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Merge branch 'master' of https://github.com/biocore/microsetta-privat…
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…e-api into return_project_ids
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@AmandaBirmingham
AmandaBirmingham committed Oct 27, 2020
2 parents 6533aea + 03410c1 commit c8af43a
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Showing 16 changed files with 709 additions and 57 deletions.
10 changes: 8 additions & 2 deletions README.md
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Expand Up @@ -43,9 +43,15 @@ In the activated conda environment, initialize a test database:

`python microsetta_private_api/LEGACY/build_db.py`

Then we'll initiate a Celery worker:
Then we'll initiate a Celery worker (Example shown is with embedded Celery Beat scheduler):

`celery -A microsetta_private_api.celery_worker.celery worker -B --loglevel=info`

*** OR (Allowing for multiple workers)***

`celery -A microsetta_private_api.celery_worker.celery worker --loglevel=info` (Start 1 worker)
`celery -A microsetta_private_api.celery_worker.celery beat --loglevel=info` (Start the Celery Beat scheduler)

`celery -A microsetta_private_api.celery_worker.celery worker --loglevel=info`

Next, start the microservice using flask's built-in server by running, e.g.,

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4 changes: 2 additions & 2 deletions microsetta_private_api/admin/admin_impl.py
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Expand Up @@ -99,12 +99,12 @@ def validate_admin_access(token_info):
raise Unauthorized()


def get_projects(token_info, is_active=None):
def get_projects(token_info, include_stats, is_active=None):
validate_admin_access(token_info)

with Transaction() as t:
admin_repo = AdminRepo(t)
projects_list = admin_repo.get_projects(is_active)
projects_list = admin_repo.get_projects(include_stats, is_active)
result = [x.to_api() for x in projects_list]
return jsonify(result), 200

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66 changes: 57 additions & 9 deletions microsetta_private_api/admin/tests/test_admin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -527,7 +527,7 @@ def test_get_survey(self):
survey)
self.assertTrue(found)

def _set_up_and_query_projects(self, t, is_active_val):
def _set_up_and_query_projects(self, t, include_stats, is_active_val):
updated_dict = self._FULL_PROJECT_DICT.copy()
updated_dict[p.PROJ_NAME_KEY] = 'test_proj'
input = p.Project.from_dict(updated_dict)
Expand Down Expand Up @@ -570,10 +570,10 @@ def _set_up_and_query_projects(self, t, is_active_val):
with t.cursor() as cur:
cur.execute(set_up_sql)

output = admin_repo.get_projects(is_active_val)
output = admin_repo.get_projects(include_stats, is_active_val)

updated_dict["project_id"] = 8
updated_dict[p.COMPUTED_STATS_KEY] = \
computed_stats = \
{p.NUM_FULLY_RETURNED_KITS_KEY: 1,
p.NUM_KITS_KEY: 5,
p.NUM_KITS_W_PROBLEMS_KEY: 1,
Expand All @@ -587,12 +587,60 @@ def _set_up_and_query_projects(self, t, is_active_val):
p.NUM_SAMPLES_RECEIVED_KEY: 5,
p.NUM_UNIQUE_SOURCES_KEY: 4}

updated_dict[p.COMPUTED_STATS_KEY] = \
computed_stats if include_stats else {}

return updated_dict, output

def test_get_projects_all(self):
def test_get_projects_all_w_stats(self):
with Transaction() as t:
updated_dict, output = self._set_up_and_query_projects(
t, include_stats=True, is_active_val=None)

# Test we have the correct number of total projects
self.assertEqual(len(output), 56)

# For one fully-characterized test project, ensure all the
# output values are what we expect (project 8)
self.assertEqual(updated_dict, output[7].to_api())

def test_get_projects_active_w_stats(self):
with Transaction() as t:
updated_dict, output = self._set_up_and_query_projects(
t, include_stats=True, is_active_val=True)

