def test_treatment_table_entry_treatment_relationship(self):
entry1 = TreatmentTableEntry()
entry2 = TreatmentTableEntry()
treatment1 = Treatment(name='Treatment 1')
treatment2 = Treatment(name='Treatment 2')
# before connecting
self.assertEqual(len(treatment1.treatment_table_entries.all()), 0)
self.assertEqual(len(treatment2.treatment_table_entries.all()), 0)
# after connecting
entry1.treatment = treatment1
entry2.treatment = treatment1
self.assertEqual(len(treatment1.treatment_table_entries.all()), 2)
self.assertEqual(treatment1, entry1.treatment)
self.assertEqual(treatment1, entry2.treatment)
self.assertTrue(entry1 in treatment1.treatment_table_entries.all())
self.assertTrue(entry2 in treatment1.treatment_table_entries.all())
self.assertEqual(len(treatment2.treatment_table_entries.all()), 0)
self.assertNotEqual(treatment2, entry1.treatment)
self.assertNotEqual(treatment2, entry2.treatment)
self.assertFalse(entry1 in treatment2.treatment_table_entries.all())
self.assertFalse(entry2 in treatment2.treatment_table_entries.all())
def setUp(self):
self.app = create_app('testing')
self.app_context = self.app.app_context()
self.app_context.push()
db.create_all()
self.client = self.app.test_client(use_cookies=True)
hospital = Hospital(name='Hospital')
user = User(first_name='userone',
last_name='userone',
username='******',
email='*****@*****.**',
password='******')
user.hospital = hospital
patient = Patient('Patient', '100', '*****@*****.**')
user.patients.append(patient)
treatment = Treatment(name='Treatment 1')
treatment.hospital = hospital
table1 = TreatmentTable(patient=patient, name='Table 1')
entry1 = TreatmentTableEntry(amount='Entry1Amount',
note='Entry1Note',
treatment=treatment,
treatment_table=table1)
db.session.add_all(
[hospital, user, patient, treatment, table1, entry1])
db.session.commit()
def test_treatments_list(self):
# create model instances
hospital1 = Hospital(name='hospital1')
hospital2 = Hospital(name='hospital2')
user1 = User(first_name='one',
last_name='one',
username='******',
email='*****@*****.**',
password='******')
user2 = User(first_name='two',
last_name='two',
username='******',
email='*****@*****.**',
password='******')
treatment1 = Treatment(name='treatment1')
treatment2 = Treatment(name='treatment2')
hospital1.treatments.append(treatment1)
hospital1.treatments.append(treatment2)
user1.hospital = hospital1
user2.hospital = hospital2
db.session.add_all(
[hospital1, hospital2, user1, user2, treatment1, treatment2])
db.session.commit()
# test for user1
with self.client:
self.client.post(url_for('auth.login'),
data={
'email': '*****@*****.**',
'password': '******'
})
response = self.client.get(url_for('treatments.list'))
data = response.get_data(as_text=True)
self.assertTrue('treatment1' in data)
self.assertTrue('treatment2' in data)
# test for user2
with self.client:
self.client.post(url_for('auth.login'),
data={
'email': '*****@*****.**',
'password': '******'
})
response = self.client.get(url_for('treatments.list'))
data = response.get_data(as_text=True)
self.assertFalse('treatment1' in data)
self.assertFalse('treatment2' in data)
def add():
form = TreatmentAddForm()
if form.validate_on_submit():
hospital = current_user.hospital
# create new treatment
treatment = Treatment(name=form.name.data)
treatment.hospital = hospital
db.session.add(treatment)
db.session.commit()
flash('Treatment Successfully Added')
return redirect(url_for('treatments.list'))
return render_template('treatments/add.html', form=form)
def test_treatments_delete(self):
hospital1 = Hospital(name='hospital1')
user = User(first_name='one',
last_name='one',
username='******',
email='*****@*****.**',
password='******')
user.hospital = hospital1
treatment = Treatment(name='treatment')
treatment.hospital = hospital1
treatment2 = Treatment(name='not part of hospital1')
