES_FILTER_KEY, genes_filter_file_path)
except:
current_app.logger.exception("Error retrieving genes filter from form")
assembly = request.form.get("assembly", DEFAULT_ASSEMBLY).lower()
project = dict(
id=project_id,
assembly=assembly,
files=[file_name])
projects = [init_project_files(project, check_paths=False)]
cb.add_value("projects", projects)
properties = dict(
analysis_type=type,
path=os.path.relpath(project_path, results_path))
current_app.logger.info("[{}] Starting analysis {} ...".format(current_user.nick, project_id))
case = current_app.wok.create_case(current_user, project_id, cb, PROJECT_NAME, MUTATIONS_FLOW_NAME,
properties=properties, start=False)
engine_case = current_app.wok.engine.case(case.engine_name)
#TODO use a background thread
upload_files(current_app.logger, case.engine_name, engine_case.storages, projects, streams=[mutations_file.stream])
current_app.logger.info("[{}] Analysis {} started on case {}...".format(
current_user.nick, project_id, case.engine_name))
engine_case.start()
return redirect(url_for("cases.index", highlight=case.id))
def run(type):
if type not in [COHORT_ANALYSIS, SINGLE_TUMOR_ANALYSIS]:
abort(400)
if current_app.wok.cases_count(current_user) >= current_app.config.get("LIMIT_NUM_CASES", 100):
flash("""There is a limit on the number of simultaneous analysis that can be managed.
You must remove finished analysis before running new ones.""", "error")
return redirect(url_for("cases.index"))
cb = ConfigBuilder()
cb.add_value("user_id", current_user.nick)
cb.add_value("workspace", DEFAULT_WORKSPACE)
if not current_user.is_anonymous():
cb.add_value("website.user_id", current_user.nick)
conf = get_project_conf()
if type == COHORT_ANALYSIS:
project_id = "cohort-example"
mutations_path = get_examples_path(conf, "meduloblastoma_cohort_tier1.muts")
elif type == SINGLE_TUMOR_ANALYSIS:
project_id = "single-tumor-example"
mutations_path = get_examples_path(conf, "pat4_crc.muts")
cb.add_value("variants_only", True)
cb.add_value("skip_oncodrivefm", True)
cb.add_value("skip_oncodriveclust", True)
project_id = unique_project_id(project_id)
cb.add_value("project.id", project_id)
results_path, project_path, project_temp_path = get_paths(project_id, conf=conf)
assembly = "hg19"
project = dict(
id=project_id,
assembly=assembly,
files=[mutations_path])
projects = [init_project_files(project)]
cb.add_value("projects", projects)
properties = dict(
analysis_type=type,
path=os.path.relpath(project_path, results_path),
data_file=mutations_path)
current_app.logger.info("[{}] Starting example {} ...".format(current_user.nick, project_id))
case = current_app.wok.create_case(current_user, project_id, cb, PROJECT_NAME, MUTATIONS_FLOW_NAME,
properties=properties, start=False)
engine_case = current_app.wok.engine.case(case.engine_name)
#TODO use a background thread
upload_files(current_app.logger, case.engine_name, engine_case.storages, projects)
current_app.logger.info("[{}] Example {} started on case {}...".format(
current_user.nick, project_id, case.engine_name))
engine_case.start()
return redirect(url_for("cases.index", highlight=case.id))