# Test we have the correct number of active projects
self.assertEqual(len(output), 55)

# For one fully-characterized test project, ensure all the
# output values are what we expect. Project 8 is now 7th in
# list (note zero-based) bc project 2 is inactive, so not returned
self.assertEqual(updated_dict, output[6].to_api())

def test_get_projects_inactive_w_stats(self):
with Transaction() as t:
with t.cursor() as cur:
cur.execute("UPDATE barcodes.project"
" SET is_active = FALSE"
" WHERE project_id = 8;")

updated_dict, output = self._set_up_and_query_projects(
t, include_stats=True, is_active_val=False)

updated_dict["is_active"] = False

# Test we have the correct number of inactive projects
self.assertEqual(len(output), 2)

# For one fully-characterized test project, ensure all the
# output values are what we expect. Project 8 is now inactive,
# and is 2nd in (zero-based) list, after project 2
self.assertEqual(updated_dict, output[1].to_api())

def test_get_projects_all_wo_stats(self):
with Transaction() as t:
updated_dict, output = self._set_up_and_query_projects(
t, is_active_val=None)
t, include_stats=False, is_active_val=None)

# Test we have the correct number of total projects
self.assertEqual(len(output), 56)
Expand All @@ -601,10 +649,10 @@ def test_get_projects_all(self):
# output values are what we expect (project 8)
self.assertEqual(updated_dict, output[7].to_api())

def test_get_projects_active(self):
def test_get_projects_active_wo_stats(self):
with Transaction() as t:
updated_dict, output = self._set_up_and_query_projects(
t, is_active_val=True)
t, include_stats=False, is_active_val=True)

# Test we have the correct number of active projects
self.assertEqual(len(output), 55)
Expand All @@ -614,15 +662,15 @@ def test_get_projects_active(self):
# list (note zero-based) bc project 2 is inactive, so not returned
self.assertEqual(updated_dict, output[6].to_api())

def test_get_projects_inactive(self):
def test_get_projects_inactive_wo_stats(self):
with Transaction() as t:
with t.cursor() as cur:
cur.execute("UPDATE barcodes.project"
" SET is_active = FALSE"
" WHERE project_id = 8;")

updated_dict, output = self._set_up_and_query_projects(
t, is_active_val=False)
t, include_stats=False, is_active_val=False)

updated_dict["is_active"] = False

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174 changes: 168 additions & 6 deletions microsetta_private_api/admin/tests/test_admin_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -282,10 +282,10 @@ def test_update_project(self):
expected_result["project_id"] = proj_id
self.assertEqual(expected_result, stored_result)

def test_get_projects_all(self):
def test_get_projects_all_w_stats(self):
# execute projects get
response = self.client.get(
"/api/admin/projects",
"/api/admin/projects?include_stats=true",
headers=MOCK_HEADERS
)

Expand Down Expand Up @@ -348,10 +348,10 @@ def test_get_projects_all(self):
self.assertEqual(56, len(response_obj))
self.assertEqual(expected_record, response_obj[7])

def test_get_projects_active(self):
def test_get_projects_active_w_stats(self):
# execute projects get
response = self.client.get(
"/api/admin/projects?is_active=true",
"/api/admin/projects?include_stats=true&is_active=true",
headers=MOCK_HEADERS
)

Expand Down Expand Up @@ -414,10 +414,10 @@ def test_get_projects_active(self):
self.assertEqual(55, len(response_obj))
self.assertEqual(expected_record, response_obj[6])

def test_get_projects_inactive(self):
def test_get_projects_inactive_w_stats(self):
# execute projects get
response = self.client.get(
"/api/admin/projects?is_active=false",
"/api/admin/projects?include_stats=true&is_active=false",
headers=MOCK_HEADERS
)

Expand Down Expand Up @@ -480,6 +480,168 @@ def test_get_projects_inactive(self):
self.assertEqual(1, len(response_obj))
self.assertEqual(expected_record, response_obj[0])

def test_get_projects_all_wo_stats(self):
# execute projects get
response = self.client.get(
"/api/admin/projects?include_stats=false",
headers=MOCK_HEADERS
)

