From 0415dc7ff6b66029030df530c911e919046eb058 Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Fri, 16 Aug 2024 22:27:05 -0700
Subject: [PATCH 01/17] Adding mem based key-value driver and testing a python
 lib

---
 gripql/python/gripql/graph.py |   6 ++
 kvi/leveldb/memdb.go          | 168 ++++++++++++++++++++++++++++++++++
 pygrip_wrapper/new.go         |  15 +++
 3 files changed, 189 insertions(+)
 create mode 100644 kvi/leveldb/memdb.go
 create mode 100644 pygrip_wrapper/new.go

diff --git a/gripql/python/gripql/graph.py b/gripql/python/gripql/graph.py
index 2b64d02b0..ccfd20ca5 100644
--- a/gripql/python/gripql/graph.py
+++ b/gripql/python/gripql/graph.py
@@ -179,6 +179,12 @@ def query(self):
         """
         return Query(self.base_url, self.graph, self.user, self.password, self.token, self.credential_file)
 
+    def V(self, *args):
+        """
+        Create a vertex query handle.
+        """
+        return Query(self.base_url, self.graph, self.user, self.password, self.token, self.credential_file).V(*args)
+
     def resume(self, job_id):
         """
         Create a query handle.
diff --git a/kvi/leveldb/memdb.go b/kvi/leveldb/memdb.go
new file mode 100644
index 000000000..66e8c2752
--- /dev/null
+++ b/kvi/leveldb/memdb.go
@@ -0,0 +1,168 @@
+package leveldb
+
+import (
+	"bytes"
+	"fmt"
+
+	"github.com/bmeg/grip/kvi"
+	"github.com/bmeg/grip/log"
+	"github.com/syndtr/goleveldb/leveldb/comparer"
+	"github.com/syndtr/goleveldb/leveldb/iterator"
+	"github.com/syndtr/goleveldb/leveldb/memdb"
+)
+
+var mem_loaded = kvi.AddKVDriver("memdb", NewMemKVInterface)
+
+type LevelMemKV struct {
+	db *memdb.DB
+}
+
+// NewKVInterface creates new LevelDB backed KVInterface at `path`
+func NewMemKVInterface(path string, opts kvi.Options) (kvi.KVInterface, error) {
+	log.Info("Starting In-Memory LevelDB")
+	db := memdb.New(comparer.DefaultComparer, 1000)
+	return &LevelMemKV{db: db}, nil
+}
+
+// BulkWrite implements kvi.KVInterface.
+func (l *LevelMemKV) BulkWrite(u func(bl kvi.KVBulkWrite) error) error {
+	ktx := &memIterator{l.db, nil, true, nil, nil}
+	return u(ktx)
+}
+
+// Close implements kvi.KVInterface.
+func (l *LevelMemKV) Close() error {
+	return nil
+}
+
+// Delete implements kvi.KVInterface.
+func (l *LevelMemKV) Delete(key []byte) error {
+	return l.db.Delete(key)
+}
+
+// DeletePrefix implements kvi.KVInterface.
+func (l *LevelMemKV) DeletePrefix(prefix []byte) error {
+	deleteBlockSize := 10000
+	for found := true; found; {
+		found = false
+		wb := make([][]byte, 0, deleteBlockSize)
+		it := l.db.NewIterator(nil)
+		for it.Seek(prefix); it.Valid() && bytes.HasPrefix(it.Key(), prefix) && len(wb) < deleteBlockSize-1; it.Next() {
+			wb = append(wb, copyBytes(it.Key()))
+		}
+		it.Release()
+		for _, i := range wb {
+			l.db.Delete(i)
+			found = true
+		}
+	}
+	return nil
+
+}
+
+// Get implements kvi.KVInterface.
+func (l *LevelMemKV) Get(key []byte) ([]byte, error) {
+	return l.db.Get(key)
+}
+
+// HasKey implements kvi.KVInterface.
+func (l *LevelMemKV) HasKey(key []byte) bool {
+	_, err := l.db.Get(key)
+	return err == nil
+}
+
+// Set implements kvi.KVInterface.
+func (l *LevelMemKV) Set(key []byte, value []byte) error {
+	return l.db.Put(key, value)
+}
+
+// Update implements kvi.KVInterface.
+func (l *LevelMemKV) Update(func(tx kvi.KVTransaction) error) error {
+	panic("unimplemented")
+}
+
+// View implements kvi.KVInterface.
+func (l *LevelMemKV) View(u func(it kvi.KVIterator) error) error {
+	it := l.db.NewIterator(nil)
+	defer it.Release()
+	lit := memIterator{l.db, it, true, nil, nil}
+	return u(&lit)
+}
+
+type memIterator struct {
+	db      *memdb.DB
+	it      iterator.Iterator
+	forward bool
+	key     []byte
+	value   []byte
+}
+
+// Get retrieves the value of key `id`
+func (lit *memIterator) Get(id []byte) ([]byte, error) {
+	return lit.db.Get(id)
+}
+
+func (lit *memIterator) Set(key, val []byte) error {
+	return lit.db.Put(key, val)
+}
+
+// Key returns the key the iterator is currently pointed at
+func (lit *memIterator) Key() []byte {
+	return lit.key
+}
+
+// Value returns the valud of the iterator is currently pointed at
+func (lit *memIterator) Value() ([]byte, error) {
+	return lit.value, nil
+}
+
+// Next move the iterator to the next key
+func (lit *memIterator) Next() error {
+	var more bool
+	if lit.forward {
+		more = lit.it.Next()
+	} else {
+		more = lit.it.Prev()
+	}
+	if !more {
+		lit.key = nil
+		lit.value = nil
+		return fmt.Errorf("Invalid")
+	}
+	lit.key = copyBytes(lit.it.Key())
+	lit.value = copyBytes(lit.it.Value())
+	return nil
+}
+
+func (lit *memIterator) Seek(id []byte) error {
+	lit.forward = true
+	if lit.it.Seek(id) {
+		lit.key = copyBytes(lit.it.Key())
+		lit.value = copyBytes(lit.it.Value())
+		return nil
+	}
+	return fmt.Errorf("Invalid")
+}
+
+func (lit *memIterator) SeekReverse(id []byte) error {
+	lit.forward = false
+	if lit.it.Seek(id) {
+		//Level iterator will land on the first value above the request
+		//if we're there, move once to get below start request
+		if bytes.Compare(id, lit.it.Key()) < 0 {
+			lit.it.Prev()
+		}
+		lit.key = copyBytes(lit.it.Key())
+		lit.value = copyBytes(lit.it.Value())
+		return nil
+	}
+	return fmt.Errorf("Invalid")
+}
+
+// Valid returns true if iterator is still in valid location
+func (lit *memIterator) Valid() bool {
+	if lit.key == nil || lit.value == nil {
+		return false
+	}
+	return true
+}
diff --git a/pygrip_wrapper/new.go b/pygrip_wrapper/new.go
new file mode 100644
index 000000000..d8ddda4b0
--- /dev/null
+++ b/pygrip_wrapper/new.go
@@ -0,0 +1,15 @@
+package pygrip_wrapper
+
+import (
+	"fmt"
+
+	"github.com/bmeg/grip/gdbi"
+)
+
+func NewMemServer() gdbi.GraphDB {
+	fmt.Printf("I got this far\n")
+	//db, _ := leveldb.NewMemKVInterface("", kvi.Options{})
+	//graphdb := kvgraph.NewKVGraph(db)
+	//return graphdb
+	return nil
+}

