removed module file

Former-commit-id: 48c08798baa9f29a97de21370e064cfbefe83f84 [formerly a147e273d739122a722a4a9a0f78bcdb607f3642]
Former-commit-id: ed0cb6561aa56c8512bcb53a81e309e872037b2b

.gitmodules

-[submodule "python_nedrex"]
-	path = python_nedrex
-	url = git@github.com:repotrial/python_nedrex.git

docker-compose.yml

@@ -12,7 +12,7 @@ services:
       - 'docker-django.env.dev'
     restart: always
 #    volumes:
-#      - ./:/usr/src/drugstone/
+#      - drugstone_backend_volume:/usr/src/drugstone/
     ports:
       - 8001:8000
     networks:
@@ -97,4 +97,5 @@ networks:
   drugstone_net:
 
 volumes:
-  drugstone_postgres_volume:
+  drugstone_postgres_volume:
\ No newline at end of file
+  drugstone_backend_volume:
\ No newline at end of file

drugstone/management/commands/import_from_nedrex.py

 from collections import defaultdict
 
+import python_nedrex as nedrex
+from python_nedrex.core import get_nodes, get_edges, get_api_key
+
+from drugstone import models
+
+
+def iter_node_collection(coll_name, eval):
+    offset = 0
+    limit = 10000
+    while True:
+        result = get_nodes(coll_name, offset=offset, limit=limit)
+        if not result:
+            return
+        for node in result:
+            eval(node)
+        offset += limit
+
+
+def iter_edge_collection(coll_name, eval):
+    offset = 0
+    limit = 10000
+    while True:
+        result = get_edges(coll_name, offset=offset, limit=limit)
+        if not result:
+            return
+        for edge in result:
+            eval(edge)
+        offset += limit
+
+
+def identify_updates(new_list, old_list):
+    u = list()
+    c = list()
+    for id in new_list:
+        if id not in old_list:
+            c.append(id)
+        elif new_list[id] != old_list[id]:
+            old_list[id].update(new_list[id])
+            u.append(old_list[id])
+    return u, c
 
-class nedrex_importer:
 
+def format_list(l):
+    if l is not None and len(l) > 0:
+        s = str(l)[1:]
+        return s[:len(s) - 1]
+    return ""
+
+
+class nedrex_importer:
     proteins = dict()
+    entrez_to_uniprot = dict()
+    gene_name_to_uniprot = defaultdict(lambda: set())
+    disorders = dict()
+    drugs = dict()
+
+    def __init__(self, base_url):
+        nedrex.config.set_url_base(base_url)
+        api_key = get_api_key(accept_eula=True)
+        nedrex.config.set_api_key(api_key)
+
+    def init_proteins(self):
+        if len(self.proteins) == 0:
+            print("Generating protein maps...")
+            for protein in models.Protein.objects.all():
+                self.proteins[protein.entrez] = protein
+                self.entrez_to_uniprot[protein.entrez] = protein.uniprot_code
+                self.gene_name_to_uniprot[protein.gene].add(protein.uniprot_code)
+
+    def init_drugs(self):
+        if len(self.drugs) == 0:
+            print("Generating drug map...")
+            for drug in models.Drug.objects.all():
+                self.drugs[drug.drug_id] = drug
 
-    def import_proteins(self):
-        import python_nedrex as nedrex
-        from python_nedrex.core import get_nodes, get_api_key, get_edges
-        from drugstone.models import Protein
+    def init_disorders(self):
+        if len(self.disorders) == 0:
+            print("Generating disorder map...")
+            for disorder in models.Disorder.objects.all():
+                self.disorders[disorder.mondo_id] = disorder
 
+    def import_proteins(self, update: bool):
+        proteins = dict()
         gene_to_prots = defaultdict(lambda: set())
 
