Update export

setup.cfg

@@ -54,16 +54,12 @@ docs =
 [options.entry_points]
 console_scripts =
     bio2bel_adeptus = bio2bel_adeptus.cli:main
+bio2bel =
+    adeptus = bio2bel_adeptus
 
 [options.packages.find]
 where = src
 
-#######################
-# Wheel Configuration #
-#######################
-[bdist_wheel]
-python-tag = py36
-
 ##########################
 # Coverage Configuration #
 # (.coveragerc)          #

src/bio2bel_adeptus/manager.py

@@ -6,79 +6,108 @@
 
 from tqdm import tqdm
 
-import pybel.dsl
 from bio2bel.manager.bel_manager import BELManagerMixin
 from pybel import BELGraph
 from pybel.constants import NEGATIVE_CORRELATION, POSITIVE_CORRELATION
+from pybel.dsl import Pathology, Rna
 from .constants import MODULE_NAME
 from .models import Base
 from .parser import get_adeptus_df
 
 
 class Manager(BELManagerMixin):
-    """Manages the Bio2BEL ADEPTUS database."""
+    """Disease-specific differential gene expression."""
 
     module_name = MODULE_NAME
     _base = Base
 
     def __init__(self, *args, **kwargs):  # noqa: D107
-        pass
+        self.graph = get_graph()
 
     @classmethod
     def _get_connection(cls):
-        return ''
+        pass
 
-    def is_populated(self) -> bool:
+    @staticmethod
+    def is_populated() -> bool:
         """Check if the Bio2BEL ADEPTUS database is populated."""
-        raise NotImplementedError
+        return True
 
     def summarize(self) -> Mapping[str, int]:
         """Summarize the contents of the Bio2BEL ADEPTUS database."""
-        raise NotImplementedError
+        return dict(
+            correlations=self.count_relations(),
+            diseases=self.count_diseases(),
+            rnas=self.count_rnas(),
+        )
 
     def populate(self) -> None:
         """Populate the Bio2BEL ADEPTUS database."""
         raise NotImplementedError
 
+    def count_diseases(self) -> int:
+        """Count the number of diseases."""
+        return sum(
+            isinstance(node, Pathology)
+            for node in self.graph
+        )
+
+    def count_rnas(self) -> int:
+        """Count the number of RNAs."""
+        return sum(
+            isinstance(node, Rna)
+            for node in self.graph
+        )
+
+    def count_relations(self) -> int:
+        """Count the number of disease-differential expressed gene relations."""
+        return self.graph.number_of_edges()
+
     def to_bel(self) -> BELGraph:
         """Output ADEPTUS as a BEL graph."""
-        graph = BELGraph(
-            name='ADEPTUS',
-            version='0.0.0',
-            description="""ADEPTUS conversion to BEL using Daniel Himmelstein's data at https://raw.githubusercontent.com/dhimmel/adeptus/master/data/gene-sets.tsv"""
+        return self.graph
+
+
+def get_graph(use_tqdm: bool = False) -> BELGraph:
+    graph = BELGraph(
+        name='ADEPTUS',
+        version='0.0.0',
+        description="""ADEPTUS conversion to BEL using Daniel Himmelstein's data at https://raw.githubusercontent.com/dhimmel/adeptus/master/data/gene-sets.tsv"""
+    )
+    graph.annotation_pattern['Database'] = '.*'
+    graph.annotation_pattern['ADEPTUS_PB_ROC'] = '.*'
+    graph.annotation_pattern['ADEPTUS_PN_ROC'] = '.*'
+
+    df = get_adeptus_df()
+
+    it = df.iterrows()
+    if use_tqdm:
+        it = tqdm(it, desc='ADEPTUS to BEL', total=len(df.index))
+    for _, (disease_doid, disease_name, entrez_id, entrez_name, pb_roc, pn_roc, direction) in it:
+        disease = Pathology(
+            namespace='doid',
+            name=disease_name,
+            identifier=disease_doid,
+        )
+        gene = Rna(
+            namespace='ncbigene',
+            name=entrez_name,
+            identifier=entrez_id,
         )
-        graph.annotation_pattern['Database'] = '.*'
-        graph.annotation_pattern['ADEPTUS_PB_ROC'] = '.*'
-        graph.annotation_pattern['ADEPTUS_PN_ROC'] = '.*'
-
-        df = get_adeptus_df()
-
-        it = tqdm(df.iterrows(), desc='ADEPTUS to BEL', total=len(df.index))
-        for _, (disease_doid, disease_name, entrez_id, entrez_name, pb_roc, pn_roc, direction) in it:
-            disease = pybel.dsl.Pathology(
-                namespace='doid',
-                name=disease_name,
-                identifier=disease_doid,
-            )
-            gene = pybel.dsl.Gene(
-                namespace='ncbigene',
-                name=entrez_name,
-                identifier=entrez_id,
-            )
-
-            relation = POSITIVE_CORRELATION if direction == 'up' else NEGATIVE_CORRELATION
-
-            graph.add_qualified_edge(
-                disease,
-                gene,
-                relation=relation,
-                citation='26261215',
-                evidence='ADEPTUS database',
-                annotations={
-                    'Database': 'ADEPTUS',
-                    'ADEPTUS_PB_ROC': pb_roc,
-                    'ADEPTUS_PN_ROC': pn_roc,
-                }
-            )
-
-        return graph
+
+        relation = POSITIVE_CORRELATION if direction == 'up' else NEGATIVE_CORRELATION
+
+        graph.add_qualified_edge(
+            disease,
+            gene,
+            relation=relation,
+            citation='26261215',
+            evidence='ADEPTUS database',
+            annotations={
+                'bio2bel': 'adeptus',
+                'ADEPTUS_PB_ROC': pb_roc,
+                'ADEPTUS_PN_ROC': pn_roc,
+            }
+        )
+
+    return graph