def study_get_req(study_id, user_id):
"""Returns information available for the given study
Parameters
----------
study_id : int
Study id to get prep template info for
user_id : str
User requesting the info
Returns
-------
dict
Data types information in the form
{'status': status,
'message': message,
'info': dict of objects
status can be success, warning, or error depending on result
message has the warnings or errors
info contains study information seperated by data type, in the form
{col_name: value, ...} with value being a string, int, or list of
strings or ints
"""
access_error = check_access(study_id, user_id)
if access_error:
return access_error
# Can only pass ids over API, so need to instantiate object
study = Study(study_id)
study_info = study.info
# Add needed info that is not part of the initial info pull
study_info['publications'] = study.publications
study_info['study_id'] = study.id
study_info['study_title'] = study.title
study_info['shared_with'] = [s.id for s in study.shared_with]
study_info['status'] = study.status
study_info['ebi_study_accession'] = study.ebi_study_accession
study_info['ebi_submission_status'] = study.ebi_submission_status
# Clean up StudyPerson objects to string for display
pi = study_info['principal_investigator']
study_info['principal_investigator'] = {
'name': pi.name,
'email': pi.email,
'affiliation': pi.affiliation}
lab_person = study_info['lab_person']
if lab_person:
study_info['lab_person'] = {
'name': lab_person.name,
'email': lab_person.email,
'affiliation': lab_person.affiliation}
samples = study.sample_template
study_info['num_samples'] = 0 if samples is None else len(list(samples))
study_info['owner'] = study.owner.id
return {'status': 'success',
'message': '',
'study_info': study_info,
'editable': study.can_edit(User(user_id))}
def study_prep_get_req(study_id, user_id):
"""Gives a summary of each prep template attached to the study
Parameters
----------
study_id : int
Study id to get prep template info for
user_id : str
User id requesting the prep templates
Returns
-------
dict of list of dict
prep template information seperated by data type, in the form
{data_type: [{prep 1 info dict}, ....], ...}
"""
access_error = check_access(study_id, user_id)
if access_error:
return access_error
# Can only pass ids over API, so need to instantiate object
study = Study(int(study_id))
prep_info = defaultdict(list)
editable = study.can_edit(User(user_id))
for dtype in study.data_types:
for prep in study.prep_templates(dtype):
if prep.status != 'public' and not editable:
continue
start_artifact = prep.artifact
info = {
'name': 'PREP %d NAME' % prep.id,
'id': prep.id,
'status': prep.status,
}
if start_artifact is not None:
youngest_artifact = prep.artifact.youngest_artifact
info['start_artifact'] = start_artifact.artifact_type
info['start_artifact_id'] = start_artifact.id
info['youngest_artifact'] = '%s - %s' % (
youngest_artifact.name, youngest_artifact.artifact_type)
info['ebi_experiment'] = bool(
[v for _, v in viewitems(prep.ebi_experiment_accessions)
if v is not None])
else:
info['start_artifact'] = None
info['start_artifact_id'] = None
info['youngest_artifact'] = None
info['ebi_experiment'] = False
prep_info[dtype].append(info)
return {'status': 'success',
'message': '',
'info': prep_info}
def study_get_req(study_id, user_id):
"""Returns information available for the given study
Parameters
----------
study_id : int
Study id to get prep template info for
user_id : str
User requesting the info
Returns
-------
dict
Data types information in the form
{'status': status,
'message': message,
'info': dict of objects
status can be success, warning, or error depending on result
message has the warnings or errors
info contains study information seperated by data type, in the form
{col_name: value, ...} with value being a string, int, or list of
strings or ints
"""
access_error = check_access(study_id, user_id)
if access_error:
return access_error
# Can only pass ids over API, so need to instantiate object
study = Study(study_id)
study_info = study.info
# Add needed info that is not part of the initial info pull
study_info['publication_doi'] = []
study_info['publication_pid'] = []
for pub, is_doi in study.publications:
if is_doi:
study_info['publication_doi'].append(pub)
else:
study_info['publication_pid'].append(pub)
study_info['study_id'] = study.id
study_info['study_title'] = study.title
study_info['shared_with'] = [s.id for s in study.shared_with]
study_info['status'] = study.status
study_info['ebi_study_accession'] = study.ebi_study_accession
study_info['ebi_submission_status'] = study.ebi_submission_status
study_info['public_raw_download'] = study.public_raw_download
study_info['notes'] = study.notes
