def parse_json_file(file):
# returns a tuple: (species,reactions,compartments)
# species: { 'id' : Species(...) }
# reactions: { 'id' : Reaction(...) }
# compartments { 'id' : ('name','outside') }
model = util.parse_json_file(file)
compartments = {}
for compartment in model['compartments']:
compartments[compartment['id']] = (compartment['name'],
compartment['outside'])
species = {}
for sp in model['species']:
species[sp['id']] = Species(sp['id'],
name=sp['name'],
compartment=sp['compartment'])
reactions = {}
for reaction in model['reactions']:
reactants = [copy.deepcopy(species[s]) for s in reaction['reactants']]
products = [copy.deepcopy(species[s]) for s in reaction['products']]
reactions[reaction['id']] = Reaction(reaction['id'],
reactants=reactants,
products=products,
reversible=reaction['reversible'],
subsystem=reaction['subsystem'])
return species, reactions, compartments
def buildPopulationList(population_list):
states = SateList()
for i in population_list:
tokens = i.split("=")
s = Species(tokens[0])
states.updateSpeciesPopulation(s, int(tokens[1]))
return states
def addSpecies2(session, species_input):
genus_id = addGenus(session, species_input["genus"])
print("creating new Species:" + species_input)
species = Species()
species.scientific_name = species_input["scientific_name"]
species.common_name = species_input["common_name"]
species.genus = genus_id
session.add(species)
session.commit()
def addSpecimen(session, specimen_input):
try: # Lets check if we can retreive the species matching the specimen record.
species = session.query(Species).filter(
Species.scientific_name == specimen_input["species"]
["scientific_name"]).one()
except:
species = Species()
species.scientific_name = specimen_input["species"]["scientific_name"]
session.add(species)
specimen = Specimen()
specimen.name = specimen_input["name"]
specimen.birth_date_time = specimen_input["birth_date_time"]
specimen.species = species
session.add(specimen)
session.commit()
def add_species():
session = dbconnect()
request_dict = request.get_json()
try:
genus_instance = session.query(Genus).filter(
Genus.scientific_name == request_dict["genus"]
["scientific_name"]).one()
except:
return "Genus does not exist, please add it", 400
species = Species()
species.scientific_name = request_dict["scientific_name"]
species.common_name = request_dict["common_name"]
species.genus_id = genus_instance.id
session.add(species)
session.commit()
return "ok"
def load_species():
"""Load species from u.species into database."""
print "Species"
Species.query.delete()
for row in open('seed_data/u.species'):
row = row.rstrip()
species_id, name = row.split('|')
species = Species(species_id=species_id, name=name)
db.session.add(species)
db.session.commit()
def addSpecies(session, species_input):
genus = Genus()
try:
genus = session.query(Genus).filter(
Genus.scientific_name == species_input["genus"]
["scientific_name"]).one()
except:
genus = Genus()
genus.scientific_name = species_input["genus"]["scientific_name"]
session.add(genus)
species = Species()
species.scientific_name = species_input["scientific_name"]
species.common_name = species_input["common_name"]
species.genus = genus
session.add(species)
session.commit()
def load_birds():
"""Load bird common names with corresponding species codes into database"""
for i, row in enumerate(open('seed_data/species.csv')):
data = row.rstrip().split(",")
common_name, species_code = data
bird = Species(common_name=common_name,
species_code=species_code)
db.session.add(bird)
# For testing, just to see it was happening
if i % 100 == 0:
print i
db.session.commit()
def _pSpecies(cls, delayedInits=None):
xml = xmlutils.parseAndValidateXML('species.xml')
sl = xml.xpath('/species-list/species')
assert len(sl) > 0
def resolveTrait(ref_xml, trait_type):
key = ref_xml.get('ref')
assert key
trait = trait_type.db.get(key)
assert trait, key
assert trait.name, key
# print(trait.name)
return trait
for xml in sl:
name = xml.get('name')
s = Species(parent=g.getApp(), identifier=Id(name))
def resolveList(modelType, xp):
l = [resolveTrait(x, modelType) for x in xml.xpath(xp)]
# for ll in l:
# print(ll.value)
return QQmlListProperty(modelType, s, l)
s.name = name
s.cost = int(xml.get('cost'))
s.baseLE = int(xml.xpath('./point-modifiers/LE-base/@value')[0])
s.baseSK = int(xml.xpath('./point-modifiers/SK-base/@value')[0])
s.baseZ = int(xml.xpath('./point-modifiers/Z-base/@value')[0])
s.baseGS = int(xml.xpath('./point-modifiers/GS-base/@value')[0])
s.unusualPerkList = resolveList(Perk, './unusual-perks/*')
s.unusualQuirkList = [] # resolveList(Quirk, './unusual-quirks/*')
s.perkList = resolveList(Perk, './usual-perks/*')
s.quirkList = [] # resolveList(Quirk, './usual-quirks/*')
#TODO
s.eyeColorList = xml.xpath('./eye_colors/eye_color/@name')
s.hairColorList = xml.xpath('./hair-colors/hair-color/@name')
s.weightLimits = xml.xpath('./weight/range/@*')
s.heightLimits = xml.xpath('./height/range/@*')
s.talentBoniList = xml.xpath('./talent-bonus/*')
s.cultureList = xml.xpath('./cultures/*')
# todo starting ages
s.assertFrozenAttrs()
yield s
def add_species():
session = dbconnect()
request_dict = request.get_json()
try:
genus_instance = session.query(Genus).filter(Genus.id == request_dict["genus"]["id"]).one()
except:
return "Genus does not exist, please add it", 400
try:
species = Species()
species.scientific_name = request_dict["scientific_name"]
species.common_name = request_dict["common_name"]
species.genus_id = genus_instance.id
session.add(species)
session.commit()
return jsonify(species.id)
except exc.IntegrityError:
session.rollback()
return "already exists", 400
def load_species(species_filename):
"""Load species from seed_data/species into database."""
# Delete all rows in table, so if we need to run this a second time,
# we won't be trying to add duplicate users
Species.query.delete()
#Read species file and insert data
for row in open(species_filename):
row = row.rstrip()
species_id, species = row.split("|")
the_species = Species(species=species)
# We need to add to the session or it won't ever be stored
db.session.add(the_species)
# Once we're done, we should commit our work
db.session.commit()
#finished the function
print("Species inserted")
def parse_species(sp):
return Species(sp.get('id'),
name=sp.get('name'),
compartment=sp.get('compartment'))