I23 haplo db

.travis.yml

@@ -3,10 +3,17 @@ dist: xenial
 
 language: python
 python:
-  - 3.7
+  - 3.7.3
 
 # Command to install dependencies, e.g. pip install -r requirements_dev.txt --use-mirrors
-install: pip install -r requirements_dev.txt
+install:
+  - pip install -r requirements_dev.txt
+  - python manage.py migrate
+
+env:
+  - DJANGO_VERSION=2.2.1
+  - DJANGO_SETTINGS_MODULE=vgbrowser.settings
 
 # Command to run tests, e.g. python setup.py test
-script: python -m unittest
+script:
+  - python manage.py test

Graph/gfa.py

@@ -60,8 +60,9 @@ def topologicalSort(self):
 
 
 class GFA:
-    def __init__(self, gfa: gfapy.Gfa):
+    def __init__(self, gfa: gfapy.Gfa, source_path: str):
         self.gfa = gfa
+        self.source_path = source_path
 
     #    @classmethod
     #    def load_from_pickle(cls, file: str):
@@ -77,15 +78,14 @@ def load_from_xg(cls, file: str, xg_bin: str):
         process.wait()
         if process.returncode != 0:
             raise OSError()
-        graph = cls(gfa)
+        instance = cls(gfa, file)
         process.stdout.close()
-        return graph
+        return instance
 
     @classmethod
     def load_from_gfa(cls, file: str):
         gfa = gfapy.Gfa.from_file(file)
-        graph = cls(gfa)
-        return graph
+        return cls(gfa, file)
 
     #    def save_as_pickle(self, outfile: str):
     #        with open(outfile, 'wb') as pickle_file:
@@ -103,67 +103,30 @@ def save_as_gfa(self, file: str):
         self.gfa.to_file(file)
 
     @classmethod
-    def from_graph(cls, graph: Graph):
+    def from_graph(cls, graph: GraphGenome):
         """Constructs the lines of a GFA file listing paths, then sequence nodes in arbitrary order."""
         gfa = gfapy.Gfa()
         for path in graph.paths:
-            node_series = ",".join([traverse.node.id + traverse.strand for traverse in path.nodes])
+            node_series = ",".join([traverse.node.name + traverse.strand for traverse in path.nodes])
             gfa.add_line('\t'.join(['P', path.accession, node_series, ",".join(['*' for _ in path.nodes])]))
-        for node in graph.nodes.values(): # in no particular order
-            gfa.add_line('\t'.join(['S', str(node.id), node.seq]))
-        return cls(gfa)
-
-    @property
-    def to_paths(self) -> List[Path]:
-        node_hash = {}
+        for node in graph.nodes:  # in no particular order
+            gfa.add_line('\t'.join(['S', str(node.name), node.seq]))
+        return cls(gfa, "from Graph")
+
+    def to_paths(self) -> GraphGenome:
+        graph = self.to_graph()
+        return graph.paths
+
+    def to_graph(self) -> GraphGenome:
+        """Create parent object for this genome and save it in the database.
+        This can create duplicates appended in Paths if it is called twice."""
+        gdb = GraphGenome.objects.get_or_create(name=self.source_path)[0]
         for segment in self.gfa.segments:
-            node_id = segment.name + "+"
-            node = Node(segment.sequence, [])
-            node_hash[node_id] = node
-
-            node_id = segment.name + "-"
-            node = Node(segment.sequence, [])
-            node_hash[node_id] = node
+            Node.objects.get_or_create(seq=segment.sequence, name=(segment.name), graph=gdb)
 
-        paths = []
-        for path in self.gfa.paths:
-            nodes = []
-            for node in path.segment_names:
-                node_index = NodeTraversal(Node(node_hash[node.name + node.orient].seq, [], node.name), node.orient)
-                nodes.append(node_index)
-            paths.append(Path(path.name, nodes))
-
-        return paths
-
-    @property
-    def to_graph(self):
-        # Extract all paths into graph
-        path_names = [p.name for p in self.gfa.paths]
-        graph = Graph(path_names)  # Paths can be empty at start
         for path in self.gfa.paths:
-            for node in path.segment_names:
-                graph.append_node_to_path(node.name, node.orient, path.name)
-        for segment in self.gfa.segments:
-            graph.nodes[segment.name].seq = segment.sequence
-        graph.paths = self.to_paths
-        return graph
-        # IMPORTANT: It's not clear to Josiah how much of the below is necessary, so it's being left unmodified.
-
-
-'''
-class XGWrapper:
-    @staticmethod
-    def save(gfa):
-        pass
-
-    @staticmethod
-    def load(gfa):
-        pass
-
-class GraphStack:
-    def __init__(graphs: List[Graph]):
-        self.graphs = graphs
-'''
-
-if __name__ == "__main__":
-    location_of_xg = sys.argv[0]
+            p = Path(accession=path.name, graph=gdb)
+            p.save()
+            p.append_gfa_nodes(path.segment_names)
+        return gdb
+

Graph/migrations/0001_initial.py

@@ -0,0 +1,51 @@
+# Generated by Django 2.2.1 on 2019-08-14 14:28
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='GraphGenome',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=1000)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Node',
+            fields=[
+                ('seq', models.CharField(blank=True, max_length=255)),
+                ('name', models.CharField(max_length=15, primary_key=True, serialize=False)),
+                ('graph', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='Graph.GraphGenome')),
+            ],
+            options={
+                'unique_together': {('graph', 'name')},
+            },
+        ),
+        migrations.CreateModel(
+            name='Path',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('accession', models.CharField(max_length=1000, unique=True)),
+                ('graph', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='Graph.GraphGenome')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='NodeTraversal',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('order', models.IntegerField(help_text='Defines the order a path lists traversals')),
+                ('strand', models.CharField(choices=[('+', '+'), ('-', '-')], default='+', max_length=1)),
+                ('node', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='Graph.Node')),
+                ('path', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='Graph.Path')),
+            ],
+        ),
+    ]

Graph/migrations/0002_Path_unique_together.py

@@ -0,0 +1,22 @@
+# Generated by Django 2.2.1 on 2019-08-19 17:47
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('Graph', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='path',
+            name='accession',
+            field=models.CharField(max_length=1000),
+        ),
+        migrations.AlterUniqueTogether(
+            name='path',
+            unique_together={('graph', 'accession')},
+        ),
+    ]