From d352fa8bb1fca71fb6d1b035a2a54fee4b4fb604 Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Tue, 20 Aug 2024 21:17:49 -0700
Subject: [PATCH 02/17] Working python wrapper library

---
 gripql/python/gripql/query.py |  25 ++++--
 pygrip/Makefile               |   4 +
 pygrip/__init__.py            |  71 +++++++++++++++
 pygrip/pygrip.h               |  86 ++++++++++++++++++
 pygrip/wrapper.go             | 158 ++++++++++++++++++++++++++++++++++
 pygrip_wrapper/new.go         |  15 ----
 test/pygrip/pygrip_test.py    |  19 ++++
 7 files changed, 356 insertions(+), 22 deletions(-)
 create mode 100644 pygrip/Makefile
 create mode 100644 pygrip/__init__.py
 create mode 100644 pygrip/pygrip.h
 create mode 100644 pygrip/wrapper.go
 delete mode 100644 pygrip_wrapper/new.go
 create mode 100644 test/pygrip/pygrip_test.py

diff --git a/gripql/python/gripql/query.py b/gripql/python/gripql/query.py
index b9e8f1bc2..738c73f24 100644
--- a/gripql/python/gripql/query.py
+++ b/gripql/python/gripql/query.py
@@ -36,16 +36,13 @@ def _wrap_dict_value(value):
     return _wrap_value(value, dict)
 
 
-class Query(BaseConnection):
-    def __init__(self, url, graph, user=None, password=None, token=None, credential_file=None, resume=None):
-        super(Query, self).__init__(url, user, password, token, credential_file)
-        self.url = self.base_url + "/v1/graph/" + graph + "/query"
-        self.graph = graph
+class QueryBuilder:
+    def __init__(self):
         self.query = []
-        self.resume = resume
+        print("QueryBuilder_init_")
 
     def __append(self, part):
-        q = self.__class__(self.base_url, self.graph, self.user, self.password, self.token, self.credential_file, self.resume)
+        q = self._builder()
         q.query = self.query[:]
         q.query.append(part)
         return q
@@ -343,6 +340,20 @@ def to_dict(self):
         """
         return {"query": self.query}
 
+
+
+class Query(BaseConnection):
+    def __init__(self, url, graph, user=None, password=None, token=None, credential_file=None, resume=None):
+        super(Query, self).__init__(url, user, password, token, credential_file)
+        super(QueryBuilder, self).__init__(self.__new)
+        self.url = self.base_url + "/v1/graph/" + graph + "/query"
+        self.graph = graph
+        self.query = []
+        self.resume = resume
+
+    def __new(self):
+        return self.__class__(self.base_url, self.graph, self.user, self.password, self.token, self.credential_file, self.resume)
+
     def __iter__(self):
         return self.__stream()
 