# Clean up StudyPerson objects to string for display
pi = study_info['principal_investigator']
study_info['principal_investigator'] = {
'name': pi.name,
'email': pi.email,
'affiliation': pi.affiliation
}
lab_person = study_info['lab_person']
if lab_person:
study_info['lab_person'] = {
'name': lab_person.name,
'email': lab_person.email,
'affiliation': lab_person.affiliation
}
samples = study.sample_template
study_info['num_samples'] = 0 if samples is None else len(list(samples))
study_info['owner'] = study.owner.id
# Study.has_access no_public=True, will return True only if the user_id is
# the owner of the study or if the study is shared with the user_id; this
# with study.public_raw_download will define has_access_to_raw_data
study_info['has_access_to_raw_data'] = study.has_access(
User(user_id), True) or study.public_raw_download
study_info['show_biom_download_button'] = 'BIOM' in [
a.artifact_type for a in study.artifacts()
]
study_info['show_raw_download_button'] = any(
[True for pt in study.prep_templates() if pt.artifact is not None])
# getting study processing status from redis
processing = False
study_info['level'] = ''
study_info['message'] = ''
job_info = r_client.get(STUDY_KEY_FORMAT % study_id)
if job_info:
job_info = defaultdict(lambda: '', loads(job_info))
job_id = job_info['job_id']
job = ProcessingJob(job_id)
job_status = job.status
processing = job_status not in ('success', 'error')
if processing:
study_info['level'] = 'info'
study_info['message'] = 'This study is currently being processed'
elif job_status == 'error':
study_info['level'] = 'danger'
study_info['message'] = job.log.msg.replace('\n', '</br>')
else:
study_info['level'] = job_info['alert_type']
study_info['message'] = job_info['alert_msg'].replace(
'\n', '</br>')
return {
'status': 'success',
'message': '',
'study_info': study_info,
'editable': study.can_edit(User(user_id))
}
def study_get_req(study_id, user_id):
"""Returns information available for the given study
Parameters
----------
study_id : int
Study id to get prep template info for
user_id : str
User requesting the info
Returns
-------
dict
Data types information in the form
{'status': status,
'message': message,
'info': dict of objects
status can be success, warning, or error depending on result
message has the warnings or errors
info contains study information seperated by data type, in the form
{col_name: value, ...} with value being a string, int, or list of
strings or ints
"""
access_error = check_access(study_id, user_id)
if access_error:
return access_error
# Can only pass ids over API, so need to instantiate object
study = Study(study_id)
study_info = study.info
# Add needed info that is not part of the initial info pull
study_info['publication_doi'] = []
study_info['publication_pid'] = []
for pub, is_doi in study.publications:
if is_doi:
study_info['publication_doi'].append(pub)
else:
study_info['publication_pid'].append(pub)
study_info['study_id'] = study.id
study_info['study_title'] = study.title
study_info['shared_with'] = [s.id for s in study.shared_with]
study_info['status'] = study.status
study_info['ebi_study_accession'] = study.ebi_study_accession
study_info['ebi_submission_status'] = study.ebi_submission_status
# Clean up StudyPerson objects to string for display
pi = study_info['principal_investigator']
study_info['principal_investigator'] = {
'name': pi.name,
'email': pi.email,
'affiliation': pi.affiliation}
lab_person = study_info['lab_person']
if lab_person:
study_info['lab_person'] = {
'name': lab_person.name,
'email': lab_person.email,
'affiliation': lab_person.affiliation}
samples = study.sample_template
study_info['num_samples'] = 0 if samples is None else len(list(samples))
study_info['owner'] = study.owner.id
# Study.has_access no_public=True, will return True only if the user_id is
# the owner of the study or if the study is shared with the user_id
study_info['has_access_to_raw_data'] = study.has_access(
User(user_id), True)
study_info['show_biom_download_button'] = 'BIOM' in [
a.artifact_type for a in study.artifacts()]
study_info['show_raw_download_button'] = any([
True for pt in study.prep_templates() if pt.artifact is not None])
# getting study processing status from redis
processing = False
study_info['level'] = ''
study_info['message'] = ''
job_info = r_client.get(STUDY_KEY_FORMAT % study_id)
if job_info:
job_info = defaultdict(lambda: '', loads(job_info))
job_id = job_info['job_id']
job = ProcessingJob(job_id)
job_status = job.status
processing = job_status not in ('success', 'error')
if processing:
study_info['level'] = 'info'
study_info['message'] = 'This study is currently being processed'
elif job_status == 'error':
study_info['level'] = 'danger'
study_info['message'] = job.log.msg.replace('\n', '</br>')
