def post(self, preprocessed_data_id): # make sure user is admin and can therefore actually submit to VAMPS if self.current_user.level != 'admin': raise HTTPError( 403, "User %s cannot submit to VAMPS!" % self.current_user.id) msg = '' msg_level = 'success' preprocessed_data = Artifact(preprocessed_data_id) state = preprocessed_data.submitted_to_vamps_status() demux = [ path for _, path, ftype in preprocessed_data.get_filepaths() if ftype == 'preprocessed_demux' ] demux_length = len(demux) if state in ('submitting', 'success'): msg = "Cannot resubmit! Current state is: %s" % state msg_level = 'danger' elif demux_length != 1: msg = "The study doesn't have demux files or have too many" % state msg_level = 'danger' else: channel = self.current_user.id job_id = submit(channel, submit_to_VAMPS, int(preprocessed_data_id)) self.render('compute_wait.html', job_id=job_id, title='VAMPS Submission', completion_redirect='/compute_complete/%s' % job_id) return self.display_template(preprocessed_data_id, msg, msg_level)
def post(self, preprocessed_data_id): # make sure user is admin and can therefore actually submit to VAMPS if self.current_user.level != "admin": raise HTTPError(403, "User %s cannot submit to VAMPS!" % self.current_user.id) msg = "" msg_level = "success" preprocessed_data = Artifact(preprocessed_data_id) state = preprocessed_data.submitted_to_vamps_status() demux = [path for _, path, ftype in preprocessed_data.get_filepaths() if ftype == "preprocessed_demux"] demux_length = len(demux) if state in ("submitting", "success"): msg = "Cannot resubmit! Current state is: %s" % state msg_level = "danger" elif demux_length != 1: msg = "The study doesn't have demux files or have too many" % state msg_level = "danger" else: channel = self.current_user.id job_id = submit(channel, submit_to_VAMPS, int(preprocessed_data_id)) self.render( "compute_wait.html", job_id=job_id, title="VAMPS Submission", completion_redirect="/compute_complete/%s" % job_id, ) return self.display_template(preprocessed_data_id, msg, msg_level)
def display_template(self, preprocessed_data_id, msg, msg_level): """Simple function to avoid duplication of code""" preprocessed_data_id = int(preprocessed_data_id) try: preprocessed_data = Artifact(preprocessed_data_id) except QiitaDBUnknownIDError: raise HTTPError( 404, "Artifact %d does not exist!" % preprocessed_data_id) else: user = self.current_user if user.level != 'admin': raise HTTPError( 403, "No permissions of admin, " "get/VAMPSSubmitHandler: %s!" % user.id) prep_template = PrepTemplate(preprocessed_data.prep_template) sample_template = SampleTemplate(preprocessed_data.study) study = Study(preprocessed_data.study) stats = [('Number of samples', len(prep_template)), ('Number of metadata headers', len(sample_template.categories()))] demux = [ path for _, path, ftype in preprocessed_data.get_filepaths() if ftype == 'preprocessed_demux' ] demux_length = len(demux) if not demux_length: msg = ("Study does not appear to have demultiplexed " "sequences associated") msg_level = 'danger' elif demux_length > 1: msg = ("Study appears to have multiple demultiplexed files!") msg_level = 'danger' elif demux_length == 1: demux_file = demux[0] demux_file_stats = demux_stats(demux_file) stats.append(('Number of sequences', demux_file_stats.n)) msg_level = 'success' self.render('vamps_submission.html', study_title=study.title, stats=stats, message=msg, study_id=study.id, level=msg_level, preprocessed_data_id=preprocessed_data_id)
def display_template(self, preprocessed_data_id, msg, msg_level): """Simple function to avoid duplication of code""" preprocessed_data_id = int(preprocessed_data_id) try: preprocessed_data = Artifact(preprocessed_data_id) except QiitaDBUnknownIDError: raise HTTPError(404, "Artifact %d does not exist!" % preprocessed_data_id) else: user = self.current_user if user.level != "admin": raise HTTPError(403, "No permissions of admin, " "get/VAMPSSubmitHandler: %s!" % user.id) prep_template = PrepTemplate(preprocessed_data.prep_template) sample_template = SampleTemplate(preprocessed_data.study) study = Study(preprocessed_data.study) stats = [ ("Number of samples", len(prep_template)), ("Number of metadata headers", len(sample_template.categories())), ] demux = [path for _, path, ftype in preprocessed_data.get_filepaths() if ftype == "preprocessed_demux"] demux_length = len(demux) if not demux_length: msg = "Study does not appear to have demultiplexed " "sequences associated" msg_level = "danger" elif demux_length > 1: msg = "Study appears to have multiple demultiplexed files!" msg_level = "danger" elif demux_length == 1: demux_file = demux[0] demux_file_stats = demux_stats(demux_file) stats.append(("Number of sequences", demux_file_stats.n)) msg_level = "success" self.render( "vamps_submission.html", study_title=study.title, stats=stats, message=msg, study_id=study.id, level=msg_level, preprocessed_data_id=preprocessed_data_id, )
self.display_template(preprocessed_data_id, "", "") @authenticated @execute_as_transaction def post(self, preprocessed_data_id): # make sure user is admin and can therefore actually submit to VAMPS <<<<<<< HEAD if self.current_user.level != 'admin': raise HTTPError(403, "User %s cannot submit to VAMPS!" % self.current_user.id) msg = '' msg_level = 'success' preprocessed_data = Artifact(preprocessed_data_id) state = preprocessed_data.submitted_to_vamps_status() demux = [path for _, path, ftype in preprocessed_data.get_filepaths() if ftype == 'preprocessed_demux'] demux_length = len(demux) if state in ('submitting', 'success'): msg = "Cannot resubmit! Current state is: %s" % state msg_level = 'danger' elif demux_length != 1: msg = "The study doesn't have demux files or have too many" % state msg_level = 'danger' else: channel = self.current_user.id job_id = submit(channel, submit_to_VAMPS, int(preprocessed_data_id)) self.render('compute_wait.html',