safety

models.py

@@ -85,6 +85,14 @@ class TaxonTree(models.Model):
 
     objects = TaxonTreeManager()
 
+
+    def save(self, *args, **kwargs):
+        if self.is_root_taxon == False and not self.parent:
+            raise ValueError('non-root taxa require a parent')
+
+        super().save(*args, **kwargs)
+        
+
     def __str__(self):
         return self.taxon_latname
 

sources/algaebase/AlgaebaseManager.py

+####################################################################################################################
+#
+#   IMPORT Algaebase.org
+#
+####################################################################################################################
+
+from taxonomy.sources.TaxonSourceManager import (TaxonSourceManager, SourceTreeTaxon,
+                                    SourceSynonymTaxon, VernacularName, TreeCache)
+
+from taxonomy.sources.algaebase.models import AlgaebaseTaxonTree, AlgaebaseTaxonSynonym, AlgaebaseTaxonLocale
+
+import psycopg2, psycopg2.extras, os, csv
+
+from html.parser import HTMLParser
+
+
+
+# the CoL2019 uses language names like "English" -> use langcodes
+import langcodes
+
+DEBUG = False
+
+
+
+# db interface for algaebase 2020 postgres db
+algaebaseCon = psycopg2.connect(dbname="algaebase2019", user="localcosmos", password="localcosmos",
+                          host="localhost", port="5432")
+
+algaebaseCursor = algaebaseCon.cursor(cursor_factory = psycopg2.extras.DictCursor)
+
+
+class AlgaebaseSourceTreeTaxon(SourceTreeTaxon):
+
+    TreeModel = AlgaebaseTaxonTree
+
+    def _get_source_object(self):
+        raise NotImplementedError('SourceTaxon subclasses need a _get_source_object method')
+
+
+    def _get_vernacular_names(self):
+        raise NotImplementedError('SourceTaxon subclasses need a _get_vernacular_names method')
+
+
+    def _get_synonyms(self):
+        raise NotImplementedError('SourceTaxon subclasses need a _get_synonyms method')
+
+
+class AlgaebaseSourceSynonymTaxon(SourceSynonymTaxon):
+    pass
+
+
+class AlgaebaseTreeCache(TreeCache):
+
+    SourceTreeTaxonClass = AlgaebaseSourceTreeTaxon
+    TaxonTreeModel = AlgaebaseTaxonTree
+    
+
+class AlgaebaseManager(TaxonSourceManager):
+
+    SourceTreeTaxonClass = AlgaebaseSourceTreeTaxon
+    SourceSynonymTaxonClass = AlgaebaseSourceSynonymTaxon
+    
+    TaxonTreeModel = AlgaebaseTaxonTree
+    TaxonSynonymModel = AlgaebaseTaxonSynonym
+    TaxonLocaleModel = AlgaebaseTaxonLocale
+
+    TreeCacheClass = AlgaebaseTreeCache
+
+    def _get_root_source_taxa(self):
+        raise NotImplementedError('Tree Managers need a _get_root_source_taxa method')
+
+
+    def _get_children(self, source_taxon):
+        raise NotImplementedError('Tree Managers need a _get_children method')
+
+    '''
+    this function has to travel right and up until the next parent taxon which has not been climbed down
+    yet has been found
+    returns a source_taxon or None
+
+    EXAMPLE:
+    - source_taxon is a taxon without children
+    - the next sibling of source taxon might have children -> check all siblings first
+    - if no siblings have children, travel up
+    '''
+
+    def _get_next_sibling(self, source_taxon):
+        raise NotImplementedError('Tree Managers need a _get_next_sibling method')
+
+    # travel one up
+    def _get_parent(self, source_taxon):
+        raise NotImplementedError('Tree Managers need a _get_parent method')

sources/algaebase/admin.py

+from django.contrib import admin
+
+# Register your models here.

sources/algaebase/apps.py

+from django.apps import AppConfig
+
+
+class AlgaebaseConfig(AppConfig):
+    name = 'algaebase'

sources/algaebase/models.py

+from django.db import models
+
+from taxonomy.models import TaxonTree, TaxonSynonym, TaxonNamesView, TaxonLocale
+
+
+class AlgaebaseTaxonTree(TaxonTree):
+    pass
+
+
+class AlgaebaseTaxonSynonym(TaxonSynonym):
+    taxon = models.ForeignKey(AlgaebaseTaxonTree, on_delete=models.CASCADE, to_field='name_uuid')
+
+    class Meta:
+        unique_together = ('taxon', 'taxon_latname', 'taxon_author')
+
+
+class AlgaebaseTaxonLocale(TaxonLocale):
+    taxon = models.ForeignKey(algaebaseTaxonTree, on_delete=models.CASCADE, to_field='name_uuid')
+
+    class Meta:
+        index_together = [
+            ['taxon', 'language'],
+        ]
+    
+
+'''
+    VIEWS
+'''
+class AlgaebaseTaxonNamesView(TaxonNamesView):
+    pass
+

sources/algaebase/tests.py

+from django.test import TestCase
+
+# Create your tests here.

sources/algaebase/views.py

+from django.shortcuts import render
+
+# Create your views here.