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Fix 2635 #2639

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Merged
merged 7 commits into from
Aug 16, 2018
Merged

Fix 2635 #2639

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ad76b13
rm QiitaStudySearch
antgonza Aug 14, 2018
19429a2
rm import search
antgonza Aug 14, 2018
f116a1f
fixing error
antgonza Aug 14, 2018
45724e8
fix #2635
antgonza Aug 14, 2018
b887031
returning private status to preps in test_generate_study_list
antgonza Aug 14, 2018
af767a7
upstream dev
antgonza Aug 15, 2018
74a5046
addressing @ElDeveloper comments
antgonza Aug 16, 2018
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24 changes: 20 additions & 4 deletions qiita_db/study.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,7 @@ def all_data_types():
return qdb.sql_connection.TRN.execute_fetchflatten()

@classmethod
def get_by_status(cls, status):
def get_ids_by_status(cls, status):
"""Returns study id for all Studies with given status

Parameters
Expand All @@ -138,7 +138,7 @@ def get_by_status(cls, status):
JOIN qiita.portal_type USING (portal_type_id)
WHERE visibility = %s AND portal = %s"""
qdb.sql_connection.TRN.add(sql, [status, qiita_config.portal])
studies = set(qdb.sql_connection.TRN.execute_fetchflatten())
sids = set(qdb.sql_connection.TRN.execute_fetchflatten())
# If status is sandbox, all the studies that are not present in the
# study_artifact table are also sandbox
if status == 'sandbox':
Expand All @@ -150,10 +150,26 @@ def get_by_status(cls, status):
SELECT study_id
FROM qiita.study_artifact)"""
qdb.sql_connection.TRN.add(sql, [qiita_config.portal])
studies = studies.union(
sids = sids.union(
qdb.sql_connection.TRN.execute_fetchflatten())

return set(cls(sid) for sid in studies)
return sids

@classmethod
def get_by_status(cls, status):
"""Returns study id for all Studies with given status

Parameters
----------
status : str
Status setting to search for

Returns
-------
set of qiita_db.study.Study
All studies in the database that match the given status
"""
return set(cls(sid) for sid in cls.get_ids_by_status(status))

@classmethod
def get_info(cls, study_ids=None, info_cols=None):
Expand Down
167 changes: 130 additions & 37 deletions qiita_db/test/test_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -858,6 +858,11 @@ def test_get_pubmed_ids_from_dois(self):
self.assertEqual(obs, exp)

def test_generate_study_list(self):
USER = qdb.user.User
STUDY = qdb.study.Study
PREP = qdb.metadata_template.prep_template.PrepTemplate
UTIL = qdb.util

# creating a new study to make sure that empty studies are also
# returned
info = {"timeseries_type_id": 1, "metadata_complete": True,
Expand All @@ -868,46 +873,134 @@ def test_generate_study_list(self):
"emp_person_id": qdb.study.StudyPerson(1),
"principal_investigator_id": qdb.study.StudyPerson(1),
"lab_person_id": qdb.study.StudyPerson(1)}
new_study = qdb.study.Study.create(
qdb.user.User('shared@foo.bar'), 'test_study_1', info=info)

exp_info = [
{'status': 'private', 'study_title': (
'Identification of the Microbiomes for Cannabis Soils'),
'metadata_complete': True, 'publication_pid': [
'123456', '7891011'], 'artifact_biom_ids': [4, 5, 6, 7],
'ebi_submission_status': 'submitted', 'study_id': 1,
'ebi_study_accession': 'EBI123456-BB', 'owner': 'Dude',
'shared': [('shared@foo.bar', 'Shared')],
'study_abstract': (
new_study = STUDY.create(
USER('shared@foo.bar'), 'test_study_1', info=info)

