def migrate_meta():
from app.models import User, Role, Permission, \
IUCNStatus, ESAStatus, OrganismType, GrowthFormRaunkiaer, ReproductiveRepetition, \
DicotMonoc, AngioGymno, SpandExGrowthType, SourceType, Database, Purpose, MissingData, ContentEmail, Ecoregion, Continent, InvasiveStatusStudy, InvasiveStatusElsewhere, StageTypeClass, \
TransitionType, MatrixComposition, StartSeason, StudiedSex, Captivity, Species, Taxonomy, Trait, \
Publication, Study, AuthorContact, AdditionalSource, Population, Stage, StageType, Treatment, \
MatrixStage, MatrixValue, Matrix, Interval, Fixed, Small, CensusTiming, PurposeEndangered, PurposeWeed, Institute
print "Migrating Meta Tables..."
try:
Role.insert_roles()
Species.migrate()
Taxonomy.migrate()
Trait.migrate()
Publication.migrate()
AuthorContact.migrate()
Population.migrate()
StageType.migrate()
MatrixValue.migrate()
Matrix.migrate()
Fixed.migrate()
Study.migrate()
User.migrate()
Version.migrate()
Institute.migrate()
except:
"Error migrating metadata"
finally:
"Done + good"
return
def study_init(row):
study = Study()
num = Study.query.filter_by(name=row['Nom']).count()
if num > 0:
Study.query.delete()
study.name = row['Nom']
study.description = row['Description']
return study
def add():
form = StudyForm()
if form.validate_on_submit():
study = Study(name=form.name.data, description=form.description.data)
db.session.add(study)
db.session.commit()
flash(_('Nouvelle etude ajouté avec succèss!'))
return redirect(url_for('study.detail', id=study.id))
return render_template('study/form.html', form=form)
def add_fake_data(number_users):
"""
Adds fake data to the database.
"""
study = Study()
study.name = 'test_study'
study.patients = 10
study.variables = 10
db.session.add(study)
db.session.commit()
variables = [Variable() for i in range(10)]
for i, v in enumerate(variables):
v.code = 'variable' + str(i)
v.path = '\\\\folder1\\folder2\\variable' + str(i)
v.type = 'NUMERIC'
v.study_id = study.id
db.session.add(v)
db.session.commit()
def study():
form = StudyForm()
if form.validate_on_submit():
study = Study(id_study=form.id_study.data, date_study=form.date_study.data, result_study=form.result_study.data)
#save the model to the database
db.session.add(study)
db.session.commit()
flash('Congratulations, you are now a registered study!')
return redirect(url_for('index'))
return render_template('study.html', title='validate', form=form)
def create_study(
client,
name="Test Study",
description="",
image="",
data_values=0,
number_of_columns=4,
number_of_rows=4,
start_date=date.today(),
end_date=date.today() + timedelta(days=3),
mail_sent=False,
creator=None,
user_group=None,
card_set_x=None,
card_set_y=None,
data_value_labels=None,
):
with client.application.test_request_context():
if not creator:
creator = create_admin(client)
if not user_group:
user_group = create_user_group(client, creator=creator)
if not card_set_x:
card_set_x = create_card_set(client, creator=creator)
if not card_set_y:
card_set_y = create_card_set(client, creator=creator)
if not data_value_labels:
data_value_labels = [
create_data_value_label(client, creator=creator, label="You get the benefit (e.g. Personalised Service)"),
create_data_value_label(client, creator=creator, label="Data Consumer gets the benefit (e.g. Supply Chain gets the benefit)")
]
study = Study(
name=name,
description=description,
image=image,
data_values=data_values,
number_of_columns=number_of_columns,
number_of_rows=number_of_rows,
start_date=start_date,
end_date=end_date,
mail_sent=mail_sent,
creator=creator,
user_group=user_group,
card_set_x=card_set_x,
card_set_y=card_set_y,
data_value_labels=data_value_labels,
)
db.session.add(study)
db.session.commit()
return study
def submit_new(data):
species = Species.query.filter_by(species_accepted=data["species_accepted"]).first()
if species == None:
species = Species(species_accepted=data["species_accepted"])
species.gbif_taxon_key = data["species_gbif_taxon_key"]
species.species_author = data["species_author"]
species.species_accepted = data["species_accepted"]
species.species_esa_status = ESAStatus.query.filter_by(status_code=data["species_esa_status_id"]).first()
species.species_common = data["species_common"]
species.species_iucn_status = IUCNStatus.query.filter_by(status_code=data["species_iucn_status_id"]).first()
db.session.add(species)
db.session.commit()
''' Species Version '''
species_version = Version()
species_version.version_number = 0
species_version.species = species
db.session.add(species_version)
db.session.commit()
species_version.version_of_id = species_version.id
species_version.checked = True
species_version.checked_count = 1
species_version.statuses = Status.query.filter_by(status_name="Green").first()
species_version.user = User.query.filter_by(username="******").first()
species_version.database = Database.query.filter_by(database_name="COMPADRE 4").first()
db.session.add(species_version)
db.session.commit()
''' Publication '''
if data["publication_DOI_ISBN"] == None:
