API first commit

models.py

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+from django.db import models
+from django.contrib.auth.models import User
+
+# these models are elements of the mangal data specification
+
+M_NAME = 400
+D_NAME = 1000
+
+# taxa
+class Taxa(models.Model):
+   name = models.CharField(max_length=M_NAME, unique=True, help_text = "The scientific name of the taxa")
+   owner = models.ForeignKey(User, related_name ="%(app_label)s_%(class)s_owner")
+   vernacular = models.CharField(max_length=M_NAME, help_text = "The vernacular name of the taxa, in English", blank=True, null=True)
+   description = models.CharField(max_length=D_NAME,blank=True,null=True, help_text = "A short description of the taxa")
+   ncbi = models.IntegerField(blank=True,null=True, unique=True, help_text = "The NCBI Taxonomy identifier of the taxa")
+   gbif = models.IntegerField(blank=True,null=True, unique=True, help_text = "The GBIF identifier of the taxa")
+   bold = models.IntegerField(blank=True,null=True, unique=True, help_text = "The BOLD identifier of the taxa")
+   itis = models.IntegerField(blank=True,null=True, unique=True, help_text = "The ITIS identifier of the taxa")
+   eol = models.IntegerField(blank=True,null=True, unique=True, help_text = "The EOL identifier of the taxa")
+   def __unicode__(self):
+       na = self.name
+       if len(self.vernacular) > 0:
+           na += " ("+self.vernacular+")"
+       return na
+
+# population
+class Population(models.Model):
+   taxa = models.ForeignKey(Taxa)
+   name = models.CharField(max_length=M_NAME, help_text = "A name allowing to identify the population")
+   owner = models.ForeignKey(User, related_name="%(app_label)s_%(class)s_owner", help_text = "The identifier of the uploader")
+   description = models.CharField(max_length=D_NAME,blank=True,null=True, help_text = "A short description of the population")
+   def __unicode__(self):
+       return u'%s, of taxa %s' % (self.name, self.taxa)
+
+# trait
+class Trait(models.Model):
+   name = models.CharField(max_length=M_NAME, help_text  = "The name of the measured trait")
+   owner = models.ForeignKey(User, related_name="%(app_label)s_%(class)s_owner", help_text = "The identifier of the uploader")
+   value = models.CharField(help_text = "The value of the trait", max_length=50)
+   units = models.CharField(max_length=50, help_text = "Units in which the trait was measured", blank=True, null=True)
+   description = models.CharField(max_length=D_NAME,blank=True,null=True, help_text = "A longer description of the trait")
+   def __unicode__(self):
+       return u'%s (%.4f %s)' % (self.name, self.value, self.units)
+
+# item
+class Item(models.Model):
+   STAGE_CHOICES = (
+           ('seed', 'Seed'),
+           ('juvenile', 'Juvenile'),
+           ('adult', 'Adult'),
+           ('dead', 'Dead'),
+           ('larva', 'Larva'),
+           ('all', 'All'),
+           )
+   public = models.BooleanField(default=True)
+   owner = models.ForeignKey(User, related_name="%(app_label)s_%(class)s_owner", help_text = "The identifier of the uploader")
+   population = models.ForeignKey(Population)
+   level = models.CharField(max_length=50, choices = (('individual', 'Individual'), ('population', 'Population'),), help_text = "Whether the item is a single individual, or a population")
+   name = models.CharField(max_length=M_NAME, help_text = "A name for the item, useful to identify it later")
+   stage = models.CharField(max_length=50, choices = STAGE_CHOICES, default = 'all', help_text = "The stage of the item, to be selected in the list of allowed values")
+   traits = models.ManyToManyField(Trait,blank=True,null=True)
+   size = models.FloatField(blank=True,null=True, help_text = "If the item is a population, the number of individuals or biomass")
+   units = models.CharField(max_length=50,blank=True,null=True, help_text = "Units in which the population size is measured")
+   description = models.CharField(max_length=D_NAME,blank=True,null=True, help_text = "A short description of the population")
+   def __unicode__(self):
+       return u'%s (%s) - belongs to %s' % (self.name, self.level, self.population)
+
+# interaction
+class Interaction(models.Model):
+   TYPE_CHOICES = (
+           ('predation', 'Predation'),
+           ('ectoparasitism', 'Ectoparasitism'),
+           ('endoparasitism', 'Endoparasitism'),
+           ('intra-cellular parasitism', 'Intra-Cellular parasitism'),
+           ('parasitoidism', 'Parasitoidism'),
+           ('mycoheterotrophy', 'Mycoheterotrophy'),
+           ('antixenosis', 'Anitxenosis'),
+           ('teletoxy', 'Teletoxy'),
+           ('amensalism', 'Amensalism'),
+           ('antibiosis', 'Antibiosis'),
+           ('allelopathy', 'Allelopathy'),
+           ('competition', 'Competition'),
+           ('facilitation', 'Facilitation'),
+           ('refuge creation', 'Refuge creation'),
+           ('inquilinism', 'Inquilinism'),
+           ('phoresis', 'Phoresis'),
+           ('epibiosis', 'Epibiosis'),
+           ('pollination', 'Pollination'),