diff --git a/pygrip/Makefile b/pygrip/Makefile
new file mode 100644
index 000000000..e3d2cad19
--- /dev/null
+++ b/pygrip/Makefile
@@ -0,0 +1,4 @@
+
+
+pygrip.so: wrapper.go
+	go build -o pygrip.so -buildmode=c-shared wrapper.go
diff --git a/pygrip/__init__.py b/pygrip/__init__.py
new file mode 100644
index 000000000..a691c8ff4
--- /dev/null
+++ b/pygrip/__init__.py
@@ -0,0 +1,71 @@
+
+
+from __future__ import print_function
+from ctypes import *
+import os, inspect
+import random, string
+import json
+from gripql.query import QueryBuilder
+
+cwd = os.getcwd()
+currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
+os.chdir(currentdir)
+_lib = cdll.LoadLibrary("./pygrip.so")
+os.chdir(cwd)
+
+_lib.ReaderNext.restype = c_char_p
+
+class GoString(Structure):
+    _fields_ = [("p", c_char_p), ("n", c_longlong)]
+
+def NewMemServer():
+    print(dir(_lib))
+    return GraphDBWrapper( _lib.NewMemServer() )
+
+def getGoString(s):
+    return GoString(bytes(s, encoding="raw_unicode_escape"), len(s))
+
+def id_generator(size=6, chars=string.ascii_uppercase + string.digits):
+    return ''.join(random.choice(chars) for _ in range(size))
+
+class QueryWrapper(QueryBuilder):
+    def __init__(self, wrapper):
+        super(QueryBuilder, self).__init__()
+        self.query = []
+        self.wrapper = wrapper
+
+    def __iter__(self):
+        jquery = json.dumps({ "graph" : "default", "query" : self.query })
+        reader = _lib.Query( self.wrapper._handle, getGoString(jquery) )
+        while not _lib.ReaderDone(reader):
+            j = _lib.ReaderNext(reader)
+            yield json.loads(j)
+
+    def _builder(self):
+        return QueryWrapper(self.wrapper)
+
+class GraphDBWrapper:
+    def __init__(self, handle) -> None:
+        self._handle = handle
+
+    def addVertex(self, gid, label, data={}):
+        """
+        Add vertex to a graph.
+        """
+        _lib.AddVertex(self._handle, getGoString(gid), getGoString(label), getGoString(json.dumps(data)))
+    
+    def addEdge(self, src, dst, label, data={}, gid=None):
+        """
+        Add edge to a graph.
+        """
+        if gid is None:
+            gid = id_generator(10)
+
+        _lib.AddEdge(self._handle, getGoString(gid), 
+                     getGoString(src), getGoString(dst), getGoString(label), 
+                     getGoString(json.dumps(data)))
+        
+
+
+    def V(self, *ids):
+        return QueryWrapper(self).V(*ids)
\ No newline at end of file
diff --git a/pygrip/pygrip.h b/pygrip/pygrip.h
new file mode 100644
index 000000000..db6abcf1c
--- /dev/null
+++ b/pygrip/pygrip.h
@@ -0,0 +1,86 @@
+/* Code generated by cmd/cgo; DO NOT EDIT. */
+
+/* package command-line-arguments */
+
+
+#line 1 "cgo-builtin-export-prolog"
+
+#include <stddef.h>
+
+#ifndef GO_CGO_EXPORT_PROLOGUE_H
+#define GO_CGO_EXPORT_PROLOGUE_H
+
+#ifndef GO_CGO_GOSTRING_TYPEDEF
+typedef struct { const char *p; ptrdiff_t n; } _GoString_;
+#endif
+
+#endif
+
+/* Start of preamble from import "C" comments.  */
+
+
+
+
+/* End of preamble from import "C" comments.  */
+
+
+/* Start of boilerplate cgo prologue.  */
+#line 1 "cgo-gcc-export-header-prolog"
+
+#ifndef GO_CGO_PROLOGUE_H
+#define GO_CGO_PROLOGUE_H
+
+typedef signed char GoInt8;
+typedef unsigned char GoUint8;
+typedef short GoInt16;
+typedef unsigned short GoUint16;
+typedef int GoInt32;
+typedef unsigned int GoUint32;
+typedef long long GoInt64;
+typedef unsigned long long GoUint64;
+typedef GoInt64 GoInt;
+typedef GoUint64 GoUint;
+typedef size_t GoUintptr;
+typedef float GoFloat32;
+typedef double GoFloat64;
+#ifdef _MSC_VER
+#include <complex.h>
+typedef _Fcomplex GoComplex64;
+typedef _Dcomplex GoComplex128;
+#else
+typedef float _Complex GoComplex64;
+typedef double _Complex GoComplex128;
+#endif
+
+/*
+  static assertion to make sure the file is being used on architecture
+  at least with matching size of GoInt.
+*/
+typedef char _check_for_64_bit_pointer_matching_GoInt[sizeof(void*)==64/8 ? 1:-1];
+
+#ifndef GO_CGO_GOSTRING_TYPEDEF
+typedef _GoString_ GoString;
+#endif
+typedef void *GoMap;
+typedef void *GoChan;
+typedef struct { void *t; void *v; } GoInterface;
+typedef struct { void *data; GoInt len; GoInt cap; } GoSlice;
+
+#endif
+
+/* End of boilerplate cgo prologue.  */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern GoUintptr NewMemServer();
+extern void AddVertex(GoUintptr graph, GoString gid, GoString label, GoString jdata);
+extern void AddEdge(GoUintptr graph, GoString gid, GoString src, GoString dst, GoString label, GoString jdata);
+extern GoUintptr Query(GoUintptr graph, GoString jquery);
+extern GoUint8 ReaderDone(GoUintptr reader);
+extern char* ReaderNext(GoUintptr reader);
+
+#ifdef __cplusplus
+}