publication = Publication.query.filter_by(authors=data["publication_authors"]).filter_by(year=data["publication_year"]).filter_by(name=data["publication_journal_name"]).first()
else:
publication = Publication.query.filter_by(DOI_ISBN=data["publication_DOI_ISBN"]).first()
if publication == None:
publication = Publication()
publication.authors = data["publication_authors"]
publication.year = data["publication_year"]
publication.DOI_ISBN = data["publication_DOI_ISBN"]
publication.additional_source_string = data["publication_additional_source_string"]
publication.name = data["publication_journal_name"]
db.session.add(publication)
db.session.commit()
''' Publication Version '''
publication_version = Version()
publication_version.version_number = 0
publication_version.publication = publication
db.session.add(publication_version)
db.session.commit()
publication_version.version_of_id = publication_version.id
publication_version.checked = True
publication_version.checked_count = 1
publication_version.statuses = Status.query.filter_by(status_name="Green").first()
publication_version.user = User.query.filter_by(username="******").first()
publication_version.database = Database.query.filter_by(database_name="COMPADRE 4").first()
db.session.add(publication_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 = Trait()
trait.species_id = species.id
trait.organism_type = organism_type
trait.dicot_monoc = dicot_monoc
trait.angio_gymno = angio_gymno
trait.spand_ex_growth_type = spand_ex_growth_type
trait.growth_form_raunkiaer = growth_form_raunkiaer
db.session.add(trait)
db.session.commit()
''' Trait Version '''
trait_version = Version()
trait_version.version_number = 0
trait_version.trait = trait
db.session.add(trait_version)
db.session.commit()
trait_version.version_of_id = trait_version.id
trait_version.checked = True
trait_version.checked_count = 1
trait_version.statuses = Status.query.filter_by(status_name="Green").first()
trait_version.user = User.query.filter_by(username="******").first()
trait_version.database = Database.query.filter_by(database_name="COMPADRE 4").first()
db.session.add(trait_version)
db.session.commit()
''' Study '''
# What if all none? Will they be grouped together?
purpose_endangered = PurposeEndangered.query.filter_by(purpose_name=data["study_purpose_endangered_id"]).first()
purpose_weed = PurposeWeed.query.filter_by(purpose_name="study_purpose_weed_id").first()
study = Study.query.filter_by(publication_id=publication.id, study_start=data["study_start"], study_end=data["study_end"]).first()
if study == None:
study = Study()
study.study_duration = data["study_duration"]
study.study_start = data["study_start"]
study.study_end = data["study_end"]
study.publication_id = publication.id
study.number_populations = data["study_number_populations"]
db.session.add(study)
db.session.commit()
''' Study Version '''
study_version = Version()
study_version.version_number = 0
study_version.study = study
db.session.add(study_version)
db.session.commit()
study_version.version_of_id = study_version.id
study_version.checked = True
study_version.checked_count = 1
study_version.statuses = Status.query.filter_by(status_name="Green").first()
study_version.user = User.query.filter_by(username="******").first()
study_version.database = Database.query.filter_by(database_name="COMPADRE 4").first()
db.session.add(study_version)
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()
pop = Population.query.filter_by(name=data["population_name"], species_id=species.id, publication_id=publication.id).first()
if pop == None:
pop = Population()
pop.species_author = data["species_author"]
pop.name = data["population_name"]
pop.species_id = species.id
pop.publication_id = publication.id
pop.study_id = study.id
pop.longitude = data["population_longitude"]
pop.latitude = data["population_latitude"]
pop.altitude = data["population_altitude"]
pop.pop_size = data["population_pop_size"]
pop.country = data["population_country"]
pop.invasive_status_study = invasive_status_study
pop.invasive_status_elsewhere = invasive_status_elsewhere
pop.ecoregion = ecoregion
pop.continent = continent
db.session.add(pop)
db.session.commit()
''' Population Version '''
population_version = Version()
population_version.version_number = 0
population_version.population = pop
db.session.add(population_version)
db.session.commit()
population_version.version_of_id = population_version.id
population_version.checked = True
population_version.checked_count = 1
population_version.statuses = Status.query.filter_by(status_name="Green").first()
population_version.user = User.query.filter_by(username="******").first()
population_version.database = Database.query.filter_by(database_name="COMPADRE 4").first()
db.session.add(population_version)
db.session.commit()
''' Taxonomy '''
tax = Taxonomy.query.filter_by(species_id=species.id).first()
if tax == None:
tax = Taxonomy()
tax.species_author = species.species_author
tax.species_accepted = species.species_accepted
