def get_prep_templates(self, raw_data, callback):
"""Get all prep templates for a list of raw data objects"""
d = {}
for rd in raw_data:
# We neeed this so PrepTemplate(p) doesn't fail if that raw
# doesn't exist but raw data has the row: #554
prep_templates = sorted(rd.prep_templates)
d[rd.id] = [PrepTemplate(p) for p in prep_templates
if PrepTemplate.exists(p)]
callback(d)
def get_prep_templates(self, raw_data, callback):
"""Get all prep templates for a list of raw data objects"""
d = {}
for rd in raw_data:
# We neeed this so PrepTemplate(p) doesn't fail if that raw
# doesn't exist but raw data has the row: #554
prep_templates = sorted(rd.prep_templates)
d[rd.id] = [PrepTemplate(p) for p in prep_templates
if PrepTemplate.exists(p)]
callback(d)
def remove_add_study_template(self, raw_data, study_id, fp_rsp):
"""Replace prep templates, raw data, and sample template with a new one
"""
for rd in raw_data():
rd = RawData(rd)
for pt in rd.prep_templates:
if PrepTemplate.exists(pt):
PrepTemplate.delete(pt)
if SampleTemplate.exists(study_id):
SampleTemplate.delete(study_id)
SampleTemplate.create(load_template_to_dataframe(fp_rsp),
Study(study_id))
remove(fp_rsp)
def remove_add_study_template(self, raw_data, study_id, fp_rsp):
"""Replace prep templates, raw data, and sample template with a new one
"""
for rd in raw_data():
rd = RawData(rd)
for pt in rd.prep_templates:
if PrepTemplate.exists(pt):
PrepTemplate.delete(pt)
if SampleTemplate.exists(study_id):
SampleTemplate.delete(study_id)
SampleTemplate.create(load_template_to_dataframe(fp_rsp),
Study(study_id))
remove(fp_rsp)
def render(self, study_id, preprocessed_data):
user = 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"
# 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"
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)
def remove_add_study_template(self, raw_data, study_id, fp_rsp, data_type, is_mapping_file):
"""Replace prep templates, raw data, and sample template with a new one
"""
if is_mapping_file and data_type == "":
raise ValueError("Please, choose a data type if uploading a QIIME " "mapping file")
for rd in raw_data():
rd = RawData(rd)
for pt in rd.prep_templates:
if PrepTemplate.exists(pt):
PrepTemplate.delete(pt)
if SampleTemplate.exists(study_id):
SampleTemplate.delete(study_id)
if is_mapping_file:
create_templates_from_qiime_mapping_file(fp_rsp, Study(study_id), int(data_type))
else:
SampleTemplate.create(load_template_to_dataframe(fp_rsp), Study(study_id))
remove(fp_rsp)
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 test_exists_false(self):
"""Exists returns false when the PrepTemplate does not exists"""
self.assertFalse(PrepTemplate.exists(self.new_raw_data))
def test_exists_true(self):
"""Exists returns true when the PrepTemplate already exists"""
self.assertTrue(PrepTemplate.exists(self.test_raw_data))
def test_exists_false(self):
"""Exists returns false when the PrepTemplate does not exists"""
self.assertFalse(PrepTemplate.exists(self.new_raw_data))
def test_exists_true(self):
"""Exists returns true when the PrepTemplate already exists"""
self.assertTrue(PrepTemplate.exists(self.test_raw_data))
def render(self, study, raw_data, full_access):
user = self.current_user
study_status = study.status
user_level = user.level
raw_data_id = raw_data.id
files = [f for _, f in get_files_from_uploads_folders(str(study.id))]
# Get the available prep template data types
data_types = sorted(viewitems(get_data_types()), key=itemgetter(1))
# 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']
# Get all the information about the prep templates
available_prep_templates = []
for p in sorted(raw_data.prep_templates):
if PrepTemplate.exists(p):
pt = PrepTemplate(p)
# if the prep template doesn't belong to this study, skip
if (study.id == pt.study_id and
(full_access or pt.status == 'public')):
available_prep_templates.append(pt)
# getting filepath_types
if raw_data.filetype == 'SFF':
fts = ['sff']
elif raw_data.filetype == 'FASTA':
fts = ['fasta', 'qual']
elif raw_data.filetype == 'FASTQ':
fts = ['barcodes', 'forward seqs', 'reverse seqs']
else:
fts = [k.split('_', 1)[1].replace('_', ' ')
for k in get_filepath_types() if k.startswith('raw_')]
# The raw data can be edited (e.i. adding prep templates and files)
# only if the study is sandboxed or the current user is an admin
is_editable = study_status == 'sandbox' or user_level == 'admin'
# Get the files linked with the raw_data
raw_data_files = raw_data.get_filepaths()
# Get the status of the data linking
raw_data_link_status = raw_data.link_filepaths_status
# By default don't show the unlink button
show_unlink_btn = False
# By default disable the the link file button
disable_link_btn = True
# Define the message for the link status
if raw_data_link_status == 'linking':
link_msg = "Linking files..."
