def family_count(args, family_id):
data = {}
family = Family.query.get_or_404(family_id)
for relation in args['relation']:
_, base = relation.rsplit('/', 1)
data[base] = utils.count_relation(family, relation)
return utils.json_response(data)
def taxon_count(args, id):
data = {}
taxon = Taxon.query.get_or_404(id)
for relation in args['relation']:
_, base = relation.rsplit('/', 1)
data[base] = utils.count_relation(taxon, relation)
return utils.json_response(data)
def genus_count(args, id):
data = {}
genus = Genus.query.get_or_404(id)
for relation in args['relation']:
_, base = relation.rsplit('/', 1)
data[base] = utils.count_relation(genus, relation)
return utils.json_response(data)
def accession_count(args, id):
data = {}
accession = Accession.query.get_or_404(id)
for relation in args['relation']:
_, base = relation.rsplit('/', 1)
data[base] = utils.count_relation(accession, relation)
return utils.json_response(data)
def post_taxon(taxon):
genus = Genus.query.filter_by(id=taxon.genus_id).first()
if not genus:
abort(422, "Invalid genus id")
db.session.add(taxon)
db.session.commit()
return utils.json_response(taxon.jsonify(), 201)
def post_plant(plant):
location_id = request.values.get('location_id', None)
if location_id is not None:
location = Location.query.filter_by(id=location_id).first()
if not location:
abort(422, "Invalid location id")
accession_id = request.values.get('accession_id', None)
if accession_id is not None:
accession = Accession.query.filter_by(id=accession_id).first()
if not accession:
abort(422, "Invalid accession id")
db.session.add(plant)
# change = PlantChange(to_location_id=plant.location_id,
# quantity=plant.quantity, # store original quantity
# person=request.user.fullname if request.user.fullname is not None else request.user.email,
# #reason=request.json['change'].get('reason', None) if 'change' in request.json else None,
# reason=None,
# date=request.json['change'].get('date', None) if 'change' in request.json else None
# )
# change.plant = plant
# request.session.add(change)
db.session.commit()
return utils.json_response(plant.jsonify(), 201)
def post_plant(plant):
location_id = request.values.get('location_id', None)
if location_id is not None:
location = Location.query.filter_by(id=location_id).first()
if not location:
abort(422, "Invalid location id")
accession_id = request.values.get('accession_id', None)
if accession_id is not None:
accession = Accession.query.filter_by(id=accession_id).first()
if not accession:
abort(422, "Invalid accession id")
db.session.add(plant)
# change = PlantChange(to_location_id=plant.location_id,
# quantity=plant.quantity, # store original quantity
# person=request.user.fullname if request.user.fullname is not None else request.user.email,
# #reason=request.json['change'].get('reason', None) if 'change' in request.json else None,
# reason=None,
# date=request.json['change'].get('date', None) if 'change' in request.json else None
# )
# change.plant = plant
# request.session.add(change)
db.session.commit()
return utils.json_response(plant.jsonify(), 201)
def family_count(args, family_id):
data = {}
family = Family.query.get_or_404(family_id)
for relation in args['relation']:
_, base = relation.rsplit('/', 1)
data[base] = utils.count_relation(family, relation)
return utils.json_response(data)
def plant_count(args, id):
data = {}
plant = Plant.query.get_or_404(id)
for relation in args['relation']:
_, base = relation.rsplit('/', 1)
data[base] = utils.count_relation(plant, relation)
return utils.json_response(data)
def genus_count(args, id):
data = {}
genus = Genus.query.get_or_404(id)
for relation in args['relation']:
_, base = relation.rsplit('/', 1)
data[base] = utils.count_relation(genus, relation)
return utils.json_response(data)
def post_taxon(taxon):
genus = Genus.query.filter_by(id=taxon.genus_id).first()
if not genus:
abort(422, "Invalid genus id")
db.session.add(taxon)
db.session.commit()
return utils.json_response(taxon.jsonify(), 201)
def location_count(args, location_id):
data = {}
location = Location.query.get_or_404(location_id)
for relation in args['relation']:
_, base = relation.rsplit('/', 1)
data[base] = utils.count_relation(location, relation)
return utils.json_response(data)
def location_count(args, location_id):
data = {}
location = Location.query.get_or_404(location_id)
for relation in args['relation']:
_, base = relation.rsplit('/', 1)
data[base] = utils.count_relation(location, relation)
return utils.json_response(data)
def post_genus(genus):
# TODO: do an exists query instead of loading the family
family = Family.query.filter_by(id=genus.family_id).first()
if not family:
abort(422, "Invalid family id")
db.session.add(genus)
db.session.commit()
return utils.json_response(genus.jsonify(), 201)
def post_genus(genus):
# TODO: do an exists query instead of loading the family
family = Family.query.filter_by(id=genus.family_id).first()
if not family:
abort(422, "Invalid family id")
db.session.add(genus)
db.session.commit()
