From b1de943d00931ef6e1371e55c7a6c43bd505a6b1 Mon Sep 17 00:00:00 2001
From: Jeremy Arbesfeld <jarbesfeld@gmail.com>
Date: Tue, 12 Jul 2022 17:48:35 -0400
Subject: [PATCH 1/2] feat #13:get statistics about variation content

---
 .gitignore                                    |  1 +
 src/anyvar/restapi/_data/openapi.yaml         | 27 +++++++++++++++++++
 .../restapi/routes/summary_statistics.py      | 13 +++++++++
 src/anyvar/storage/postgres.py                | 15 ++++++++++-
 4 files changed, 55 insertions(+), 1 deletion(-)
 create mode 100644 src/anyvar/restapi/routes/summary_statistics.py

diff --git a/.gitignore b/.gitignore
index e46a0a0..7ff73c3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,6 +12,7 @@ build/
 develop-eggs/
 dist/
 downloads/
+*.DS_Store
 eggs/
 .eggs/
 .idea/
diff --git a/src/anyvar/restapi/_data/openapi.yaml b/src/anyvar/restapi/_data/openapi.yaml
index 59437a9..02127a5 100644
--- a/src/anyvar/restapi/_data/openapi.yaml
+++ b/src/anyvar/restapi/_data/openapi.yaml
@@ -433,6 +433,33 @@ paths:
                 type: object
                 # This seems to be working: $ref: "file:vr.json#/definitions/Location"
 
+  #######################################################################
+  # Summary Statistics
+
+  /summary_statistics/{vartype}:
+    get:
+      tags: ["Statistics"]
+      summary: Summary Statistics for Variations in anyvar
+      description: Output summary statistics
+      parameters:
+        - name: vartype
+          in: path
+          description: variation type
+          required: true
+          schema:
+            type: string
+            enum:
+              - substitution
+              - deletion
+              - insertion
+              - all
+      responses:
+        200:
+          description: OK
+          content:
+            application/json:
+              schema:
+                type: integer
 
 
 # ######################################################################
diff --git a/src/anyvar/restapi/routes/summary_statistics.py b/src/anyvar/restapi/routes/summary_statistics.py
new file mode 100644
index 0000000..40fdd57
--- /dev/null
+++ b/src/anyvar/restapi/routes/summary_statistics.py
@@ -0,0 +1,13 @@
+from ..globals import get_anyvar
+
+def get(vartype):
+    av = get_anyvar()
+    if vartype == "substitution":
+        out = av.object_store.substitution_count()
+    elif vartype == "deletion":
+        out = av.object_store.deletion_count()
+    elif vartype == "insertion":
+        out = av.object_store.insertion_count()
+    elif vartype == "all":
+        out = len(av.object_store)
+    return out, 200
diff --git a/src/anyvar/storage/postgres.py b/src/anyvar/storage/postgres.py
index bfe367d..9fa17a8 100644
--- a/src/anyvar/storage/postgres.py
+++ b/src/anyvar/storage/postgres.py
@@ -54,7 +54,20 @@ def __del__(self):
         self._db.close()
 
     def __len__(self):
-        return self._db.__len__()
+        data = self.conn._fetchone(f"select count(*) as c from vrs_objects where vrs_object ->> 'type' = 'Allele'")
+        return data[0]
+
+    def deletion_count(self):
+        data = self.conn._fetchone(f"select count(*) as c from vrs_objects where length(vrs_object -> 'state' ->> 'sequence') = 0")
+        return data[0]
+
+    def substitution_count(self):
+        data = self.conn._fetchone(f"select count(*) as c from vrs_objects where length(vrs_object -> 'state' ->> 'sequence') = 1")
+        return data[0]
+
+    def insertion_count(self):
+        data = self.conn._fetchone(f"select count(*) as c from vrs_objects where length(vrs_object -> 'state' ->> 'sequence') > 1")
+        return data[0]
 
     def __iter__(self):
         return self._db.__iter__()

From eb1b0cf520f5f67c5791643c55339e5f0c5c2684 Mon Sep 17 00:00:00 2001
From: Jeremy Arbesfeld <jarbesfeld@gmail.com>
Date: Tue, 12 Jul 2022 18:06:44 -0400
Subject: [PATCH 2/2] set enum default to all

---
 src/anyvar/restapi/_data/openapi.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/anyvar/restapi/_data/openapi.yaml b/src/anyvar/restapi/_data/openapi.yaml
index 02127a5..5eefa52 100644
--- a/src/anyvar/restapi/_data/openapi.yaml
+++ b/src/anyvar/restapi/_data/openapi.yaml
@@ -448,6 +448,7 @@ paths:
           required: true
           schema:
             type: string
+            default: all
             enum:
               - substitution
               - deletion