+#endif
diff --git a/pygrip/wrapper.go b/pygrip/wrapper.go
new file mode 100644
index 000000000..033b947b1
--- /dev/null
+++ b/pygrip/wrapper.go
@@ -0,0 +1,158 @@
+package main
+
+/*
+#include <stdint.h> // for uintptr_t
+*/
+
+import "C"
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+
+	"runtime/cgo"
+
+	"github.com/bmeg/grip/engine"
+	"github.com/bmeg/grip/engine/core"
+	"github.com/bmeg/grip/engine/pipeline"
+	"github.com/bmeg/grip/gdbi"
+	"github.com/bmeg/grip/gripql"
+	"github.com/bmeg/grip/kvgraph"
+	"github.com/bmeg/grip/kvi"
+	"github.com/bmeg/grip/kvi/leveldb"
+	"google.golang.org/protobuf/encoding/protojson"
+)
+
+var graphDB gdbi.GraphDB
+
+type GraphHandle uintptr
+type QueryReaderHandle uintptr
+
+type Reader interface {
+	Done() bool
+	Next() string
+}
+
+//export NewMemServer
+func NewMemServer() GraphHandle {
+	db, _ := leveldb.NewMemKVInterface("", kvi.Options{})
+	graphDB = kvgraph.NewKVGraph(db)
+	err := graphDB.AddGraph("default")
+	if err != nil {
+		fmt.Printf("Graph init error: %s\n", err)
+	}
+	g, err := graphDB.Graph("default")
+	if err != nil {
+		fmt.Printf("Graph init error: %s\n", err)
+	}
+	return GraphHandle(cgo.NewHandle(g))
+}
+
+//export AddVertex
+func AddVertex(graph GraphHandle, gid, label, jdata string) {
+	data := map[string]any{}
+	err := json.Unmarshal([]byte(jdata), &data)
+	if err != nil {
+		fmt.Printf("Data error: %s : %s\n", err, jdata)
+	}
+
+	g := cgo.Handle(graph).Value().(gdbi.GraphInterface)
+
+	g.AddVertex([]*gdbi.Vertex{
+		{ID: gid, Label: label, Data: data},
+	})
+}
+
+//export AddEdge
+func AddEdge(graph GraphHandle, gid, src, dst, label, jdata string) {
+	data := map[string]any{}
+	err := json.Unmarshal([]byte(jdata), &data)
+	if err != nil {
+		fmt.Printf("Data error: %s : %s\n", err, jdata)
+	}
+
+	g := cgo.Handle(graph).Value().(gdbi.GraphInterface)
+
+	g.AddEdge([]*gdbi.Edge{
+		{ID: gid, To: dst, From: src, Label: label, Data: data},
+	})
+}
+
+type QueryReader struct {
+	pipe    gdbi.Pipeline
+	results chan *gripql.QueryResult
+	current *gripql.QueryResult
+}
+
+//export Query
+func Query(graph GraphHandle, jquery string) QueryReaderHandle {
+	query := gripql.GraphQuery{}
+	err := protojson.Unmarshal([]byte(jquery), &query)
+	if err != nil {
+		fmt.Printf("Query error: %s : %s\n", err)
+	}
+
+	g := cgo.Handle(graph).Value().(gdbi.GraphInterface)
+	compiler := core.NewCompiler(g)
+	pipe, err := compiler.Compile(query.Query, nil)
+	if err != nil {
+		fmt.Printf("Compile error: %s : %s\n", err)
+	}
+
+	ctx := context.Background()
+
+	bufsize := 5000
+	resch := make(chan *gripql.QueryResult, bufsize)
+	go func() {
+		defer close(resch)
+		graph := pipe.Graph()
+		dataType := pipe.DataType()
+		markTypes := pipe.MarkTypes()
+		man := engine.NewManager("./") //TODO: in memory option
+		rPipe := pipeline.Start(ctx, pipe, man, bufsize, nil, nil)
+		for t := range rPipe.Outputs {
+			if !t.IsSignal() {
+				resch <- pipeline.Convert(graph, dataType, markTypes, t)
+			}
+		}
+		man.Cleanup()
+	}()
+	var o = &QueryReader{
+		pipe:    pipe,
+		results: resch,
+		current: nil,
+	}
+	return QueryReaderHandle(cgo.NewHandle(o))
+}
+
+//export ReaderDone
+func ReaderDone(reader QueryReaderHandle) bool {
+	r := cgo.Handle(reader).Value().(*QueryReader)
+	return r.Done()
+}
+
+//export ReaderNext
+func ReaderNext(reader QueryReaderHandle) *C.char {
+	r := cgo.Handle(reader).Value().(*QueryReader)
+	o := r.Next()
+	return C.CString(o)
+}
+
+func (r *QueryReader) Next() string {
+	out, _ := protojson.Marshal(r.current)
+	return string(out)
+}
+
+func (r *QueryReader) Done() bool {
+	select {
+	case i, ok := <-r.results:
+		if ok {
+			r.current = i
+			return false
+		}
+		return true
+	}
+}
+
+func main() {}
diff --git a/pygrip_wrapper/new.go b/pygrip_wrapper/new.go
deleted file mode 100644
index d8ddda4b0..000000000
--- a/pygrip_wrapper/new.go
+++ /dev/null
@@ -1,15 +0,0 @@
-package pygrip_wrapper
-
-import (
-	"fmt"
-
-	"github.com/bmeg/grip/gdbi"
-)
-
-func NewMemServer() gdbi.GraphDB {
-	fmt.Printf("I got this far\n")
-	//db, _ := leveldb.NewMemKVInterface("", kvi.Options{})
-	//graphdb := kvgraph.NewKVGraph(db)
-	//return graphdb
-	return nil
-}
diff --git a/test/pygrip/pygrip_test.py b/test/pygrip/pygrip_test.py
new file mode 100644
index 000000000..8eb6e2e71
--- /dev/null
+++ b/test/pygrip/pygrip_test.py
@@ -0,0 +1,19 @@
+import pygrip
+
+w = pygrip.NewMemServer()
+
+
+w.addVertex("1", "Person", {"age":30, "eyes":"brown"})
+w.addVertex("2", "Person", {"age":40, "eyes":"blue"})
+
+w.addEdge("1", "2", "knows")
+
+for row in w.V().hasLabel("Person"):
+    print("hasLabel", row)
+
+for row in w.V().out("knows"):
+    print("out", row)
+
+for row in w.V().count():
+    print("count", row)
+