+           ('mutualistic symbiosis', 'Mutualistic symbiosis'),
+           ('zoochory', 'Zoochory'),
+           ('mutual protection', 'Mutual protection'),
+        )
+   OBSERVATION_CHOICES = (
+           ('unspecified', 'Unspecified'),
+           ('observation', 'Observation'),
+           ('litterature', 'Litterature'),
+           ('absence', 'Confirmed absence'),
+           ('inferred', 'Inferred'),
+           )
+   link_type = models.CharField(max_length=50, choices = TYPE_CHOICES, help_text  ="The type of interaction")
+   obs_type = models.CharField(max_length=50, choices = OBSERVATION_CHOICES, help_text  ="How the interaction was observed")
+   owner = models.ForeignKey(User, related_name="%(app_label)s_%(class)s_owner")
+   taxa_from = models.ForeignKey(Taxa, related_name='taxa_from')
+   taxa_to = models.ForeignKey(Taxa, related_name='taxa_to')
+   pop_from = models.ForeignKey(Population, related_name='pop_from', blank=True, null=True)
+   pop_to = models.ForeignKey(Population, related_name='pop_to', blank=True, null=True)
+   item_from = models.ForeignKey(Item, related_name='item_from', blank=True, null=True)
+   item_to = models.ForeignKey(Item, related_name='item_to', blank=True, null=True)
+   strength_f = models.FloatField(blank=True,null=True, help_text = "The strength of the interaction for the item ESTABLISHING the interaction")
+   strength_t = models.FloatField(blank=True,null=True, help_text = "The strength of the interaction for the item RECEVING the interaction")
+   units_f = models.CharField(max_length=50,blank=True,null=True, help_text = "Units in which the interaction strength is measured")
+   units_t = models.CharField(max_length=50,blank=True,null=True, help_text = "Units in which the interaction strength is measured")
+   description = models.CharField(max_length=D_NAME,blank=True,null=True, help_text = "A description of the interaction")
+   def __unicode__(self):
+       From = self.taxa_from
+       To = self.taxa_to
+       if self.pop_from :
+          From = self.pop_from
+       if self.pop_to:
+          To = self.pop_to
+       if self.item_from :
+          From = self.item_from
+       if self.item_to:
+          To = self.item_to
+       return u'%s of %s by %s'% (self.ecotype, To, From)
+
+
+# environment
+class Environment(models.Model):
+   name = models.CharField(max_length=M_NAME, help_text = "The environmental property being measured")
+   owner = models.ForeignKey(User, related_name="%(app_label)s_%(class)s_owner")
+   value = models.CharField(help_text = "The value of the environmental property", max_length = 50)
+   units = models.CharField(max_length=50, help_text = "The units in which the environmental property is measured", blank=True, null=True)
+   description = models.CharField(max_length=D_NAME,blank=True,null=True, help_text = "A description of the environmental property")
+   def __unicode__(self):
+      return u'%s (%.4f %s)' % (self.name, self.value, self.units)
+
+# network
+class Network(models.Model):
+   public = models.BooleanField(default=True)
+   owner = models.ForeignKey(User, related_name="%(app_label)s_%(class)s_owner")
+   name = models.CharField(max_length=M_NAME, help_text = "The name of the network")
+   description = models.CharField(max_length=D_NAME,blank=True,null=True, help_text = "A short description of the network")
+   interactions = models.ManyToManyField(Interaction)
+   date = models.CharField(max_length=10,blank=True,null=True, help_text = "The date at which the network was sampled")
+   latitude = models.CharField(max_length=20,blank=True,null=True, help_text = "Latitude")
+   longitude = models.CharField(max_length=20,blank=True,null=True, help_text = "Longitude")
+   environment = models.ManyToManyField(Environment,blank=True,null=True)
+   def __unicode__(self):
+       return self.name
+
+# reference
+class Ref(models.Model):
+   doi = models.CharField(max_length=200, blank=True, null=True, help_text = "DOI of the reference object")
+   owner = models.ForeignKey(User, related_name="%(app_label)s_%(class)s_owner")
+   jstor = models.CharField(max_length=200, blank=True, null=True, help_text = "JSTOR identifier of the reference object")
+   pmid = models.CharField(max_length=200, blank=True, null=True, help_text = "PubMed ID of the reference object")
+   url = models.CharField(max_length=200, blank=True, null=True, help_text = "URL of the reference object")
+
+# dataset
+class Dataset(models.Model):
+   public = models.BooleanField(default=True)
+   owner = models.ForeignKey(User, related_name="%(app_label)s_%(class)s_owner")
+   name = models.CharField(max_length=M_NAME, help_text = "The name of the dataset")
+   description = models.CharField(max_length=D_NAME,blank=True,null=True, help_text = "A short description of the dataset")
+   papers = models.ManyToManyField(Ref, related_name='papers',blank=True,null=True)
+   data = models.ManyToManyField(Ref, related_name='data',blank=True,null=True)
+   networks = models.ManyToManyField(Network,blank=True,null=True)
+   def __unicode__(self):
+       return self.name