db.session.add_all([user, hospital1, treatment, treatment2])
db.session.commit()
with self.client:
self.client.post(url_for('auth.login'),
data={
'email': '*****@*****.**',
'password': '******'
})
# treatment id does not exist
response = self.client.get(url_for('treatments.delete', id=100))
self.assertEqual(response.status_code, 404)
# user not validated
response = self.client.get(url_for('treatments.delete', id=2))
self.assertEqual(response.status_code, 403)
# successful deletion
self.assertEqual(len(current_user.hospital.treatments.all()), 1)
response = self.client.get(url_for('treatments.delete', id=1),
follow_redirects=True)
data = response.get_data(as_text=True)
self.assertEqual(response.status_code, 200)
self.assertTrue('Treatment Successfully Deleted' in data)
self.assertEqual(len(current_user.hospital.treatments.all()), 0)
def test_treatment_hospital_relationship(self):
hospital1 = Hospital('hospital1')
hospital2 = Hospital('hospital2')
treatment1 = Treatment('treatment1')
treatment2 = Treatment('treatment2')
# before connecting
self.assertEqual(len(hospital1.treatments.all()), 0)
self.assertEqual(len(hospital2.treatments.all()), 0)
# after connecting
treatment1.hospital = hospital1
treatment2.hospital = hospital1
self.assertEqual(len(hospital1.treatments.all()), 2)
self.assertEqual(hospital1, treatment1.hospital)
self.assertEqual(hospital1, treatment2.hospital)
self.assertTrue(treatment1 in hospital1.treatments.all())
self.assertTrue(treatment2 in hospital1.treatments.all())
self.assertEqual(len(hospital2.treatments.all()), 0)
self.assertNotEqual(hospital2, treatment1.hospital)
self.assertNotEqual(hospital2, treatment2.hospital)
self.assertFalse(treatment1 in hospital2.treatments.all())
self.assertFalse(treatment2 in hospital2.treatments.all())
def test_appointments_relationship(self):
start = datetime.utcnow()
end = datetime.utcnow() + timedelta(days=1)
appointment1 = Appointment(title='title1',
description='description1',
date_start=start,
date_end=end)
appointment2 = Appointment(title='title2',
description='description2',
date_start=start,
date_end=end)
patient = Patient(first_name='John',
last_name='Elliot',
email="*****@*****.**")
user = User(first_name='John',
last_name='Elliot',
username='******',
email="*****@*****.**",
password='******')
treatment = Treatment(name='Tylenol')
# before connecting
self.assertEqual(len(patient.appointments.all()), 0)
self.assertEqual(len(user.appointments.all()), 0)
self.assertEqual(len(treatment.appointments.all()), 0)
# after connecting appointment1
appointment1.patient = patient
appointment1.user = user
appointment1.treatment = treatment
db.session.add_all(
[patient, user, treatment, appointment1, appointment2])
db.session.commit()
self.assertEqual(len(patient.appointments.all()), 1)
self.assertTrue(appointment1 in patient.appointments.all())
self.assertEqual(appointment1.patient_id, patient.id)
self.assertFalse(appointment2 in patient.appointments.all())
self.assertNotEqual(appointment2.patient_id, patient.id)
self.assertEqual(len(user.appointments.all()), 1)
self.assertTrue(appointment1 in user.appointments.all())
self.assertEqual(appointment1.user_id, user.id)
self.assertFalse(appointment2 in user.appointments.all())
self.assertNotEqual(appointment2.user_id, user.id)
self.assertEqual(len(treatment.appointments.all()), 1)
self.assertTrue(appointment1 in treatment.appointments.all())
self.assertEqual(appointment1.treatment_id, treatment.id)
self.assertFalse(appointment2 in treatment.appointments.all())
self.assertNotEqual(appointment2.treatment_id, treatment.id)
def test_attributes_assignment(self):
date = datetime.utcnow()
amount = "1 mg Dose"
note = "Additional Note"
treatment = Treatment(name='Treatment 1')
patient = Patient(first_name='John',
last_name='Doe',
email='*****@*****.**')
