pinnacle df reformatting

tdc/resource/pinnacle.py

@@ -61,12 +61,28 @@ def get_keys(self):
     def get_embeds(self):
         prots = self.get_keys()
         emb = self.get_embeds_raw()
-        nemb = {'--'.join(prots.iloc[k]): v for k, v in emb.items()}
+        # nemb = {'--'.join(prots.iloc[k]): v for k, v in emb.items()}
         x = {}
-        for k, v in nemb.items():
+        ctr = 0
+        for _, v in emb.items():
             if isinstance(v, torch.Tensor):
-                x[k] = pd.DataFrame(v.detach().numpy())
+                if v.size()[0] == 1:
+                    k = "--".join(prots.iloc[ctr])
+                    ctr += 1
+                    x[k] = v.detach().numpy()
+                    continue
+                for t in v:
+                    assert len(t.size()) == 1, t.size()
+                    k = "--".join(prots.iloc[ctr])
+                    ctr += 1
+                    x[k] = t.detach().numpy()
             else:
                 raise Exception("encountered non-tensor")
-        df = pd.concat(x, axis=0)
+        assert len(x) == len(prots), "dict len {} vs keys length {}".format(
+            len(x), len(prots))
+        df = pd.DataFrame.from_dict(x)
+        df = df.transpose()
+        assert len(df) == len(
+            x), "dims not mantained when translated to pandas. {} vs {}".format(
+                len(df), len(x))
         return df

tdc/test/test_resources.py

@@ -97,6 +97,16 @@ def test_embeddings(self):
         assert len(keys) > 0, "PINNACLE keys is empty"
         assert len(keys) == len(embeds), "{} vs {}".format(
             len(keys), len(embeds))
+        num_targets = len(keys["target"].unique())
+        num_cells = len(keys["cell type"].unique())
+        all_entries = embeds.index
+        prots = [x.split("--")[0] for x in all_entries]
+        cells = [x.split("--")[1] for x in all_entries]
+        assert len(
+            set(prots)) == num_targets, "{} vs {} for target proteins".format(
+                len(prots), num_targets)
+        assert len(set(cells)) == num_cells, "{} vs {} for cell_types".format(
+            len(cells), num_cells)
 
 
 if __name__ == "__main__":

tdc/version.py

@@ -19,4 +19,4 @@
 # Dev branch marker is: 'X.Y.dev' or 'X.Y.devN' where N is an integer.
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
-__version__ = "1.0.0"  # pragma: no cover
+__version__ = "1.0.6"  # pragma: no cover