From 80b165211a65c53107135fa9d75b6b5553711ffd Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Tue, 20 Aug 2024 22:07:53 -0700
Subject: [PATCH 03/17] Fixing client

---
 gripql/python/gripql/query.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gripql/python/gripql/query.py b/gripql/python/gripql/query.py
index 738c73f24..728658d84 100644
--- a/gripql/python/gripql/query.py
+++ b/gripql/python/gripql/query.py
@@ -39,7 +39,6 @@ def _wrap_dict_value(value):
 class QueryBuilder:
     def __init__(self):
         self.query = []
-        print("QueryBuilder_init_")
 
     def __append(self, part):
         q = self._builder()
@@ -342,16 +341,16 @@ def to_dict(self):
 
 
 
-class Query(BaseConnection):
+class Query(BaseConnection, QueryBuilder):
     def __init__(self, url, graph, user=None, password=None, token=None, credential_file=None, resume=None):
         super(Query, self).__init__(url, user, password, token, credential_file)
-        super(QueryBuilder, self).__init__(self.__new)
+        super(QueryBuilder, self).__init__()
         self.url = self.base_url + "/v1/graph/" + graph + "/query"
         self.graph = graph
         self.query = []
         self.resume = resume
 
-    def __new(self):
+    def _builder(self):
         return self.__class__(self.base_url, self.graph, self.user, self.password, self.token, self.credential_file, self.resume)
 
     def __iter__(self):

From 4e79dd7aae24b5d5aa88c060a17a3a05ad08a17c Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Thu, 22 Aug 2024 15:02:04 -0700
Subject: [PATCH 04/17] Adding setup.py for pygrip

---
 gripql/python/gripql/__init__.py |  2 +-
 pygrip/__init__.py               |  5 +++--
 setup.py                         | 33 ++++++++++++++++++++++++++++++++
 3 files changed, 37 insertions(+), 3 deletions(-)
 create mode 100644 setup.py

diff --git a/gripql/python/gripql/__init__.py b/gripql/python/gripql/__init__.py
index 8cc78e544..bbacd739d 100644
--- a/gripql/python/gripql/__init__.py
+++ b/gripql/python/gripql/__init__.py
@@ -36,4 +36,4 @@
     count
 ]
 
-__version__ = "0.7.1"
+__version__ = "0.8.0"
diff --git a/pygrip/__init__.py b/pygrip/__init__.py
index a691c8ff4..df19dd8cd 100644
--- a/pygrip/__init__.py
+++ b/pygrip/__init__.py
@@ -2,7 +2,8 @@
 
 from __future__ import print_function
 from ctypes import *
-import os, inspect
+from ctypes.util import find_library
+import os, inspect, sysconfig
 import random, string
 import json
 from gripql.query import QueryBuilder
@@ -10,7 +11,7 @@
 cwd = os.getcwd()
 currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
 os.chdir(currentdir)
-_lib = cdll.LoadLibrary("./pygrip.so")
+_lib = cdll.LoadLibrary("./_pygrip" + sysconfig.get_config_vars()["EXT_SUFFIX"])
 os.chdir(cwd)
 
 _lib.ReaderNext.restype = c_char_p
diff --git a/setup.py b/setup.py
new file mode 100644
index 000000000..4dba5c58c
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,33 @@
+"""Setup for checksig package"""
+import sys
+from distutils.errors import CompileError
+from subprocess import call
+
+from setuptools import Extension, setup, find_packages
+from setuptools.command.build_ext import build_ext
+ 
+
+class build_go_ext(build_ext):
+    """Custom command to build extension from Go source files"""
+    def build_extension(self, ext):
+        ext_path = self.get_ext_fullpath(ext.name)
+        cmd = ['go', 'build', '-buildmode=c-shared', '-o', ext_path]
+        cmd += ext.sources
+        out = call(cmd)
+        if out != 0:
+            raise CompileError('Go build failed')
+
+setup(
+    name='pygrip',
+    version='0.8.0',
+    packages=find_packages(include=['pygrip']), 
+    #py_modules=['pygrip'],
+    ext_modules=[
+        Extension('pygrip/_pygrip', ['./pygrip/wrapper.go'])
+    ],
+    cmdclass={'build_ext': build_go_ext},
+    install_requires=[
+        "gripql>=0.8.0"
+    ],
+    zip_safe=False,
+)
\ No newline at end of file

From ebc227afba7bd0555b720e60c0ced4205c184966 Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Thu, 22 Aug 2024 15:34:56 -0700
Subject: [PATCH 05/17] Working on adding unit tests

---
 .github/workflows/tests.yml | 20 ++++++++++++++++++--
 pygrip/__init__.py          |  1 +
 test/pygrip/pygrip_test.py  | 19 -------------------
 3 files changed, 19 insertions(+), 21 deletions(-)
 delete mode 100644 test/pygrip/pygrip_test.py

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 91ef26d2e..fb4bf88cc 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -233,8 +233,24 @@ jobs:
           fi          
           # run specialized role based tests
           make test-authorization ARGS="--grip_config_file_path test/badger-auth.yml"
-  
-    
+
+  pygripTest:
+    needs: build
+    name: PyGrip UnitTest
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v2
+      - name: Python Dependencies for Conformance
+        run: pip install requests numpy PyYAML
+      - name: install gripql
+        run: |
+          cd gripql/python
+          python setup.py install
+      - name: install gripql
+        run: |
+          python setup.py install
+      
     
 
     #gridsTest:
diff --git a/pygrip/__init__.py b/pygrip/__init__.py
index df19dd8cd..3aa41f97c 100644
--- a/pygrip/__init__.py
+++ b/pygrip/__init__.py
@@ -10,6 +10,7 @@
 
 cwd = os.getcwd()
 currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
+print("cd to %s" % (currentdir))
 os.chdir(currentdir)
 _lib = cdll.LoadLibrary("./_pygrip" + sysconfig.get_config_vars()["EXT_SUFFIX"])
 os.chdir(cwd)
diff --git a/test/pygrip/pygrip_test.py b/test/pygrip/pygrip_test.py
deleted file mode 100644
index 8eb6e2e71..000000000
--- a/test/pygrip/pygrip_test.py
+++ /dev/null
@@ -1,19 +0,0 @@
-import pygrip
-
-w = pygrip.NewMemServer()
-
-
-w.addVertex("1", "Person", {"age":30, "eyes":"brown"})
-w.addVertex("2", "Person", {"age":40, "eyes":"blue"})
-
-w.addEdge("1", "2", "knows")
-
-for row in w.V().hasLabel("Person"):
-    print("hasLabel", row)
-
-for row in w.V().out("knows"):
-    print("out", row)
-
-for row in w.V().count():
-    print("count", row)
-

From da288a3f74a4e5ec528483f7145d76d39ba9d957 Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Thu, 22 Aug 2024 15:44:09 -0700
Subject: [PATCH 06/17] Doing user install for python