-        def iter_node_collection(coll_name, eval):
-            offset = 0
-            limit = 10000
-            while True:
-                result = get_nodes(coll_name, offset=offset, limit=limit)
-                if not result:
-                    return
-                for node in result:
-                    eval(node)
-                offset += limit
-
-        def iter_edge_collection(coll_name, eval):
-            offset = 0
-            limit = 10000
-            while True:
-                result = get_edges(coll_name, offset=offset, limit=limit)
-                if not result:
-                    return
-                for edge in result:
-                    eval(edge)
-                offset += limit
+        if update:
+            self.init_proteins()
 
         def add_protein(node):
-            id = node['primaryDomainId']
-            self.proteins[id] = Protein(uniprot_code=id.split('.')[1], gene=node['geneName'])
+            print(node)
+            id = node['primaryDomainId'].split('.')[1]
+            name = node['geneName']
+            if len(node['synonyms']) > 0:
+                name = node['synonyms'][0]
+                idx = name.index('{')
+                if idx > 0:
+                    name = name[idx - 1:]
+            proteins[id] = models.Protein(uniprot_code=id, name=name, gene=node['geneName'])
 
         def add_edges(edge):
-            id = edge['sourceDomainId']
-            protein = self.proteins[id]
+            id = edge['sourceDomainId'].split('.')[1]
+            protein = proteins[id]
             protein.entrez = edge['targetDomainId'].split('.')[1]
             gene_to_prots[edge['targetDomainId']].add(id)
 
         def add_genes(node):
-            id = node['primaryDomainId']
+            id = node['primaryDomainId'].split('.')[1]
             for prot_id in gene_to_prots[id]:
-                protein = self.proteins[prot_id]
+                protein = proteins[prot_id]
                 try:
                     protein.protein_name = node['synonyms'][0]
                 except:
                     pass
 
-        nedrex.config.set_url_base("http://82.148.225.92:8123/")
-        api_key = get_api_key(accept_eula=True)
-        nedrex.config.set_api_key(api_key)
-
-
-
-        print('Importing Proteins')
         iter_node_collection('protein', add_protein)
-        print('Importing Protein-Gene mapping')
         iter_edge_collection('protein_encoded_by_gene', add_edges)
-        print('Mapping Gene information')
         iter_node_collection('gene', add_genes)
-        Protein.objects.bulk_create(self.proteins.values())
+        # TODO test updating ideas
+        if update:
+            (updates, creates) = identify_updates(proteins, self.proteins)
+            models.Protein.objects.bulk_update(updates)
+            models.Protein.objects.bulk_create(creates)
+            for protein in creates:
+                self.proteins[protein.uniprot_code] = protein
+        else:
+            models.Protein.objects.bulk_create(self.proteins.values())
+            self.proteins = proteins
         return len(self.proteins)
+
+    def import_drugs(self, update):
+        drugs = dict()
+        if update:
+            self.init_drugs()
+
+        def add_drug(node):
+            id = node['primaryDomainId'].split('.')[1]
+            drugs[id] = models.Drug(drug_id=id, name=node['displayName'], status=format_list(node['drugGroups']))
+
+        iter_node_collection('drug', add_drug)
+
+        # TODO test updating ideas
+        if update:
+            (updates, creates) = identify_updates(drugs, self.drugs)
+            models.Drug.objects.bulk_update(updates)
+            models.Drug.objects.bulk_create(creates)
+            for drug in creates:
+                self.drugs[drug.drug_id] = drug
+        else:
+            models.Drug.objects.bulk_create(self.drugs.values())
+            self.drugs = drugs
+
+        self.drugs = drugs
+        return len(self.drugs)
+
+    def import_disorders(self, update):
+        disorders = dict()
+        if update:
+            self.init_disorders()
+
+        def add_disorder(node):
+            id = node['primaryDomainId'].split('.')[1]
+            self.disorders[id] = models.Disorder(mondo_id=id, label=node['displayName'], icd10=format_list(node['icd10']))
+
+        iter_node_collection('disorder', add_disorder)
+
+        # TODO test updating ideas
+        if update:
+            (updates, creates) = identify_updates(disorders, self.disorders)
+            models.Disorder.objects.bulk_update(updates)
+            models.Disorder.objects.bulk_create(creates)
+            for disorder in creates:
+                self.disorders[disorder.uniprot_code] = disorder
+        else:
+            models.Disorder.objects.bulk_create(self.disorders.values())
+            self.disorders = disorders
+
+        self.disorders = disorders
+        return len(self.disorders)

drugstone/management/commands/populate_db.py

@@ -99,7 +99,7 @@ class Command(BaseCommand):
                                         tissue_expression_file=exp_file,
                                         )
 