sinfo = {
'study_id': 1,
'owner': 'Dude',
'study_alias': 'Cannabis Soils',
'status': 'private',
'study_abstract':
'This is a preliminary study to examine the microbiota '
'associated with the Cannabis plant. Soils samples from '
'the bulk soil, soil associated with the roots, and the '
'rhizosphere were extracted and the DNA sequenced. Roots '
'from three independent plants of different strains were '
'examined. These roots were obtained November 11, 2011 from '
'plants that had been harvested in the summer. Future studies '
'will attempt to analyze the soils and rhizospheres from the '
'same location at different time points in the plant '
'lifecycle.'), 'pi': ('PI_dude@foo.bar', 'PIDude'),
'publication_doi': ['10.100/123456', '10.100/7891011'],
'study_alias': 'Cannabis Soils', 'study_tags': None,
'number_samples_collected': 27},
{'status': 'sandbox', 'study_title': 'test_study_1',
'metadata_complete': True, 'publication_pid': [],
'artifact_biom_ids': None,
'ebi_submission_status': 'not submitted',
'study_id': new_study.id, 'ebi_study_accession': None,
'owner': 'Shared', 'shared': [],
'study_abstract': 'Some abstract goes here',
'pi': ('lab_dude@foo.bar', 'LabDude'), 'publication_doi': [],
'study_alias': 'TST', 'study_tags': None,
'number_samples_collected': 0}]
obs_info = qdb.util.generate_study_list([1, 2, 3, 4])
self.assertEqual(obs_info, exp_info)
'associated with the Cannabis plant. Soils samples '
'from the bulk soil, soil associated with the roots, '
'and the rhizosphere were extracted and the DNA '
'sequenced. Roots from three independent plants of '
'different strains were examined. These roots were '
'obtained November 11, 2011 from plants that had been '
'harvested in the summer. Future studies will attempt '
'to analyze the soils and rhizospheres from the same '
'location at different time points in the plant '
'lifecycle.',
'metadata_complete': True,
'ebi_study_accession': 'EBI123456-BB',
'ebi_submission_status': 'submitted',
'study_title':
'Identification of the Microbiomes for Cannabis Soils',
'number_samples_collected': 27,
'shared': [('shared@foo.bar', 'Shared')],
'publication_doi': ['10.100/123456', '10.100/7891011'],
'publication_pid': ['123456', '7891011'],
'pi': ('PI_dude@foo.bar', 'PIDude'),
'artifact_biom_ids': [4, 5, 6, 7],
'study_tags': None,
}
snew_info = {
'status': 'sandbox', 'study_title': 'test_study_1',
'metadata_complete': True, 'publication_pid': [],
'artifact_biom_ids': None,
'ebi_submission_status': 'not submitted',
'study_id': new_study.id, 'ebi_study_accession': None,
'owner': 'Shared', 'shared': [],
'study_abstract': 'Some abstract goes here',
'pi': ('lab_dude@foo.bar', 'LabDude'), 'publication_doi': [],
'study_alias': 'TST', 'study_tags': None,
'number_samples_collected': 0}
exp1 = [sinfo]
exp2 = [snew_info]
exp_both = [sinfo, snew_info]

# let's make sure that everything is private for stiudy 1
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stiudy -> study

for a in STUDY(1).artifacts():
a.visibility = 'private'

# owner of study
obs = UTIL.generate_study_list(USER('test@foo.bar'), 'user')
self.assertEqual(obs, exp1)
# shared with
obs = UTIL.generate_study_list(USER('shared@foo.bar'), 'user')
self.assertEqual(obs, exp_both)
# admin
obs = UTIL.generate_study_list(USER('admin@foo.bar'), 'user')
self.assertEqual(obs, exp_both)
# no access/hidden
obs = UTIL.generate_study_list(USER('demo@microbio.me'), 'user')
self.assertEqual(obs, [])
# public - none for everyone
obs = UTIL.generate_study_list(USER('test@foo.bar'), 'public')
self.assertEqual(obs, [])
obs = UTIL.generate_study_list(USER('shared@foo.bar'), 'public')
self.assertEqual(obs, [])
obs = UTIL.generate_study_list(USER('admin@foo.bar'), 'public')
self.assertEqual(obs, [])
obs = UTIL.generate_study_list(USER('demo@microbio.me'), 'public')
self.assertEqual(obs, [])

# deleting the old study
def _avoid_duplicated_tests(all_artifacts=False):
# nothing should shange for owner, shared
obs = UTIL.generate_study_list(USER('test@foo.bar'), 'user')
self.assertEqual(obs, exp1)
obs = UTIL.generate_study_list(USER('shared@foo.bar'), 'user')
self.assertEqual(obs, exp_both)
# for admin it should be shown in public and user cause there are
# 2 preps and only one is public
obs = UTIL.generate_study_list(USER('admin@foo.bar'), 'user')
if not all_artifacts:
self.assertEqual(obs, exp_both)
else:
self.assertEqual(obs, exp2)
obs = UTIL.generate_study_list(USER('demo@microbio.me'), 'user')
self.assertEqual(obs, [])
# for the public query, everything should be same for owner, share
# and admin but demo should now see it as public but with limited
# artifacts
obs = UTIL.generate_study_list(USER('test@foo.bar'), 'public')
self.assertEqual(obs, [])
obs = UTIL.generate_study_list(USER('shared@foo.bar'), 'public')
self.assertEqual(obs, [])
obs = UTIL.generate_study_list(USER('admin@foo.bar'), 'public')
if not all_artifacts:
exp1[0]['artifact_biom_ids'] = [7]
self.assertEqual(obs, exp1)
obs = UTIL.generate_study_list(USER('demo@microbio.me'), 'public')
self.assertEqual(obs, exp1)

# returning artifacts
exp1[0]['artifact_biom_ids'] = [4, 5, 6, 7]

# make artifacts of prep 2 public
PREP(2).artifact.visibility = 'public'
exp1[0]['status'] = 'public'
exp_both[0]['status'] = 'public'
_avoid_duplicated_tests()

# make artifacts of prep 1 awaiting_approval
PREP(1).artifact.visibility = 'awaiting_approval'
_avoid_duplicated_tests()

# making all studies public
PREP(1).artifact.visibility = 'public'
_avoid_duplicated_tests(True)

# deleting the new study study and returning artifact status
qdb.study.Study.delete(new_study.id)
PREP(1).artifact.visibility = 'private'
PREP(2).artifact.visibility = 'private'

def test_generate_study_list_errors(self):
with self.assertRaises(ValueError):
qdb.util.generate_study_list(qdb.user.User('test@foo.bar'), 'bad')

def test_generate_study_list_without_artifacts(self):
# creating a new study to make sure that empty studies are also
Expand Down
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