---
 .github/workflows/tests.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index fb4bf88cc..fa47bc2ea 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -246,10 +246,10 @@ jobs:
       - name: install gripql
         run: |
           cd gripql/python
-          python setup.py install
-      - name: install gripql
+          python setup.py install --user
+      - name: install pygrip
         run: |
-          python setup.py install
+          python setup.py install --user
       
     
 

From cf3613cf30f71131ac5427f4ad206c6370953722 Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Thu, 22 Aug 2024 15:51:33 -0700
Subject: [PATCH 07/17] add step to actually run the pygrip unit tests

---
 .github/workflows/tests.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index fa47bc2ea..d5e51e998 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -250,9 +250,10 @@ jobs:
       - name: install pygrip
         run: |
           python setup.py install --user
-      
-    
-
+      - name: unit tests
+        run: |
+          python -m unittest discover -s ./test/pygrip      
+  
     #gridsTest:
     #  needs: build
     #  name: GRIDs Conformance

From 1441f5dc39f79af5ad4e7aea35f3f799760bfc85 Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Thu, 22 Aug 2024 15:55:47 -0700
Subject: [PATCH 08/17] Adding missing file

---
 test/pygrip/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 test/pygrip/__init__.py

diff --git a/test/pygrip/__init__.py b/test/pygrip/__init__.py
new file mode 100644
index 000000000..e69de29bb

From 2200d28413c56b57b0bd037f067ae8148c913c22 Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Thu, 22 Aug 2024 16:04:16 -0700
Subject: [PATCH 09/17] Debugging unit test running

---
 .github/workflows/tests.yml              |  3 ++-
 pygrip/__init__.py                       |  4 ++--
 test/{pygrip => pygrip_test}/__init__.py |  0
 test/pygrip_test/test_pygrip.py          | 29 ++++++++++++++++++++++++
 4 files changed, 33 insertions(+), 3 deletions(-)
 rename test/{pygrip => pygrip_test}/__init__.py (100%)
 create mode 100644 test/pygrip_test/test_pygrip.py

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index d5e51e998..5ea5226e7 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -252,7 +252,8 @@ jobs:
           python setup.py install --user
       - name: unit tests
         run: |
-          python -m unittest discover -s ./test/pygrip      
+          cd test
+          python -m unittest discover -s ./pygrip_test
   
     #gridsTest:
     #  needs: build
diff --git a/pygrip/__init__.py b/pygrip/__init__.py
index 3aa41f97c..d04f14c13 100644
--- a/pygrip/__init__.py
+++ b/pygrip/__init__.py
@@ -10,7 +10,8 @@
 
 cwd = os.getcwd()
 currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
-print("cd to %s" % (currentdir))
+#print("frame: %s" % (inspect.getfile(inspect.currentframe())))
+#print("cd to %s" % (currentdir))
 os.chdir(currentdir)
 _lib = cdll.LoadLibrary("./_pygrip" + sysconfig.get_config_vars()["EXT_SUFFIX"])
 os.chdir(cwd)
@@ -21,7 +22,6 @@ class GoString(Structure):
     _fields_ = [("p", c_char_p), ("n", c_longlong)]
 
 def NewMemServer():
-    print(dir(_lib))
     return GraphDBWrapper( _lib.NewMemServer() )
 
 def getGoString(s):
diff --git a/test/pygrip/__init__.py b/test/pygrip_test/__init__.py
similarity index 100%
rename from test/pygrip/__init__.py
rename to test/pygrip_test/__init__.py
diff --git a/test/pygrip_test/test_pygrip.py b/test/pygrip_test/test_pygrip.py
new file mode 100644
index 000000000..a21f881d2
--- /dev/null
+++ b/test/pygrip_test/test_pygrip.py
@@ -0,0 +1,29 @@
+
+import pygrip
+import unittest
+
+class TestPyGRIP(unittest.TestCase):
+
+    def test_query(self):
+
+        w = pygrip.NewMemServer()
+
+        w.addVertex("1", "Person", {"age":30, "eyes":"brown"})
+        w.addVertex("2", "Person", {"age":40, "eyes":"blue"})
+        w.addEdge("1", "2", "knows")
+
+        count = 0
+        for row in w.V().hasLabel("Person"):
+            count += 1        
+        self.assertEqual(count, 2)
+
+        count = 0
+        for row in w.V().out("knows"):
+            count += 1
+        self.assertEqual(count, 1)
+        
+        for row in w.V().count():
+            self.assertEqual(row["count"], 2)
+
+if __name__ == '__main__':
+    unittest.main()

From 7421fe8260e2d8ecbd70680250d62ec1cc087088 Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Wed, 28 Aug 2024 11:13:31 -0700
Subject: [PATCH 10/17] Removing stdout error statements

---
 pygrip/__init__.py |  3 ++-
 pygrip/wrapper.go  | 18 +++++++++++-------
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/pygrip/__init__.py b/pygrip/__init__.py
index d04f14c13..33964bf1a 100644
--- a/pygrip/__init__.py
+++ b/pygrip/__init__.py
@@ -54,7 +54,8 @@ def addVertex(self, gid, label, data={}):
         """
         Add vertex to a graph.
         """
-        _lib.AddVertex(self._handle, getGoString(gid), getGoString(label), getGoString(json.dumps(data)))
+        _lib.AddVertex(self._handle, getGoString(gid), getGoString(label), 
+                       getGoString(json.dumps(data)))
     
     def addEdge(self, src, dst, label, data={}, gid=None):
         """
diff --git a/pygrip/wrapper.go b/pygrip/wrapper.go
index 033b947b1..0657f2c81 100644
--- a/pygrip/wrapper.go
+++ b/pygrip/wrapper.go
@@ -9,7 +9,6 @@ import "C"
 import (
 	"context"
 	"encoding/json"
-	"fmt"
 
 	"runtime/cgo"
 