elif raw_data_link_status == 'unlinking':
link_msg = "Unlinking files..."
else:
# The link button is only disable if raw data link status is
# linking or unlinking, so we can enable it here
disable_link_btn = False
# The unlink button is only shown if the study is editable, the raw
# data linking status is not in linking or unlinking, and there are
# files attached to the raw data. At this point, we are sure that
# the raw data linking status is not in linking or unlinking so we
# still need to check if it is editable or there are files attached
show_unlink_btn = is_editable and raw_data_files
if raw_data_link_status.startswith('failed'):
link_msg = "Error (un)linking files: %s" % raw_data_link_status
else:
link_msg = ""
# Get the raw_data filetype
raw_data_filetype = raw_data.filetype
return self.render_string(
"study_description_templates/raw_data_editor_tab.html",
study_id=study.id,
study_status=study_status,
user_level=user_level,
raw_data_id=raw_data_id,
files=files,
data_types=data_types,
ena_terms=ena_terms,
user_defined_terms=user_defined_terms,
available_prep_templates=available_prep_templates,
filepath_types=fts,
is_editable=is_editable,
show_unlink_btn=show_unlink_btn,
link_msg=link_msg,
raw_data_files=raw_data_files,
raw_data_filetype=raw_data_filetype,
disable_link_btn=disable_link_btn)
def render(self, study, raw_data):
user = self.current_user
study_status = study.status
user_level = user.level
raw_data_id = raw_data.id
files = [f for _, f in get_files_from_uploads_folders(str(study.id))]
# Get the available prep template data types
data_types = sorted(viewitems(get_data_types()), key=itemgetter(1))
# 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']
# Get all the information about the prep templates
available_prep_templates = []
for p in sorted(raw_data.prep_templates):
if PrepTemplate.exists(p):
pt = PrepTemplate(p)
# if the prep template doesn't belong to this study, skip
if study.id == pt.study_id:
available_prep_templates.append(pt)
# getting filepath_types
if raw_data.filetype == 'SFF':
fts = ['sff']
elif raw_data.filetype == 'FASTA':
fts = ['fasta', 'qual']
elif raw_data.filetype == 'FASTQ':
fts = ['barcodes', 'forward seqs', 'reverse seqs']
else:
fts = [
k.split('_', 1)[1].replace('_', ' ')
for k in get_filepath_types() if k.startswith('raw_')
]
# The raw data can be edited (e.i. adding prep templates and files)
# only if the study is sandboxed or the current user is an admin
is_editable = study_status == 'sandbox' or user_level == 'admin'
# Get the files linked with the raw_data
raw_data_files = raw_data.get_filepaths()
# Get the status of the data linking
raw_data_link_status = raw_data.link_filepaths_status
# By default don't show the unlink button
show_unlink_btn = False
# By default disable the the link file button
disable_link_btn = True
# Define the message for the link status
if raw_data_link_status == 'linking':
link_msg = "Linking files..."
elif raw_data_link_status == 'unlinking':
link_msg = "Unlinking files..."
else:
# The link button is only disable if raw data link status is
# linking or unlinking, so we can enable it here
disable_link_btn = False
# The unlink button is only shown if the study is editable, the raw
# data linking status is not in linking or unlinking, and there are
# files attached to the raw data. At this point, we are sure that
# the raw data linking status is not in linking or unlinking so we
# still need to check if it is editable or there are files attached
show_unlink_btn = is_editable and raw_data_files
if raw_data_link_status.startswith('failed'):
link_msg = "Error (un)linking files: %s" % raw_data_link_status
else:
link_msg = ""
# Get the raw_data filetype
raw_data_filetype = raw_data.filetype
return self.render_string(
"study_description_templates/raw_data_editor_tab.html",
study_id=study.id,
study_status=study_status,
user_level=user_level,
raw_data_id=raw_data_id,
files=files,
data_types=data_types,
ena_terms=ena_terms,
user_defined_terms=user_defined_terms,
available_prep_templates=available_prep_templates,
filepath_types=fts,
is_editable=is_editable,
show_unlink_btn=show_unlink_btn,
link_msg=link_msg,
raw_data_files=raw_data_files,
raw_data_filetype=raw_data_filetype,
disable_link_btn=disable_link_btn)