table = TreatmentTable(name='Table 1', patient=patient)
entry = TreatmentTableEntry(timestamp=date,
amount=amount,
note=note,
treatment=treatment,
treatment_table=table)
self.assertEqual(entry.timestamp, date)
self.assertEqual(entry.amount, '1 mg Dose')
self.assertEqual(entry.note, "Additional Note")
self.assertEqual(entry.treatment, treatment)
self.assertEqual(entry.treatment_table, table)
def submit_new(data):
import datetime
version = {
'checked': True,
'checked_count': 1,
'statuses': Status.query.filter_by(status_name="Green").first()
}
if data["population_database_id"] == "XXX" or data[
"population_database_id"] == "X.X.X":
version = {
'checked': False,
'checked_count': 0,
'statuses': Status.query.filter_by(status_name="Pending").first()
}
# When checking for null data later, these need to be excluded, as they will always have a value
ignore_keys = ['version_ok', 'version_latest', 'version_original']
''' DigitizationProtocol '''
# digitization_protocol = DigitizationProtocol.query.filter_by(field_name=data["digitization_protocol"]).first()
# if digitization_protocol == None:
# ac_dict = {'protocol_id' : protocol.id,
# 'field_name' : data['field_name'],
# 'name_in_csv' : data["name_in_csv"],
# 'database_model' : data["database_model"],
# 'field_description' : data["field_description"],
# 'field_short_description' : data["field_short_description"]
# }
# ac_cleaned = data_clean(ac_dict)
# digitization_protocol = Protocol(**ac_cleaned["kwargs"])
# db.session.add(digitization_protocol)
# db.session.commit()
''' Publication '''
publications_protocol = PublicationsProtocol.query.filter_by(
protocol_number=data["publications_protocol_id"]).first()
if data["publication_DOI_ISBN"] == None:
publication = Publication.query.filter_by(
authors=data["publication_authors"]
).filter_by(year=data["publication_year"]).filter_by(
journal_name=data["publication_journal_name"]).filter_by(
additional_source_string=data[
"publication_additional_source_string"]).filter_by(
study_notes=data["publication_study_notes"]).first()
else:
publication = Publication.query.filter_by(
DOI_ISBN=data["publication_DOI_ISBN"]).first()
if publication == None:
purposes = {
"Comparative Demography":
data["publication_purpose_comparative_demography"],
"Spatial Demography":
data["publication_purpose_spatial_demography"],
"Abiotic Impacts":
data["publication_purpose_abiotic"],
"PVA":
data["publication_purpose_pva"],
"Species Dynamics Description":
data["publication_purpose_species_dynamics_description"],
"Interspecific Interactions":
data["publication_purpose_interspecific_interactions"],
"Management Evaluation":
data["publication_purpose_management_evaluation"],
"Methodological Advancement":
data["publication_purpose_methodological_advancement"]
}
queryset = [
Purpose.query.filter(Purpose.purpose_name == key).first()
for key, val in purposes.items() if val == '1'
]
if data['publication_missing_data'] != 'NDY' and data[
'publication_missing_data']:
missing_data_unicode = data['publication_missing_data'].replace(
" ", "").split(';')
missing_data = [
MissingData.query.filter_by(missing_code=key).first()
for key in missing_data_unicode
if MissingData.query.filter_by(missing_code=key).first()
]
else:
missing_data = 'NDY'
pub_dict = {
'authors':
data["publication_authors"],
'year':
data["publication_year"],
'publications_protocol':
publications_protocol,
'DOI_ISBN':
data["publication_DOI_ISBN"],
'additional_source_string':
data["publication_additional_source_string"],
'journal_name':
data["publication_journal_name"],
'date_digitised':
datetime.datetime.strptime(data['publication_date_digitization'],
"%d/%m/%Y").strftime("%Y-%m-%d")
if data['publication_date_digitization'] else None,
'purposes':
queryset,
'study_notes':
data["publication_study_notes"]
}
pub_cleaned = data_clean(pub_dict)