return utils.json_response(genus.jsonify(), 201)
def render_json(self, model, status=200):
if isinstance(model, (list, tuple))and len(model) > 0:
data = type(model[0]).jsonify(model, many=True)
elif isinstance(model, db.Model):
data = model.jsonify()
else:
data = model
return utils.json_response(data, status=status)
def index(args, ext=None):
query = args.get("q", None)
results = search(query, db.session) if query is not None else {}
data = {}
if request.prefers_json:
value_factory = lambda k, v: [obj.jsonify() for obj in v]
response_factory = lambda d: utils.json_response(d)
else:
value_factory = lambda k, v: [
{"url": result_resource_map.get(key).format(obj.id), "str": obj.str()} for obj in v
]
response_factory = lambda d: render_template("search/index.html", results=d)
for key, values in results.items():
if len(values) > 0:
data[key] = value_factory(key, values)
return response_factory(data)
def index(args, ext=None):
query = args.get('q', None)
results = search(query, db.session) if query is not None else {}
data = {}
if request.prefers_json:
value_factory = lambda k, v: [obj.jsonify() for obj in v]
response_factory = lambda d: utils.json_response(d)
else:
value_factory = lambda k, v: [{
'url': result_resource_map.get(key).format(obj.id),
'str': obj.str()
} for obj in v]
response_factory = lambda d: render_template('search/index.html', results=d)
for key, values in results.items():
if len(values) > 0:
data[key] = value_factory(key, values)
return response_factory(data)
def patch_plant(plant, id):
location_id = request.values.get('location_id', None)
if location_id is not None:
location = Location.query.filter_by(id=location_id).first()
if not location:
abort(422, "Invalid location id")
accession_id = request.values.get('accession_id', None)
if accession_id is not None:
accession = Accession.query.filter_by(id=accession_id).first()
if not accession:
abort(422, "Invalid accession id")
# create the plant change
# change = PlantChange(plant_id=request.plant.id,
# from_location_id=request.plant.location_id,
# quantity=request.plant.quantity, # store original quantity
# person=request.user.fullname if request.user.fullname is not None else request.user.email,
# # reason=request.json['change'].get('reason', None) if 'change' in request.json else None,
# reason=None,
# date=request.json['change'].get('date', None) if 'change' in request.json else None
# )
# request.session.add(change)
# if change.from_location_id != request.plant.location_id:
# # the change quantity represent the number of plants tranferred to a new location
# change.quantity = request.plant.quantity
# change.to_location_id = request.plant.location_id
# elif request.plant.quantity < change.quantity:
# # the change quantity represents the number of plants removed from a location
# change.quantity = request.plant.quantity - change.quantity
# else:
# # the change quantity represents the number of plants added to a location
# change.quantity = request.plant.quantity - change.quantity
db.session.commit()
return utils.json_response(plant.jsonify())
def patch_plant(plant, id):
location_id = request.values.get('location_id', None)
if location_id is not None:
location = Location.query.filter_by(id=location_id).first()
if not location:
abort(422, "Invalid location id")
accession_id = request.values.get('accession_id', None)
if accession_id is not None:
accession = Accession.query.filter_by(id=accession_id).first()
if not accession:
abort(422, "Invalid accession id")
# create the plant change
# change = PlantChange(plant_id=request.plant.id,
# from_location_id=request.plant.location_id,
# quantity=request.plant.quantity, # store original quantity
# person=request.user.fullname if request.user.fullname is not None else request.user.email,
# # reason=request.json['change'].get('reason', None) if 'change' in request.json else None,
# reason=None,
# date=request.json['change'].get('date', None) if 'change' in request.json else None
# )
# request.session.add(change)
# if change.from_location_id != request.plant.location_id:
# # the change quantity represent the number of plants tranferred to a new location
# change.quantity = request.plant.quantity
# change.to_location_id = request.plant.location_id
# elif request.plant.quantity < change.quantity:
# # the change quantity represents the number of plants removed from a location
# change.quantity = request.plant.quantity - change.quantity
# else:
# # the change quantity represents the number of plants added to a location
# change.quantity = request.plant.quantity - change.quantity
db.session.commit()
return utils.json_response(plant.jsonify())
def patch_accession(accession, id):