@@ -21,6 +20,7 @@ import (
 	"github.com/bmeg/grip/kvgraph"
 	"github.com/bmeg/grip/kvi"
 	"github.com/bmeg/grip/kvi/leveldb"
+	"github.com/bmeg/grip/log"
 	"google.golang.org/protobuf/encoding/protojson"
 )
 
@@ -40,21 +40,25 @@ func NewMemServer() GraphHandle {
 	graphDB = kvgraph.NewKVGraph(db)
 	err := graphDB.AddGraph("default")
 	if err != nil {
-		fmt.Printf("Graph init error: %s\n", err)
+		log.Errorf("Graph init error: %s\n", err)
 	}
 	g, err := graphDB.Graph("default")
 	if err != nil {
-		fmt.Printf("Graph init error: %s\n", err)
+		log.Errorf("Graph init error: %s\n", err)
 	}
 	return GraphHandle(cgo.NewHandle(g))
 }
 
+func CloseServer(graph GraphHandle) {
+	cgo.Handle(graph).Delete()
+}
+
 //export AddVertex
 func AddVertex(graph GraphHandle, gid, label, jdata string) {
 	data := map[string]any{}
 	err := json.Unmarshal([]byte(jdata), &data)
 	if err != nil {
-		fmt.Printf("Data error: %s : %s\n", err, jdata)
+		log.Errorf("Data error: %s : %s\n", err, jdata)
 	}
 
 	g := cgo.Handle(graph).Value().(gdbi.GraphInterface)
@@ -69,7 +73,7 @@ func AddEdge(graph GraphHandle, gid, src, dst, label, jdata string) {
 	data := map[string]any{}
 	err := json.Unmarshal([]byte(jdata), &data)
 	if err != nil {
-		fmt.Printf("Data error: %s : %s\n", err, jdata)
+		log.Errorf("Data error: %s : %s\n", err, jdata)
 	}
 
 	g := cgo.Handle(graph).Value().(gdbi.GraphInterface)
@@ -90,14 +94,14 @@ func Query(graph GraphHandle, jquery string) QueryReaderHandle {
 	query := gripql.GraphQuery{}
 	err := protojson.Unmarshal([]byte(jquery), &query)
 	if err != nil {
-		fmt.Printf("Query error: %s : %s\n", err)
+		log.Errorf("Query error: %s : %s\n", err)
 	}
 
 	g := cgo.Handle(graph).Value().(gdbi.GraphInterface)
 	compiler := core.NewCompiler(g)
 	pipe, err := compiler.Compile(query.Query, nil)
 	if err != nil {
-		fmt.Printf("Compile error: %s : %s\n", err)
+		log.Errorf("Compile error: %s : %s\n", err)
 	}
 
 	ctx := context.Background()

From 0467c4e79bdc379b8a32acee9c207ff46b7e244f Mon Sep 17 00:00:00 2001
From: Brian Walsh <brian@bwalsh.com>
Date: Wed, 28 Aug 2024 16:56:46 -0700
Subject: [PATCH 11/17] adds pythonpath for pytest

---
 pytest.ini | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 pytest.ini

diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 000000000..fdfcb6508
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,2 @@
+[pytest]
+pythonpath = . gripql/python  grip

From 0b16fbe1f09527963066868963c0199728ec0393 Mon Sep 17 00:00:00 2001
From: Brian Walsh <brian@bwalsh.com>
Date: Wed, 28 Aug 2024 16:57:30 -0700
Subject: [PATCH 12/17] make ./test a package

---
 test/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 test/__init__.py

diff --git a/test/__init__.py b/test/__init__.py
new file mode 100644
index 000000000..e69de29bb

From 951532272beb3a1b7d393f22aa476e2445da8f35 Mon Sep 17 00:00:00 2001
From: Brian Walsh <brian@bwalsh.com>
Date: Wed, 28 Aug 2024 16:59:22 -0700
Subject: [PATCH 13/17] test FHIR load, dataframe traversals

test FHIR load

adds jsonpath-ng for reference searches

improves traversal tests
---
 test/pygrip_test/fhir/README.md               |   5 +
 test/pygrip_test/fhir/__init__.py             |   0
 .../META/DocumentReference.ndjson             |   1 +
 .../META/Observation.ndjson                   |   3 +
 .../META/Organization.ndjson                  |   1 +
 .../fhir-compbio-examples/META/Patient.ndjson |   1 +
 .../META/ResearchStudy.ndjson                 |   1 +
 .../META/ResearchSubject.ndjson               |   1 +
 .../META/Specimen.ndjson                      |   1 +
 .../fixtures/fhir-compbio-examples/README.md  |  11 +
 test/pygrip_test/fhir/test_load.py            | 264 ++++++++++++++++++
 11 files changed, 289 insertions(+)
 create mode 100644 test/pygrip_test/fhir/README.md
 create mode 100644 test/pygrip_test/fhir/__init__.py
 create mode 100644 test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/DocumentReference.ndjson
 create mode 100644 test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Observation.ndjson
 create mode 100644 test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Organization.ndjson
 create mode 100644 test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Patient.ndjson
 create mode 100644 test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/ResearchStudy.ndjson
 create mode 100644 test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/ResearchSubject.ndjson
 create mode 100644 test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Specimen.ndjson
 create mode 100644 test/pygrip_test/fhir/fixtures/fhir-compbio-examples/README.md
 create mode 100644 test/pygrip_test/fhir/test_load.py

