def __load_case_info(case, except_enabled=False, quality_enabled=False): wok = current_app.wok case_info = dict( id=case.id, name=case.name, state=case.state.title if case.state is not None else None,created=case.created, started=case.started, finished=case.finished, removed=case.removed) if case.state is not None: case_info["state"] = case.state.title if case.properties is not None: conf = get_project_conf() results_path = get_results_path(conf) project_path = os.path.join(results_path, case.properties["path"]) quality = None if quality_enabled: project_results = ProjectResults(path=project_path) quality = project_results.load_quality_control() zip_path = os.path.join(project_path, "results.zip") website_path = os.path.join(project_path, "website", "results", "project.tsv") case_info.update( analysis_type=case.properties["analysis_type"], results_available=os.path.exists(zip_path), website_available=os.path.exists(website_path), quality=quality if quality is not None and len(quality) > 0 else None) engine_case = wok.engine.case(case.engine_name) if engine_case is not None: exceptions = None if except_enabled: exceptions = __engine_case_exceptions(engine_case) case_info.update( state=engine_case.state.title, started=engine_case.started, finished=engine_case.finished, elapsed=engine_case.elapsed, progress=__engine_case_progress(engine_case), exceptions=exceptions) return case_info
def download(case_id):
case = current_app.wok.case_by_id(case_id, current_user)
if case is None:
flash("Case does not exist, there is nothing to download", "error")
return redirect(url_for(".index"))
current_app.logger.info("[{}] Downloading case results {} ({})...".format(current_user.nick, case.name, case.engine_name))
conf = get_project_conf()
results_path = get_results_path(conf)
project_path = os.path.join(results_path, case.properties["path"])
dest_path = os.path.join(project_path, "results.zip")
if not os.path.exists(dest_path):
flash("Sorry, there were an internal error and the results are not available", "error")
app.logger.error("[{}] results.zip not available for case {} at {}".format(current_user.nick, case.id, project_path))
return redirect(url_for(".index"))
return send_file(
dest_path,
mimetype="application/x-gzip",
as_attachment=True,
attachment_filename="IntOGen-Mutations-{}.zip".format(case.name))
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))