def execute(self):
workspace_path = os.path.join(self.results_path, self.args.workspace)
projects_path = os.path.join(workspace_path, "projects")
qc_path = os.path.join(workspace_path, "quality_control")
self.log.info("Preparing output path at {} ...".format(os.path.relpath(qc_path, self.runtime_path)))
self.create_output_path(qc_path)
loader = ChoiceLoader([
PackageLoader(__name__, 'qc_templates'),
FileSystemLoader(os.path.join(self.root_path, "web", "templates"))
])
env = Environment(loader=loader, autoescape=False)
env.globals.update(
version=VERSION,
creation_date=str(datetime.now())
)
env.filters["tojson"] = tojson
self.log.info("Looking for projects ...")
projects = []
quality_controls = []
for project_path in sorted(os.listdir(projects_path)):
project_path = os.path.join(projects_path, project_path)
proj_res = ProjectResults(path=project_path)
project = proj_res.load_def()
quality = proj_res.load_quality_control()
projects += [project]
quality_controls += [quality]
self.log.info("Processing {} projects ...".format(len(projects)))
for i, project in enumerate(projects):
self.log.info("Processing report for project {} ...".format(project["id"]))
quality = quality_controls[i]
t = env.get_template("project.html")
context=dict(
index=i,
project=project,
quality=quality,
projects=projects)
t.stream(context).dump(os.path.join(qc_path, "project_{}.html".format(project["id"])))
self.log.info("Generating index.html ...")
t = env.get_template("index.html")
t.stream(projects=projects).dump(os.path.join(qc_path, "index.html"))
def __load_case_info(case, except_enabled=False, quality_enabled=False): wok = current_app.wok case_info = dict( id=case.id, name=case.name, created=case.created, removed=case.removed) if case.properties is not None: case_path = case.properties["path"] quality = None if quality_enabled: project_results = ProjectResults(path=case_path) quality = project_results.load_quality_control() zip_path = os.path.join(case_path, "results.zip") website_path = os.path.join(case_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