-        importer = nedrex_importer()
+        importer = nedrex_importer("http://82.148.225.92:8123/")
 
         if kwargs['delete_model'] is not None:
             model_list = kwargs['delete_model'].split(',')
@@ -111,6 +111,7 @@ class Command(BaseCommand):
         if kwargs['drug_file'] is not None:
             print('Populating Drugs...')
             n = DataPopulator.populate_drugs(populator)
+            # n = nedrex_importer.import_drugs(importer,False)
             print(f'Populated {n} Drugs.')
 
         # if kwargs['protein_file'] is not None:
@@ -130,8 +131,8 @@ class Command(BaseCommand):
         if kwargs['proteins'] is not None:
             print('Populating Proteins...')
 
-            n = nedrex_importer.import_proteins(nedrex_importer)
-            # n = DataPopulator.populate_proteins(populator)
+            # n = nedrex_importer.import_proteins(importer, False)
+            n = DataPopulator.populate_proteins(populator)
             print(f'Populated {n} Proteins.')
             
             print('Populating ENSG IDs...')
@@ -140,6 +141,7 @@ class Command(BaseCommand):
 
         if kwargs['disorders'] is not None:
             print('Populating Disorders...')
+            # n = nedrex_importer.import_disorders(importer, False)
             n = DataPopulator.populate_disorders(populator)
             print(f'Populated {n} Disorders.')
 

drugstone/management/includes/DataPopulator.py

@@ -8,7 +8,6 @@ class DataPopulator:
     proteins = dict()
     uniprot_to_ensembl = dict()
     gene_name_to_ensembl = defaultdict(lambda: set())
-    # protein_name_to_ensembl = dict()
     disorders = dict()
     drugs = dict()
 
@@ -19,7 +18,6 @@ class DataPopulator:
                 self.proteins[protein.entrez]=protein
                 self.uniprot_to_ensembl[protein.uniprot_code] = protein.entrez
                 self.gene_name_to_ensembl[protein.gene].add(protein.entrez)
-                # self.protein_name_to_ensembl[protein.protein_name] = protein.entrez
 
     def init_drugs(self):
         if len(self.drugs)== 0:
@@ -49,7 +47,6 @@ class DataPopulator:
                 protein_name=row['protein_name'])
             self.uniprot_to_ensembl[row['protein_ac']] = row['entrez_id']
             self.gene_name_to_ensembl[row['gene_name']].add(row['entrez_id'])
-            # self.protein_name_to_ensembl[row['protein_name']] = row['entrez_id']
 
         models.Protein.objects.bulk_create(self.proteins.values())
         return len(self.proteins)

drugstone/models.py

@@ -79,7 +79,7 @@ class Protein(models.Model):
     # are either 6 or 10 characters long
 
     uniprot_code = models.CharField(max_length=10)
-    gene = models.CharField(max_length=128, default='')   # symbol
+    gene = models.CharField(max_length=128, default='')  # symbol
     protein_name = models.CharField(max_length=128, default='')
     entrez = models.CharField(max_length=128, default='')
     drugs = models.ManyToManyField('Drug', through='ProteinDrugInteraction',
@@ -93,10 +93,21 @@ class Protein(models.Model):
     def __str__(self):
         return self.gene
 
+    def __eq__(self, other):
+        return self.uniprot_code == other.uniprot_code and self.gene == other.gene and self.protein_name == other.protein_name and self.entrez == other.entrez
+
+    def __ne__(self, other):
+        return not self.__eq__(other)
+
+    def update(self, other):
+        self.uniprot_code = other.uniprot_code
+        self.gene = other.gene
+        self.protein_name = other.protein_name
+        self.entrez = other.entrez
 
 class Disorder(models.Model):
     mondo_id = models.CharField(max_length=7)
-    label = models.CharField(max_length=256, default='')   # symbol
+    label = models.CharField(max_length=256, default='')  # symbol
     icd10 = models.CharField(max_length=128, default='')
     proteins = models.ManyToManyField(
         'Protein', through='ProteinDisorderAssociation', related_name='associated_proteins')
@@ -107,6 +118,40 @@ class Disorder(models.Model):
     def __str__(self):
         return self.label
 