else:
study_info['level'] = job_info['alert_type']
study_info['message'] = job_info['alert_msg'].replace(
'\n', '</br>')
return {'status': 'success',
'message': '',
'study_info': study_info,
'editable': study.can_edit(User(user_id))}
def study_get_req(study_id, user_id):
"""Returns information available for the given study
Parameters
----------
study_id : int
Study id to get prep template info for
user_id : str
User requesting the info
Returns
-------
dict
Data types information in the form
{'status': status,
'message': message,
'info': dict of objects
status can be success, warning, or error depending on result
message has the warnings or errors
info contains study information seperated by data type, in the form
{col_name: value, ...} with value being a string, int, or list of
strings or ints
"""
access_error = check_access(study_id, user_id)
if access_error:
return access_error
# Can only pass ids over API, so need to instantiate object
study = Study(study_id)
study_info = study.info
# Add needed info that is not part of the initial info pull
study_info['publication_doi'] = []
study_info['publication_pid'] = []
for pub, is_doi in study.publications:
if is_doi:
study_info['publication_doi'].append(pub)
else:
study_info['publication_pid'].append(pub)
study_info['study_id'] = study.id
study_info['study_title'] = study.title
study_info['shared_with'] = [s.id for s in study.shared_with]
study_info['status'] = study.status
study_info['ebi_study_accession'] = study.ebi_study_accession
study_info['ebi_submission_status'] = study.ebi_submission_status
# Clean up StudyPerson objects to string for display
pi = study_info['principal_investigator']
study_info['principal_investigator'] = {
'name': pi.name,
'email': pi.email,
'affiliation': pi.affiliation}
lab_person = study_info['lab_person']
if lab_person:
study_info['lab_person'] = {
'name': lab_person.name,
'email': lab_person.email,
'affiliation': lab_person.affiliation}
samples = study.sample_template
study_info['num_samples'] = 0 if samples is None else len(list(samples))
study_info['owner'] = study.owner.id
# Study.has_access no_public=True, will return True only if the user_id is
# the owner of the study or if the study is shared with the user_id
study_info['has_access_to_raw_data'] = study.has_access(
User(user_id), True)
study_info['show_biom_download_button'] = 'BIOM' in [
a.artifact_type for a in study.artifacts()]
study_info['show_raw_download_button'] = any([
True for pt in study.prep_templates() if pt.artifact is not None])
return {'status': 'success',
'message': '',
'study_info': study_info,
'editable': study.can_edit(User(user_id))}
def study_prep_get_req(study_id, user_id):
"""Gives a summary of each prep template attached to the study
Parameters
----------
study_id : int
Study id to get prep template info for
user_id : str
User id requesting the prep templates
Returns
-------
dict of list of dict
prep template information seperated by data type, in the form
{data_type: [{prep 1 info dict}, ....], ...}
"""
access_error = check_access(study_id, user_id)
if access_error:
return access_error
# Can only pass ids over API, so need to instantiate object
study = Study(int(study_id))
prep_info = defaultdict(list)
editable = study.can_edit(User(user_id))
for dtype in study.data_types:
dtype_infos = list()
for prep in study.prep_templates(dtype):
if prep.status != 'public' and not editable:
continue
start_artifact = prep.artifact
info = {
'name': prep.name,
'id': prep.id,
'status': prep.status,
'total_samples': len(prep),
'creation_timestamp': prep.creation_timestamp,
'modification_timestamp': prep.modification_timestamp
}
if start_artifact is not None:
youngest_artifact = prep.artifact.youngest_artifact
info['start_artifact'] = start_artifact.artifact_type
info['start_artifact_id'] = start_artifact.id
info['num_artifact_children'] = len(start_artifact.children)
info['youngest_artifact_name'] = youngest_artifact.name
info['youngest_artifact_type'] = \
youngest_artifact.artifact_type
info['youngest_artifact'] = '%s - %s' % (
youngest_artifact.name, youngest_artifact.artifact_type)
info['ebi_experiment'] = len([
v for _, v in prep.ebi_experiment_accessions.items()
if v is not None
])
else:
info['start_artifact'] = None
info['start_artifact_id'] = None
info['youngest_artifact'] = None
info['num_artifact_children'] = 0
info['youngest_artifact_name'] = None
info['youngest_artifact_type'] = None
info['ebi_experiment'] = 0
dtype_infos.append(info)
# default sort is in ascending order of creation timestamp
sorted_info = sorted(dtype_infos,
key=lambda k: k['creation_timestamp'],
reverse=False)
prep_info[dtype] = sorted_info
return {'status': 'success', 'message': '', 'info': prep_info}