# if 'source' in request.json:
# if request.accession.source is None:
# request.accession.source = Source()
# source = request.accession.source # shorthand
# source_json = request.json['source']
# source_data = {col: source_json[col] for col in source_json.keys()
# if col in source_mutable}
# source_data['source_detail_id'] = source_data.pop('id', None)
# # make a copy of the data for only those fields that are columns
# source.set_attributes(source_data)
# # make sure the propagation type is not empty b/c we'll get an error
# # trying to set the propagation details (even if it's an empty dict) if
# # the prop_type hasn't been set
# if 'propagation' in source_json and len(source_json['propagation']) > 0:
# # TODO: validate prop_type
# if source.propagation is None:
# source.propagation = Propagation()
# prop_data = source_json['propagation']
# source.propagation.prop_type = prop_data.pop('prop_type', source.propagation.prop_type)
# prop_mutable = prop_seed_mutable if source.propagation.prop_type == 'Seed' \
# else prop_cutting_mutable
# source.propagation.details = {col: prop_data[col] for col in prop_data.keys()
# if col in prop_mutable}
# if 'collection' in source_json and len(source_json['collection']) > 0:
# # TODO: validate collection datand set mutable properties
# if source.collection is None:
# source.collection = Collection()
# coll_data = {col: value for col, value in source_json['collection'].items()
# if col in coll_mutable}
# source.collection.set_attributes(coll_data)
db.session.commit()
return utils.json_response(accession.jsonify())
def post_accession(accession):
taxon = Taxon.query.filter_by(id=accession.taxon_id).first()
if not taxon:
abort(422, "Invalid taxon id")
# if 'source' in request.json:
# source_json = request.json['source']
# source_data = {col: source_json[col] for col in source_json.keys()
# if col in source_mutable}
# source_data['source_detail_id'] = source_data.pop('id', None)
# # make a copy of the data for only those fields that are columns
# source = Source(**source_data)
# request.session.add(source)
# if 'propagation' in source_json:
# # TODO: validate prop_type
# prop_data = source_json['propagation']
# propagation = Propagation(prop_type=prop_data.pop('prop_type'))
# prop_mutable = prop_seed_mutable if propagation.prop_type == 'Seed' \
# else prop_cutting_mutable
# propagation.details = {col: prop_data[col] for col in prop_data.keys()
# if col in prop_mutable}
# source.propagation = propagation
# collection = Collection()
# if 'collection' in source_json:
# # TODO: validate collection datand set mutable properties
# coll_data = {col: value for col, value in source_json['collection'].items()
# if col in coll_mutable}
# collection = Collection(**coll_data)
# source.collection = collection
db.session.add(accession)
db.session.commit()
return utils.json_response(accession.jsonify(), 201)
def post_location(location):
db.session.add(location)
db.session.commit()
return utils.json_response(location.jsonify(), 201)
def patch_location(location, id):
db.session.commit()
return utils.json_response(location.jsonify())
def get(family, id):
return utils.json_response(family.jsonify())
def index_taxon():
taxon = Taxon.query.all()
data = Taxon.jsonify(taxon, many=True)
return utils.json_response(data)
def index_accession():
accession = Accession.query.all()
data = Accession.jsonify(accession, many=True)
return utils.json_response(data)
def list_geography():
geographies = Geography.query.all()
return utils.json_response(Geography.jsonify(geographies, many=True))
def index_taxon():
taxon = Taxon.query.all()
data = Taxon.jsonify(taxon, many=True)
return utils.json_response(data)
def post_family(family):
db.session.add(family)
db.session.commit()
return utils.json_response(family.jsonify(), 201)
def patch_family(family, id):
db.session.commit()
return utils.json_response(family.jsonify())
def get_family(family, family_id):
return utils.json_response(family.jsonify())
def get_source(source_detail, id):
return utils.json_response(source_detail.jsonify())
def patch_source(source_detail, id):
db.session.commit()
return utils.json_response(source_detail.jsonify())
def patch(family, id):
return utils.json_response(family.jsonify())
def patch_taxon(taxon, taxon_id):
db.session.commit()
return utils.json_response(taxon.jsonify())
def get_geography(geography_id):
geography = Geography.query.get_or_404(geography_id)
return utils.json_response(geography.jsonify())
def get_taxon(taxon, id):
return utils.json_response(taxon.jsonify())
def get_taxon(taxon, id):
return utils.json_response(taxon.jsonify())
def patch_taxon(taxon, taxon_id):
db.session.commit()
return utils.json_response(taxon.jsonify())
def get_accession(accession, id):
return utils.json_response(accession.jsonify())
def index_source():
sources = SourceDetail.query.all()
data = SourceDetail.jsonify(sources, many=True)
return utils.json_response(data)
def index_location():
locations = Location.query.all()
data = Location.jsonify(locations, many=True)
return utils.json_response(data)
def get_location(location, id):
return utils.json_response(location.jsonify())
def index_family():
families = Family.query.all()
data = Family.jsonify(families, many=True)
return utils.json_response(data)
def post_source(source_detail):
db.session.add(source_detail)
db.session.commit()
return utils.json_response(source_detail.jsonify(), 201)