+    def __eq__(self, other):
+        return self.mondo_id == other.mondo_id and self.label == other.label and self.icd10 == other.icd10
+
+    def __ne__(self, other):
+        return not self.__eq__(other)
+
+    def update(self,other):
+        self.mondo_id = other.mondo_id
+        self.label = other.label
+        self.icd10 = other.icd10
+
+
+class Drug(models.Model):
+    drug_id = models.CharField(max_length=10, unique=True)
+    name = models.CharField(max_length=256, default='')
+    status = models.CharField(max_length=128, default='')
+    # in_trial = models.BooleanField(default=False)
+    # in_literature = models.BooleanField(default=False)
+    links = models.CharField(max_length=16 * 1024, default='')
+
+    def __str__(self):
+        return self.drug_id
+
+    def __eq__(self, other):
+        return self.drug_id == other.uniprot_code and self.name == other.name and self.status == other.status
+
+    def __ne__(self,other):
+        return not self.__eq__(other)
+
+    def update(self, other):
+        self.drug_id = other.drug_id
+        self.name = other.name
+        self.status = other.status
+        self.links = other.links
 
 class ProteinDisorderAssociation(models.Model):
     pdis_dataset = models.ForeignKey(
@@ -121,7 +166,6 @@ class ProteinDisorderAssociation(models.Model):
     def __str__(self):
         return f'{self.pdis_dataset}-{self.protein}-{self.disorder}'
 
-
 class DrugDisorderIndication(models.Model):
     drdi_dataset = models.ForeignKey(
         'DrDiDataset', null=True, on_delete=models.CASCADE, related_name='drdi_dataset_relation')
@@ -135,18 +179,6 @@ class DrugDisorderIndication(models.Model):
         return f'{self.drdi_dataset}-{self.drug}-{self.disorder}'
 
 
-class Drug(models.Model):
-    drug_id = models.CharField(max_length=10, unique=True)
-    name = models.CharField(max_length=256, default='')
-    status = models.CharField(max_length=128, default='')
-    # in_trial = models.BooleanField(default=False)
-    # in_literature = models.BooleanField(default=False)
-    links = models.CharField(max_length=16*1024, default='')
-
-    def __str__(self):
-        return self.drug_id
-
-
 class ProteinProteinInteraction(models.Model):
     ppi_dataset = models.ForeignKey(
         'PPIDataset', null=True, on_delete=models.CASCADE, related_name='ppi_dataset_relation')
@@ -158,12 +190,12 @@ class ProteinProteinInteraction(models.Model):
             from_protein=self.from_protein,
             to_protein=self.to_protein,
             ppi_dataset=self.ppi_dataset
-            )
+        )
         p2p1_q = ProteinProteinInteraction.objects.filter(
             from_protein=self.to_protein,
             to_protein=self.from_protein,
             ppi_dataset=self.ppi_dataset
-            )
+        )
 
         if p1p2_q.exists() or p2p1_q.exists():
             raise ValidationError('Protein-Protein interaction must be unique!')
@@ -175,7 +207,6 @@ class ProteinProteinInteraction(models.Model):
     def __str__(self):
         return f'{self.ppi_dataset}-{self.from_protein}-{self.to_protein}'
 
-
 class ProteinDrugInteraction(models.Model):
     pdi_dataset = models.ForeignKey(
         'PDIDataset', null=True, on_delete=models.CASCADE, related_name='pdi_dataset_relation')
@@ -188,7 +219,6 @@ class ProteinDrugInteraction(models.Model):
     def __str__(self):
         return f'{self.pdi_dataset}-{self.protein}-{self.drug}'
 
-
 class Task(models.Model):
     token = models.CharField(max_length=32, unique=True)
     created_at = models.DateTimeField(auto_now_add=True)
@@ -208,7 +238,6 @@ class Task(models.Model):
 
     result = models.TextField(null=True)
 
-
 class Network(models.Model):
     id = models.CharField(primary_key=True, max_length=32, unique=True)
     created_at = models.DateTimeField(auto_now_add=True)