# if not all(value == None for key, value in pub_cleaned["kwargs"].items() if key not in ignore_keys) and study_present:
publication = Publication(**pub_cleaned["kwargs"])
db.session.add(publication)
db.session.commit()
publication.missing_data = missing_data if type(
missing_data) == list else []
db.session.add(publication)
db.session.commit()
''' Publication Version '''
#version = version_data(pub_cleaned)
publication_version = Version(**version)
publication_version.publication = publication
publication.colour = gen_hex_code()
possible_user = User.query.filter_by(
name=data["publication_student"]).first()
na_user = User.query.filter_by(name="N/A").first()
if possible_user == None:
possible_user = na_user
publication_version.entered_by_id = possible_user.id if possible_user else None,
publication_version.checked_by_id = na_user.id if na_user else None,
db.session.add(publication_version)
db.session.commit()
publication_version.original_version_id = publication_version.id
db.session.add(publication_version)
db.session.commit()
''' Author contact '''
author_contacts = AuthorContact.query.filter_by(
corresponding_author=data["publication_corresponding_author"]
).filter_by(
corresponding_author_email=data["publication_corresponding_email"]
).first()
if author_contacts == None:
ac_dict = {
'publication_id':
publication.id,
'date_contacted':
datetime.datetime.strptime(data['date_author_contacted'],
"%d/%m/%Y").strftime("%Y-%m-%d")
if data['date_author_contacted'] else None,
'date_contacted_again':
datetime.datetime.strptime(data['date_author_contacted_again'],
"%d/%m/%Y").strftime("%Y-%m-%d")
if data['date_author_contacted_again'] else None,
'extra_content_email':
data["correspondence_email_content"],
'author_reply':
data["correspondence_author_reply"],
'corresponding_author':
data["publication_corresponding_author"],
'corresponding_author_email':
data["publication_corresponding_email"],
'correspondence_email_content':
data["correspondence_email_content"],
'extra_content_email':
data["extra_content_email"],
'contacting_user_id':
possible_user.id if possible_user else None
}
ac_cleaned = data_clean(ac_dict)
author_contact = AuthorContact(**ac_cleaned["kwargs"])
db.session.add(author_contact)
db.session.commit()
''' Author Contact Version '''
#version = version_data(ac_cleaned)
author_contact_version = Version(**version)
author_contact_version.author_contact = author_contact
db.session.add(author_contact_version)
db.session.commit()
author_contact_version.original_version_id = author_contact_version.id
db.session.add(author_contact_version)
db.session.commit()
''' Species '''
species = Species.query.filter_by(
species_accepted=data["species_accepted"]).first()
iucn = IUCNStatus.query.filter_by(
status_code=data["species_iucn_status_id"]).first()
if species == None:
species_dict = {
'gbif_taxon_key': data["species_gbif_taxon_key"],
'species_iucn_taxonid': data["species_iucn_taxonid"],
'species_accepted': data["species_accepted"],
'species_common': data["species_common"],
'iucn_status_id': iucn.id if iucn else None,
'image_path': data["image_path"],
'image_path2': data["image_path2"]
}
species_cleaned = data_clean(species_dict)
species = Species(**species_cleaned["kwargs"])
db.session.add(species)
db.session.commit()
''' Species Version '''
#version = version_data(species_cleaned)
species_version = Version(**version)
species_version.species = species
db.session.add(species_version)
db.session.commit()
species_version.original_version_id = species_version.id
db.session.add(species_version)
db.session.commit()
''' Trait '''
spand_ex_growth_type = SpandExGrowthType.query.filter_by(
type_name=data["trait_spand_ex_growth_type_id"]).first()
dicot_monoc = DicotMonoc.query.filter_by(
dicot_monoc_name=data["trait_dicot_monoc_id"]).first()