tax.authority = None
tax.tpl_version = None
tax.infraspecies_accepted = None
tax.species_epithet_accepted = None
tax.genus_accepted = data["taxonomy_genus_accepted"]
tax.genus = data["taxonomy_genus"]
tax.family = data["taxonomy_family"]
tax.tax_order = data["taxonomy_order"]
tax.tax_class = data["taxonomy_class"]
tax.phylum = data["taxonomy_phylum"]
tax.kingdom = data["taxonomy_kingdom"]
tax.species = species
tax.publication = publication
tax.col_check_date = data["taxonomy_col_check_date"]
tax.col_check_ok = data["taxonomy_col_check_ok"]
db.session.add(tax)
db.session.commit()
''' Taxonomy Version '''
taxonomy_version = Version()
taxonomy_version.version_number = 0
taxonomy_version.taxonomy = tax
db.session.add(taxonomy_version)
db.session.commit()
taxonomy_version.version_of_id = taxonomy_version.id
taxonomy_version.checked = True
taxonomy_version.checked_count = 1
taxonomy_version.statuses = Status.query.filter_by(status_name="Green").first()
taxonomy_version.user = User.query.filter_by(username="******").first()
taxonomy_version.database = Database.query.filter_by(database_name="COMPADRE 4").first()
db.session.add(taxonomy_version)
db.session.commit()
''' Matrix '''
matrix = Matrix()
treatment = Treatment.query.filter_by(treatment_name=data["matrix_treatment_id"]).first()
if treatment == None:
treatment = Treatment(treatment_name=data["matrix_treatment_id"])
matrix.treatment = treatment
matrix.matrix_split = data["matrix_split"]
composition = MatrixComposition.query.filter_by(comp_name=data["matrix_composition_id"]).first()
matrix.matrix_composition = composition
matrix.survival_issue = data["matrix_survival_issue"]
matrix.periodicity = data["matrix_periodicity"]
matrix.matrix_criteria_size = data["matrix_criteria_size"]
matrix.matrix_criteria_ontogeny = coerce_boolean(data["matrix_criteria_ontogeny"])
matrix.matrix_criteria_age = coerce_boolean(data["matrix_criteria_age"])
matrix.matrix_start_month = data["matrix_start_month"]
matrix.matrix_end_month = data["matrix_end_month"]
matrix.matrix_start_year = data["matrix_start_year"]
matrix.matrix_end_year = data["matrix_end_year"]
matrix.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()
end_season = EndSeason.query.filter_by(season_id=data["matrix_end_season_id"]).first()
if start_season != None:
matrix.start_season = start_season
if end_season != None:
matrix.end_season = end_season
matrix.matrix_fec = coerce_boolean(data["matrix_fec"])
matrix.matrix_a_string = data["matrix_a_string"]
matrix.matrix_f_string = data["matrix_f_string"]
matrix.matrix_u_string = data["matrix_u_string"]
matrix.matrix_c_string = data["matrix_c_string"]
matrix.non_independence = data["matrix_non_independence"]
matrix.dimension = data["matrix_dimension"]
matrix.non_independence_author = data["matrix_non_independence_author"]
matrix.matrix_complete = data["matrix_complete"]
matrix.vectors_includes_na = data["matrix_vectors_includes_na"]
matrix.class_number = data["matrix_class_number"]
matrix.observations = data["matrix_observations"]
captivities = Captivity.query.filter_by(cap_code=data["matrix_captivity_id"]).first()
matrix.captivities = captivities
matrix.class_author = data["matrix_class_author"]
matrix.matrix_difficulty = data["matrix_difficulty"]
matrix.independent = data["matrix_independent"]
matrix.seasonal = data["matrix_seasonal"]
matrix.uid = generate_uid(species, publication, pop, matrix)
matrix.population = pop
matrix.study = study
db.session.add(matrix)
db.session.commit()
''' matrix Version '''
matrix_version = Version()
matrix_version.version_number = 0
matrix_version.matrix = matrix
db.session.add(matrix_version)
db.session.commit()
matrix_version.version_of_id = matrix_version.id
matrix_version.checked = True
matrix_version.checked_count = 1
matrix_version.statuses = Status.query.filter_by(status_name="Green").first()
matrix_version.user = User.query.filter_by(username="******").first()
matrix_version.database = Database.query.filter_by(database_name="COMPADRE 4").first()
db.session.add(matrix_version)
db.session.commit()
''' Fixed '''
fixed = Fixed.query.filter_by(matrix=matrix).first()
if fixed == None:
fixed = Fixed()
fixed.matrix = matrix
fixed.census_timings = CensusTiming.query.filter_by(census_name=data["fixed_census_timing_id"]).first()
fixed.seed_stage_error = data["fixed_seed_stage_error"]
fixed.smalls = Small.query.filter_by(small_name=data["fixed_small_id"]).first()
db.session.add(fixed)
db.session.commit()
''' fixed Version '''
fixed_version = Version()
fixed_version.version_number = 0
fixed_version.fixed = fixed
db.session.add(fixed_version)
db.session.commit()
fixed_version.version_of_id = fixed_version.id
fixed_version.checked = True
fixed_version.checked_count = 1
fixed_version.statuses = Status.query.filter_by(status_name="Green").first()
fixed_version.user = User.query.filter_by(username="******").first()
fixed_version.database = Database.query.filter_by(database_name="COMPADRE 4").first()
db.session.add(fixed_version)
db.session.commit()
