def test_generate_param_str(self):
params = DefaultParameters(10)
obs = generate_param_str(params)
exp = ("<b>Reference:</b> Greengenes 13_8<br/>"
"<b>similarity:</b> 0.97<br/>"
"<b>sortmerna_e_value:</b> 1<br/>"
"<b>sortmerna_max_pos:</b> 10000<br/>"
"<b>threads:</b> 1<br/>"
"<b>sortmerna_coverage:</b> 0.97")
self.assertEqual(obs, exp)
def test_generate_param_str(self):
params = ProcessedSortmernaParams(1)
obs = generate_param_str(params)
exp = ("<b>Reference:</b> Greengenes 13_8<br/>"
"<b>similarity:</b> 0.97<br/>"
"<b>sortmerna_e_value:</b> 1.0<br/>"
"<b>sortmerna_max_pos:</b> 10000<br/>"
"<b>threads:</b> 1<br/>"
"<b>sortmerna_coverage:</b> 0.97")
self.assertEqual(obs, exp)
def test_generate_param_str(self):
params = DefaultParameters(10)
obs = generate_param_str(params)
exp = ('<b>Reference:</b> Greengenes 13_8<br/>'
'<b>sortmerna_e_value:</b> 1<br/>'
'<b>sortmerna_max_pos:</b> 10000<br/>'
'<b>similarity:</b> 0.97<br/>'
'<b>sortmerna_coverage:</b> 0.97<br/>'
'<b>threads:</b> 1')
self.assertEqual(obs, exp)
def render(self, study_id, preprocessed_data):
user = self.current_user
ppd_id = preprocessed_data.id
ebi_status = preprocessed_data.submitted_to_insdc_status()
ebi_study_accession = preprocessed_data.ebi_study_accession
ebi_submission_accession = preprocessed_data.ebi_submission_accession
vamps_status = preprocessed_data.submitted_to_vamps_status()
filepaths = preprocessed_data.get_filepaths()
is_local_request = self._is_local()
show_ebi_btn = user.level == "admin"
processing_status = preprocessed_data.processing_status
processed_data = preprocessed_data.processed_data
# Get all the ENA terms for the investigation type
ontology = Ontology(convert_to_id('ENA', 'ontology'))
# make "Other" show at the bottom of the drop down menu
ena_terms = []
for v in sorted(ontology.terms):
if v != 'Other':
ena_terms.append('<option value="%s">%s</option>' % (v, v))
ena_terms.append('<option value="Other">Other</option>')
# New Type is for users to add a new user-defined investigation type
user_defined_terms = ontology.user_defined_terms + ['New Type']
if PrepTemplate.exists(preprocessed_data.prep_template):
prep_template_id = preprocessed_data.prep_template
prep_template = PrepTemplate(prep_template_id)
raw_data_id = prep_template.raw_data
inv_type = prep_template.investigation_type or "None Selected"
else:
prep_template_id = None
raw_data_id = None
inv_type = "None Selected"
process_params = {param.id: (generate_param_str(param), param.name)
for param in ProcessedSortmernaParams.iter()}
# We just need to provide an ID for the default parameters,
# so we can initialize the interface
default_params = 1
return self.render_string(
"study_description_templates/preprocessed_data_info_tab.html",
ppd_id=ppd_id,
show_ebi_btn=show_ebi_btn,
ebi_status=ebi_status,
ebi_study_accession=ebi_study_accession,
ebi_submission_accession=ebi_submission_accession,
filepaths=filepaths,
is_local_request=is_local_request,
prep_template_id=prep_template_id,
raw_data_id=raw_data_id,
inv_type=inv_type,
ena_terms=ena_terms,
vamps_status=vamps_status,
user_defined_terms=user_defined_terms,
process_params=process_params,
default_params=default_params,
study_id=preprocessed_data.study,
processing_status=processing_status,
processed_data=processed_data)
def render(self, study_id, preprocessed_data):
user = self.current_user
ppd_id = preprocessed_data.id
vamps_status = preprocessed_data.is_submitted_to_vamps
filepaths = preprocessed_data.filepaths
is_local_request = is_localhost(self.request.headers['host'])
show_ebi_btn = user.level == "admin"
processing_status, processing_status_msg = \
get_artifact_processing_status(preprocessed_data)
processed_data = sorted([pd.id for pd in preprocessed_data.children])
# Get all the ENA terms for the investigation type
ontology = Ontology(convert_to_id('ENA', 'ontology'))
# make "Other" show at the bottom of the drop down menu
ena_terms = []
for v in sorted(ontology.terms):
if v != 'Other':
ena_terms.append('<option value="%s">%s</option>' % (v, v))
ena_terms.append('<option value="Other">Other</option>')