growth_form_raunkiaer = GrowthFormRaunkiaer.query.filter_by(
form_name=data["trait_growth_form_raunkiaer_id"]).first()
organism_type = OrganismType.query.filter_by(
type_name=data["trait_organism_type_id"]).first()
angio_gymno = AngioGymno.query.filter_by(
angio_gymno_name=data["trait_angio_gymno_id"]).first()
trait = Trait.query.filter_by(species_id=species.id).first()
if trait == None:
trait_dict = {
'species_id':
species.id,
'organism_type':
organism_type,
'dicot_monoc':
dicot_monoc,
'angio_gymno':
angio_gymno,
'species_seedbank':
coerce_boolean(data["species_seedbank"]),
'species_gisd_status':
coerce_boolean(data["species_gisd_status"]),
'species_clonality':
coerce_boolean(data["species_clonality"]),
'spand_ex_growth_type_id':
spand_ex_growth_type.id if spand_ex_growth_type else None,
'growth_form_raunkiaer_id':
growth_form_raunkiaer.id if growth_form_raunkiaer else None
}
trait_cleaned = data_clean(trait_dict)
trait = Trait(**trait_cleaned["kwargs"])
db.session.add(trait)
db.session.commit()
''' Trait Version '''
#version = version_data(trait_cleaned)
trait_version = Version(**version)
trait_version.trait = trait
db.session.add(trait_version)
db.session.commit()
trait_version.original_version_id = trait_version.id
db.session.add(trait_version)
db.session.commit()
''' Taxonomy '''
tax = Taxonomy.query.filter_by(species_id=species.id).first()
if tax == None:
tax_dict = {
'authority':
None,
'tpl_version':
None,
'infraspecies_accepted':
None,
'species_epithet_accepted':
None,
'genus_accepted':
data["taxonomy_genus_accepted"],
'genus':
data["taxonomy_genus"],
'family':
data["taxonomy_family"],
'tax_order':
data["taxonomy_order"],
'tax_class':
data["taxonomy_class"],
'phylum':
data["taxonomy_phylum"],
'kingdom':
data["taxonomy_kingdom"],
'col_check_date':
datetime.datetime.strptime(data["taxonomy_col_check_date"],
"%d/%m/%Y").strftime("%Y-%m-%d")
if data['taxonomy_col_check_date'] else None,
'col_check_ok':
coerce_boolean(data["taxonomy_col_check_ok"])
}
tax_cleaned = data_clean(tax_dict)
# if not all(value == None for key, value in tax_cleaned["kwargs"].items() if key not in ignore_keys):
tax = Taxonomy(**tax_cleaned["kwargs"])
db.session.add(tax)
db.session.commit()
tax.species = species
db.session.add(tax)
db.session.commit()
''' Taxonomy Version '''
#version = version_data(tax_cleaned)
taxonomy_version = Version(**version)
taxonomy_version.version_number = 1
taxonomy_version.taxonomy = tax
db.session.add(taxonomy_version)
db.session.commit()
taxonomy_version.original_version_id = taxonomy_version.id
db.session.add(taxonomy_version)
db.session.commit()
''' Study '''
# What if all none? Will they be grouped together?
# study = Study.query.filter_by(publication_id=publication.id, study_start=data["study_start"], study_end=data["study_end"]).first()
# if study == None:
# purpose_endangered = PurposeEndangered.query.filter_by(purpose_name=data["study_purpose_endangered_id"]).first() if data["study_purpose_endangered_id"] else data["study_purpose_endangered_id"]
#
# purpose_weed = PurposeWeed.query.filter_by(purpose_name="study_purpose_weed_id").first() if data["study_purpose_weed_id"] else data["study_purpose_weed_id"]
# database_source = Institute.query.filter_by(institution_name=data["study_database_source"]).first()# if data["study_purpose_weed_id"] else data["study_purpose_endangered_id"]
#
# study_dict = {'study_duration' : data["study_duration"],
# 'study_start' : data["study_start"],
# 'study_end' : data["study_end"],
# 'number_populations' : data["study_number_populations"],
# 'purpose_endangered_id' : purpose_endangered.id if purpose_endangered else None,
# 'purpose_weed_id' : purpose_weed.id if purpose_weed else None,
# 'database_source' : database_source}
#
# study_cleaned = data_clean(study_dict)
#
# # if not all(value == None for key, value in