# check response code
self.assertEqual(200, response.status_code)

# load the response body
response_obj = json.loads(response.data)

expected_record = {'additional_contact_name': None,
'alias': None,
'bank_samples': False,
'branding_associated_instructions': None,
'branding_status': None,
'collection': None,
'computed_stats': {},
'contact_email': None,
'contact_name': None,
'coordination': None,
'deadlines': None,
'disposition_comments': None,
'do_16s': None,
'do_mass_spec': None,
'do_metatranscriptomics': None,
'do_other': None,
'do_rt_qpcr': None,
'do_serology': None,
'do_shallow_shotgun': None,
'do_shotgun': None,
'is_blood': None,
'is_fecal': None,
'is_microsetta': False,
'is_other': None,
'is_saliva': None,
'is_skin': None,
'mass_spec_comments': None,
'mass_spec_contact_email': None,
'mass_spec_contact_name': None,
'num_subjects': None,
'num_timepoints': None,
'plating_start_date': None,
'project_id': 8,
'project_name': 'Project - %u[zGmÅq=g',
'sponsor': None,
'start_date': None,
'subproject_name': None,
'is_active': True}
self.assertEqual(56, len(response_obj))
self.assertEqual(expected_record, response_obj[7])

def test_get_projects_active_wo_stats(self):
# execute projects get
response = self.client.get(
"/api/admin/projects?include_stats=false&is_active=true",
headers=MOCK_HEADERS
)

# check response code
self.assertEqual(200, response.status_code)

# load the response body
response_obj = json.loads(response.data)

expected_record = {'additional_contact_name': None,
'alias': None,
'bank_samples': False,
'branding_associated_instructions': None,
'branding_status': None,
'collection': None,
'computed_stats': {},
'contact_email': None,
'contact_name': None,
'coordination': None,
'deadlines': None,
'disposition_comments': None,
'do_16s': None,
'do_mass_spec': None,
'do_metatranscriptomics': None,
'do_other': None,
'do_rt_qpcr': None,
'do_serology': None,
'do_shallow_shotgun': None,
'do_shotgun': None,
'is_blood': None,
'is_fecal': None,
'is_microsetta': False,
'is_other': None,
'is_saliva': None,
'is_skin': None,
'mass_spec_comments': None,
'mass_spec_contact_email': None,
'mass_spec_contact_name': None,
'num_subjects': None,
'num_timepoints': None,
'plating_start_date': None,
'project_id': 8,
'project_name': 'Project - %u[zGmÅq=g',
'sponsor': None,
'start_date': None,
'subproject_name': None,
'is_active': True}
self.assertEqual(55, len(response_obj))
self.assertEqual(expected_record, response_obj[6])

def test_get_projects_inactive_wo_stats(self):
# execute projects get
response = self.client.get(
"/api/admin/projects?include_stats=false&is_active=false",
headers=MOCK_HEADERS
)

# check response code
self.assertEqual(200, response.status_code)

# load the response body
response_obj = json.loads(response.data)

expected_record = {'additional_contact_name': None,
'alias': None,
'bank_samples': False,
'branding_associated_instructions': None,
'branding_status': None,
'collection': None,
'computed_stats': {},
'contact_email': None,
'contact_name': None,
'coordination': None,
'deadlines': None,
'disposition_comments': None,
'do_16s': None,
'do_mass_spec': None,
'do_metatranscriptomics': None,
'do_other': None,
'do_rt_qpcr': None,
'do_serology': None,
'do_shallow_shotgun': None,
'do_shotgun': None,
'is_active': False,
'is_blood': None,
'is_fecal': None,
'is_microsetta': False,
'is_other': None,
'is_saliva': None,
'is_skin': None,
'mass_spec_comments': None,
'mass_spec_contact_email': None,
'mass_spec_contact_name': None,
'num_subjects': None,
'num_timepoints': None,
'plating_start_date': None,
'project_id': 2,
'project_name': 'Project - /J/xL_|Eãt',
'sponsor': None,
'start_date': None,
'subproject_name': None}
self.assertEqual(1, len(response_obj))
self.assertEqual(expected_record, response_obj[0])

def test_scan_barcode_success(self):
"""Store info on new scan for valid barcode"""

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3 changes: 2 additions & 1 deletion microsetta_private_api/api/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
from ._survey import (
read_survey_template, read_survey_templates, read_answered_survey,
read_answered_surveys, submit_answered_survey,
read_answered_survey_associations,
read_answered_survey_associations, top_food_report,
)
from ._sample import (
read_sample_association, associate_sample, read_sample_associations,
Expand All @@ -39,6 +39,7 @@
'read_answered_survey',
'read_answered_surveys',
'read_answered_survey_associations',
'top_food_report',
'read_sample_association',
'associate_sample',
'read_sample_associations',
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