# New Type is for users to add a new user-defined investigation type
user_defined_terms = ontology.user_defined_terms + ['New Type']
# ppd can only have 1 prep template
prep_template = preprocessed_data.prep_templates[0]
# this block might seem wrong but is here due to a possible
# pathological case that we used to have in the system: preprocessed
# data without valid prep_templates
prep_templates = preprocessed_data.prep_templates
if len(prep_templates) == 1:
prep_template_id = prep_template.id
raw_data_id = prep_template.artifact.id
inv_type = prep_template.investigation_type or "None selected"
else:
prep_template_id = None
raw_data_id = None
inv_type = "None Selected"
process_params = {
param.id: (generate_param_str(param), param.name)
for param in Command(3).default_parameter_sets
}
# We just need to provide an ID for the default parameters,
# so we can initialize the interface
default_params = min(process_params.keys())
ebi_link = None
if preprocessed_data.is_submitted_to_ebi:
ebi_link = EBI_LINKIFIER.format(
Study(study_id).ebi_study_accession)
return self.render_string(
"study_description_templates/preprocessed_data_info_tab.html",
ppd_id=ppd_id,
show_ebi_btn=show_ebi_btn,
filepaths=filepaths,
is_local_request=is_local_request,
prep_template_id=prep_template_id,
raw_data_id=raw_data_id,
inv_type=inv_type,
ena_terms=ena_terms,
vamps_status=vamps_status,
user_defined_terms=user_defined_terms,
process_params=process_params,
default_params=default_params,
study_id=preprocessed_data.study.id,
processing_status=processing_status,
processing_status_msg=processing_status_msg,
processed_data=processed_data,
ebi_link=ebi_link)
def render(self, study_id, preprocessed_data):
user = self.current_user
ppd_id = preprocessed_data.id
vamps_status = preprocessed_data.is_submitted_to_vamps
filepaths = preprocessed_data.filepaths
is_local_request = is_localhost(self.request.headers['host'])
show_ebi_btn = user.level == "admin"
processing_status, processing_status_msg = \
get_artifact_processing_status(preprocessed_data)
processed_data = sorted([pd.id for pd in preprocessed_data.children])
# Get all the ENA terms for the investigation type
ontology = Ontology(convert_to_id('ENA', 'ontology'))
# make "Other" show at the bottom of the drop down menu
ena_terms = []
for v in sorted(ontology.terms):
if v != 'Other':
ena_terms.append('<option value="%s">%s</option>' % (v, v))
ena_terms.append('<option value="Other">Other</option>')
# New Type is for users to add a new user-defined investigation type
user_defined_terms = ontology.user_defined_terms + ['New Type']
# ppd can only have 1 prep template
prep_template = preprocessed_data.prep_templates[0]
# this block might seem wrong but is here due to a possible
# pathological case that we used to have in the system: preprocessed
# data without valid prep_templates
prep_templates = preprocessed_data.prep_templates
if len(prep_templates) == 1:
prep_template_id = prep_template.id
raw_data_id = prep_template.artifact.id
inv_type = prep_template.investigation_type or "None selected"
else:
prep_template_id = None
raw_data_id = None
inv_type = "None Selected"
process_params = {param.id: (generate_param_str(param), param.name)
for param in Command(3).default_parameter_sets}
# We just need to provide an ID for the default parameters,
# so we can initialize the interface
default_params = min(process_params.keys())
ebi_link = None
if preprocessed_data.is_submitted_to_ebi:
ebi_link = EBI_LINKIFIER.format(
Study(study_id).ebi_study_accession)
return self.render_string(
"study_description_templates/preprocessed_data_info_tab.html",
ppd_id=ppd_id,
show_ebi_btn=show_ebi_btn,
filepaths=filepaths,
is_local_request=is_local_request,
prep_template_id=prep_template_id,
raw_data_id=raw_data_id,
inv_type=inv_type,
ena_terms=ena_terms,
vamps_status=vamps_status,
user_defined_terms=user_defined_terms,
process_params=process_params,
default_params=default_params,
study_id=preprocessed_data.study.id,
processing_status=processing_status,
processing_status_msg=processing_status_msg,
processed_data=processed_data,
ebi_link=ebi_link)