study_cleaned["kwargs"].items() if key not in ignore_keys) and population_present:
# study = Study(**study_cleaned["kwargs"])
# db.session.add(study)
# db.session.commit()
#
# study.publication_id = publication.id
# study.species_id = species.id
# db.session.add(study)
# db.session.commit()
#
#
# ''' Study Version '''
# version = version_data(study_cleaned)
# study_version = Version(**version)
# study_version.version_number = 1
# study_version.study = study
# db.session.add(study_version)
# db.session.commit()
# study_version.original_version_id = study_version.id
# db.session.add(study_version)
# db.session.commit()
''' Protocol '''
# digitization_protocol = DigitizationProtocol.query.filter_by(field_name=data["digitization_protocol_id"]).first()
# commonterm = CommonTerm.query.filter_by(common_value_name=data["commonterm_id"]).first()
# protocol = Protocol.query.filter_by(protocol_id=protocol.id).first()
# if protocol == None:
# protocol_dict = {'protocol_id' : protocol.id,
# 'digitization_protocol_id' : digitization_protocol.id if digitization_protocol else None,
# 'commonterm_id' : commonterm.id if commonterm else None}
# protocol_cleaned = data_clean(protocol_dict)
# protocol = Protocol(**protocol_cleaned["kwargs"])
# db.session.add(protocol)
# db.session.commit()
''' Population '''
''' '''
invasive_status_study = InvasiveStatusStudy.query.filter_by(
status_name=data["population_invasive_status_study_id"]).first()
invasive_status_elsewhere = InvasiveStatusStudy.query.filter_by(
status_name=data["population_invasive_status_elsewhere_id"]).first()
ecoregion = Ecoregion.query.filter_by(
ecoregion_code=data["population_ecoregion_id"]).first()
continent = Continent.query.filter_by(
continent_name=data["population_continent_id"]).first()
###Danny trying add database meta-table in correct location
database = Database.query.filter_by(
database_master_version=data["population_database_id"]).first()
purpose_endangered = PurposeEndangered.query.filter_by(
purpose_name=data["study_purpose_endangered_id"]).first(
) if data["study_purpose_endangered_id"] else data[
"study_purpose_endangered_id"]
purpose_weed = PurposeWeed.query.filter_by(
purpose_name="study_purpose_weed_id").first(
) if data["study_purpose_weed_id"] else data["study_purpose_weed_id"]
database_source = Institute.query.filter_by(
institution_name=data["study_database_source_id"]).first()
pop = Population.query.filter_by(population_name=data["population_name"],
publication_id=publication.id,
species_id=species.id).first()
if pop == None:
pop_dict = {
'population_name':
data["population_name"],
'latitude':
data["population_latitude"],
'lat_ns':
data["lat_ns"],
'lat_deg':
data["lat_deg"],
'lat_min':
data["lat_min"],
'lat_sec':
data["lat_sec"],
'longitude':
data["population_longitude"],
'lon_ew':
data["lon_ew"],
'lon_deg':
data["lon_deg"],
'lon_min':
data["lon_min"],
'lon_sec':
data["lon_sec"],
'altitude':
data["population_altitude"],
#'pop_size' : data["population_pop_size"],
'country':
data["population_country"],
'invasive_status_study_id':
invasive_status_study.id if invasive_status_study else None,
'invasive_status_elsewhere_id':
invasive_status_elsewhere.id
if invasive_status_elsewhere else None,
'ecoregion':
ecoregion,
'continent':
continent,
'database':
database,
'within_site_replication':
data['population_within_site_replication'],
'study_duration':
data["study_duration"],
'study_start':
data["study_start"],
'study_end':
data["study_end"],
'number_populations':
data["study_number_populations"],
'purpose_endangered_id':
purpose_endangered.id if purpose_endangered else None,
'purpose_weed_id':
purpose_weed.id if purpose_weed else None,
'database_source':
database_source
}
pop_cleaned = data_clean(pop_dict)
# if not all(value == None for key, value in pop_cleaned["kwargs"].items() if key not in ignore_keys) and matrix_present:
pop = Population(**pop_cleaned["kwargs"])
