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improve loading times of studies #3350

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Jan 29, 2024
Merged

improve loading times of studies #3350

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d06bf76
improve loading times of studies
antgonza Jan 26, 2024
9e57e9b
self.status == 'public'
antgonza Jan 26, 2024
c9a5777
prep_info
antgonza Jan 26, 2024
4192334
add extra case for not no_public
antgonza Jan 26, 2024
f58de06
improving study_prep_get_req
antgonza Jan 29, 2024
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34 changes: 27 additions & 7 deletions qiita_db/study.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1175,17 +1175,37 @@ def has_access(self, user, no_public=False):
Whether user has access to study or not
"""
with qdb.sql_connection.TRN:
# if admin or superuser, just return true
# return True if the user is one of the admins
if user.level in {'superuser', 'admin'}:
return True

if no_public:
study_set = user.user_studies | user.shared_studies
else:
study_set = user.user_studies | user.shared_studies | \
self.get_by_status('public')
# if no_public is False then just check if the study is public
# and return True
if not no_public and self.status == 'public':
return True

# let's check if the study belongs to this user or has been
# shared with them
sql = """SELECT EXISTS (
SELECT study_id
FROM qiita.study
JOIN qiita.study_portal USING (study_id)
JOIN qiita.portal_type USING (portal_type_id)
WHERE email = %s AND portal = %s AND study_id = %s
UNION
SELECT study_id
FROM qiita.study_users
JOIN qiita.study_portal USING (study_id)
JOIN qiita.portal_type USING (portal_type_id)
WHERE email = %s AND portal = %s AND study_id = %s
)
"""
qdb.sql_connection.TRN.add(
sql, [user.email, qiita_config.portal, self.id,
user.email, qiita_config.portal, self.id])
result = qdb.sql_connection.TRN.execute_fetchlast()

return self in study_set
return result

def can_edit(self, user):
"""Returns whether the given user can edit the study
Expand Down
94 changes: 57 additions & 37 deletions qiita_pet/handlers/api_proxy/studies.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@
from qiita_core.exceptions import IncompetentQiitaDeveloperError
from qiita_core.util import execute_as_transaction
from qiita_core.qiita_settings import r_client
from qiita_db.artifact import Artifact
from qiita_db.sql_connection import TRN
from qiita_db.user import User
from qiita_db.study import Study
from qiita_db.exceptions import QiitaDBColumnError, QiitaDBLookupError
Expand Down Expand Up @@ -114,8 +116,8 @@ def study_get_req(study_id, user_id):
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_biom_download_button'] = len(
study.artifacts(artifact_type='BIOM')) != 0
study_info['show_raw_download_button'] = any([
True for pt in study.prep_templates() if pt.artifact is not None])

Expand Down Expand Up @@ -201,53 +203,71 @@ def study_prep_get_req(study_id, user_id):
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)
prep_info = {dtype: [] for dtype in study.data_types}
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:
with TRN:
sql = """SELECT prep_template_id, pt.name as name, data_type,
artifact_id,
creation_timestamp, modification_timestamp, visibility,
(SELECT COUNT(sample_id)
FROM qiita.prep_template_sample
WHERE prep_template_id = spt.prep_template_id)
as total_samples,
(SELECT COUNT(sample_id)
FROM qiita.prep_template_sample
WHERE prep_template_id = spt.prep_template_id
AND ebi_experiment_accession != '')
as ebi_experiment
FROM qiita.study_prep_template spt
LEFT JOIN qiita.prep_template pt USING (prep_template_id)
LEFT JOIN qiita.data_type USING (data_type_id)
LEFT JOIN qiita.artifact USING (artifact_id)
LEFT JOIN qiita.visibility USING (visibility_id)
WHERE study_id = %s
GROUP BY prep_template_id, pt.name, data_type, artifact_id,
creation_timestamp, modification_timestamp,
visibility
ORDER BY creation_timestamp"""

TRN.add(sql, [study_id])
for row in TRN.execute_fetchindex():
row = dict(row)
if row['visibility'] != 'public' and not editable:
continue
start_artifact = prep.artifact
# for those preps that have no artifact
if row['visibility'] is None:
row['visibility'] = 'sandbox'

info = {
'name': prep.name,
'id': prep.id,
'status': prep.status,
'total_samples': len(prep),
'creation_timestamp': prep.creation_timestamp,
'modification_timestamp': prep.modification_timestamp
'name': row['name'],
'id': row['prep_template_id'],
'status': row['visibility'],
'total_samples': row['total_samples'],
'creation_timestamp': row['creation_timestamp'],
'modification_timestamp': row['modification_timestamp'],
'start_artifact': None,
'start_artifact_id': None,
'youngest_artifact': None,
'num_artifact_children': 0,
'youngest_artifact_name': None,
'youngest_artifact_type': None,
'ebi_experiment': row['ebi_experiment']
}
if start_artifact is not None:
youngest_artifact = prep.artifact.youngest_artifact
if row['artifact_id'] is not None:
start_artifact = Artifact(row['artifact_id'])
youngest_artifact = start_artifact.youngest_artifact
info['start_artifact'] = start_artifact.artifact_type
info['start_artifact_id'] = start_artifact.id
info['start_artifact_id'] = row['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

prep_info[row['data_type']].append(info)

return {'status': 'success',
'message': '',
Expand Down
5 changes: 2 additions & 3 deletions qiita_pet/handlers/api_proxy/tests/test_studies.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -229,8 +229,7 @@ def test_study_prep_get_req_failed_EBI(self):

# actual test
obs = study_prep_get_req(study.id, user_email)
temp_info = defaultdict(list)
temp_info['16S'] = [
temp_info = {'16S': [
{"status": 'sandbox',
'name': 'Prep information %d' % pt.id,
'start_artifact': None, 'youngest_artifact': None,
Expand All @@ -241,7 +240,7 @@ def test_study_prep_get_req_failed_EBI(self):
'num_artifact_children': 0,
'youngest_artifact_name': None,
'youngest_artifact_type': None,
'total_samples': 3}]
'total_samples': 3}]}

exp = {
'info': temp_info,
Expand Down
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