db.session.add(pop)
db.session.commit()
pop.species_author = data["species_author"]
pop.publication_id = publication.id
pop.species_id = species.id
db.session.add(pop)
db.session.commit()
''' Population Version '''
#version = version_data(pop_cleaned)
population_version = Version(**version)
population_version.version_number = 1
population_version.population = pop
db.session.add(population_version)
db.session.commit()
population_version.original_version_id = population_version.id
db.session.add(population_version)
db.session.commit()
''' Matrix '''
treatment_string = data["matrix_treatment_id"]
if treatment_string == 'NDY':
treatment = 'NDY'
elif treatment_string == None:
treatment = None
else:
treatment = Treatment.query.filter_by(
treatment_name=data["matrix_treatment_id"]
).first() if Treatment.query.filter_by(
treatment_name=data["matrix_treatment_id"]).first() else Treatment(
treatment_name=data["matrix_treatment_id"])
db.session.add(treatment)
db.session.commit()
matrix_dict = {
'treatment':
treatment,
'matrix_split':
coerce_boolean(data["matrix_split"]),
'matrix_composition':
MatrixComposition.query.filter_by(
comp_name=data["matrix_composition_id"]).first(),
'matrix_criteria_size':
data["matrix_criteria_size"],
'matrix_criteria_ontogeny':
coerce_boolean(data["matrix_criteria_ontogeny"]),
'matrix_criteria_age':
coerce_boolean(data["matrix_criteria_age"]),
'matrix_start_month':
data["matrix_start_month"],
'matrix_end_month':
data["matrix_end_month"],
'matrix_start_year':
data["matrix_start_year"],
'matrix_end_year':
data["matrix_end_year"],
'studied_sex':
StudiedSex.query.filter_by(
sex_code=data["matrix_studied_sex_id"]).first(),
'start_season':
StartSeason.query.filter_by(
season_id=data["matrix_start_season_id"]).first()
if data["matrix_start_season_id"] else None,
'end_season':
EndSeason.query.filter_by(
season_id=data["matrix_end_season_id"]).first()
if data["matrix_end_season_id"] else None,
'matrix_fec':
coerce_boolean(data["matrix_fec"]),
'matrix_a_string':
data["matrix_a_string"],
'matrix_f_string':
data["matrix_f_string"],
'matrix_u_string':
data["matrix_u_string"],
'matrix_c_string':
data["matrix_c_string"],
'non_independence':
data["matrix_non_independence"],
'matrix_dimension':
data["matrix_dimension"],
'non_independence_author':
data["matrix_non_independence_author"],
'matrix_complete':
coerce_boolean(data["matrix_complete"]),
'class_number':
data["matrix_class_number"],
'observations':
data["matrix_observations"],
'captivities':
Captivity.query.filter_by(
cap_code=data["matrix_captivity_id"]).first(),
'class_author':
data["matrix_class_author"],
'class_organized':
data["matrix_class_organized"],
'matrix_difficulty':
data["matrix_difficulty"],
'seasonal':
coerce_boolean(data["matrix_seasonal"]),
'survival_issue':
calc_surv_issue(data["matrix_u_string"]),
'periodicity':
data["matrix_periodicity"],
'matrix_irreducible':
is_matrix_irreducible(data["matrix_a_string"]),
'matrix_primitive':
is_matrix_primitive(data["matrix_a_string"]),
'matrix_ergodic':
is_matrix_ergodic(data["matrix_a_string"]),
'matrix_lambda':
calc_lambda(data["matrix_a_string"])
}
matrix_cleaned = data_clean(matrix_dict)
# if not all(value == None for key, value in matrix_cleaned["kwargs"].items() if key not in ignore_keys):
matrix = Matrix(**matrix_cleaned["kwargs"])
db.session.add(matrix)
db.session.commit()
matrix.population_id = pop.id
db.session.add(matrix)
db.session.commit()
''' matrix Version '''
#version = version_data(matrix_cleaned)
matrix_version = Version(**version)
matrix_version.version_number = 1
matrix_version.matrix = matrix
db.session.add(matrix_version)
db.session.commit()
matrix_version.original_version_id = matrix_version.id
db.session.add(matrix_version)
db.session.commit()
''' Fixed '''
fixed = Fixed.query.filter_by(matrix=matrix).first()
if fixed == None:
fixed_dict = {
'matrix':
matrix,
'census_timings':
CensusTiming.query.filter_by(
census_name=data["fixed_census_timing_id"]).first(),
'seed_stage_error':
coerce_boolean(data["fixed_seed_stage_error"]),
'smalls':
Small.query.filter_by(small_name=data["fixed_small_id"]).first(),
'vector_str':
data["matrix_vectors_includes_na"]
}
fixed_cleaned = data_clean(fixed_dict)
fixed = Fixed(**fixed_cleaned["kwargs"])
db.session.add(fixed)
db.session.commit()
''' fixed Version '''
#version = version_data(fixed_cleaned)
fixed_version = Version(**version)
fixed_version.version_number = 1
fixed_version.fixed = fixed
db.session.add(fixed_version)
db.session.commit()
fixed_version.original_version_id = fixed_version.id
db.session.add(fixed_version)
db.session.commit()
def test_database_cascade(self):
# User and PatientNote
user = User(first_name='one',
last_name='one',
username='******',
email='*****@*****.**',
password='******')
patient_note = PatientNote(title='title', notes='notes')
patient_note.user = user
db.session.add_all([user, patient_note])
db.session.commit()
db.session.delete(user)
db.session.commit()
self.assertEqual(len(PatientNote.query.all()), 0)
# User and Appointment
user = User(first_name='one',
last_name='one',
username='******',
email='*****@*****.**',
password='******')
today = datetime.utcnow()
appointment = Appointment(title='title',
description='description',
date_start=today,
date_end=today)
appointment.user = user
db.session.add_all([user, appointment])
db.session.commit()
db.session.delete(user)
db.session.commit()
self.assertEqual(len(Appointment.query.all()), 0)
# Patient and PatientNote
patient = Patient(first_name='patient1',
last_name='patient1',
email='*****@*****.**')
patient_note = PatientNote(title='title', notes='notes')
patient_note.patient = patient
db.session.add_all([patient, patient_note])
db.session.commit()
db.session.delete(patient)
db.session.commit()
self.assertEqual(len(PatientNote.query.all()), 0)
# Patient and Appointment
patient = Patient(first_name='patient1',
last_name='patient1',
email='*****@*****.**')
appointment = Appointment(title='title',
description='description',
date_start=today,
date_end=today)
appointment.patient = patient
db.session.add_all([patient, appointment])
db.session.commit()
db.session.delete(patient)
db.session.commit()
self.assertEqual(len(Appointment.query.all()), 0)
# Treatment and Appointment
treatment = Treatment(name='treatment1')
appointment = Appointment(title='title',
description='description',
date_start=today,
date_end=today)
appointment.treatment = treatment
db.session.add_all([treatment, appointment])
db.session.commit()
db.session.delete(treatment)
db.session.commit()
self.assertEqual(len(Appointment.query.all()), 0)
# Hospital and User
user = User(first_name='one',
last_name='one',
username='******',
email='*****@*****.**',
password='******')
hospital = Hospital(name='hospital')
user.hospital = hospital
db.session.add_all([hospital, user])
db.session.commit()
db.session.delete(hospital)
db.session.commit()
self.assertEqual(len(User.query.all()), 0)
# Hospital and Treatment
treatment = Treatment(name='treatment1')
hospital = Hospital(name='hospital')
treatment.hospital = hospital
db.session.add_all([hospital, treatment])
db.session.commit()
db.session.delete(hospital)
db.session.commit()
self.assertEqual(len(Treatment.query.all()), 0)
def test_name_assignment(self):
treatment = Treatment(name='medicine')
self.assertEqual(treatment.name, 'medicine')
def test_repr(self):
treatment = Treatment(name='therapy')
self.assertEqual(treatment.__repr__(), 'therapy')
def test_id(self):
treatment = Treatment(name='medicine')
db.session.add(treatment)
db.session.commit()
self.assertEqual(treatment.id, 1)