diff --git a/test/pygrip_test/fhir/README.md b/test/pygrip_test/fhir/README.md
new file mode 100644
index 000000000..c41134976
--- /dev/null
+++ b/test/pygrip_test/fhir/README.md
@@ -0,0 +1,5 @@
+This test has a dependency
+```commandline
+pip install  jsonpath-ng
+
+```
\ No newline at end of file
diff --git a/test/pygrip_test/fhir/__init__.py b/test/pygrip_test/fhir/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/DocumentReference.ndjson b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/DocumentReference.ndjson
new file mode 100644
index 000000000..8da14c2b2
--- /dev/null
+++ b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/DocumentReference.ndjson
@@ -0,0 +1 @@
+{"resourceType":"DocumentReference","id":"9ae7e542-767f-4b03-a854-7ceed17152cb","identifier":[{"use":"official","system":"https://my_demo.org/labA","value":"9ae7e542-767f-4b03-a854-7ceed17152cb"}],"status":"current","docStatus":"final","subject":{"reference":"Specimen/60c67a06-ea2d-4d24-9249-418dc77a16a9"},"date":"2024-08-21T10:53:00+00:00","content":[{"attachment":{"extension":[{"url":"http://aced-idp.org/fhir/StructureDefinition/md5","valueString":"227f0a5379362d42eaa1814cfc0101b8"},{"url":"http://aced-idp.org/fhir/StructureDefinition/source_path","valueUrl":"file:///home/LabA/specimen_1234_labA.fq.gz"}],"contentType":"text/fastq","url":"file:///home/LabA/specimen_1234_labA.fq.gz","size":5595609484,"title":"specimen_1234_labA.fq.gz","creation":"2024-08-21T10:53:00+00:00"}}]}
\ No newline at end of file
diff --git a/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Observation.ndjson b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Observation.ndjson
new file mode 100644
index 000000000..774b7051d
--- /dev/null
+++ b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Observation.ndjson
@@ -0,0 +1,3 @@
+{"resourceType":"Observation","id":"cec32723-9ede-5f24-ba63-63cb8c6a02cf","identifier":[{"use":"official","system":"https://my_demo.org/labA","value":"patientX_1234-9ae7e542-767f-4b03-a854-7ceed17152cb-sequencer"}], "status":"final","category":[{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/observation-category","code":"laboratory","display":"Laboratory"}]}],"code":{"coding":[{"system":"https://my_demo.org/labA","code":"Gen3 Sequencing Metadata","display":"Gen3 Sequencing Metadata"}]},"subject":{"reference":"Patient/bc4e1aa6-cb52-40e9-8f20-594d9c84f920"},"focus":[{"reference":"DocumentReference/9ae7e542-767f-4b03-a854-7ceed17152cb"}],"specimen":{"reference":"Specimen/60c67a06-ea2d-4d24-9249-418dc77a16a9"},"component":[{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"sequencer","display":"sequencer"}],"text":"sequencer"},"valueString":"Illumina Seq 1000"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"index","display":"index"}],"text":"index"},"valueString":"100bp Single index"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"type","display":"type"}],"text":"type"},"valueString":"Exome"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"project_id","display":"project_id"}],"text":"project_id"},"valueString":"labA_projectXYZ"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"read_length","display":"read_length"}],"text":"read_length"},"valueString":"100"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"instrument_run_id","display":"instrument_run_id"}],"text":"instrument_run_id"},"valueString":"234_ABC_1_8899"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"capture_bait_set","display":"capture_bait_set"}],"text":"capture_bait_set"},"valueString":"Human Exom 2X"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"end_type","display":"end_type"}],"text":"end_type"},"valueString":"Paired-End"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"capture","display":"capture"}],"text":"capture"},"valueString":"emitter XT"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"sequencing_site","display":"sequencing_site"}],"text":"sequencing_site"},"valueString":"AdvancedGeneExom"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"construction","display":"construction"}],"text":"construction"},"valueString":"library_construction"}]}
+{"resourceType":"Observation","id":"4e3c6b59-b1fd-5c26-a611-da4cde9fd061","identifier":[{"use":"official","system":"https://my_demo.org/labA","value":"patientX_1234-specimen_1234_labA-sample_type"}],"status":"final","category":[{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/observation-category","code":"laboratory","display":"Laboratory"}],"text":"Laboratory"}],"code":{"coding":[{"system":"https://my_demo.org/labA","code":"labA specimen metadata","display":"labA specimen metadata"}],"text":"sample type abc"},"subject":{"reference":"Patient/bc4e1aa6-cb52-40e9-8f20-594d9c84f920"},"focus":[{"reference":"Specimen/60c67a06-ea2d-4d24-9249-418dc77a16a9"}],"component":[{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"sample_type","display":"sample_type"}],"text":"sample_type"},"valueString":"Primary Solid Tumor"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"library_id","display":"library_id"}],"text":"library_id"},"valueString":"12345"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"tissue_type","display":"tissue_type"}],"text":"tissue_type"},"valueString":"Tumor"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"treatments","display":"treatments"}],"text":"treatments"},"valueString":"Trastuzumab"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"allocated_for_site","display":"allocated_for_site"}],"text":"allocated_for_site"},"valueString":"TEST Clinical Research"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"pathology_data","display":"pathology_data"}],"text":"pathology_data"}},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"clinical_event","display":"clinical_event"}],"text":"clinical_event"}},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"indexed_collection_date","display":"indexed_collection_date"}],"text":"indexed_collection_date"},"valueInteger":365},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"biopsy_specimens_bems_id","display":"biopsy_specimens_bems_id"}],"text":"biopsy_specimens"},"valueString":"specimenA, specimenB, specimenC"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"biopsy_procedure_type","display":"biopsy_procedure_type"}],"text":"biopsy_procedure_type"},"valueString":"Biopsy - Core"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"biopsy_anatomical_location","display":"biopsy_anatomical_location"}],"text":"biopsy_anatomical_location"},"valueString":"top axillary lymph node"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"percent_tumor","display":"percent_tumor"}],"text":"percent_tumor"},"valueString":"30"}]}
+{"resourceType":"Observation","id":"21f3411d-89a4-4bcc-9ce7-b76edb1c745f","identifier":[{"use":"official","system":"https://my_demo.org/labA","value":"patientX_1234-9ae7e542-767f-4b03-a854-7ceed17152cb-Gene"}], "status":"final","category":[{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/observation-category","code":"laboratory","display":"Laboratory"}]}],"code":{"coding":[{"system":"https://loinc.org","code":"81247-9","display":"Genomic structural variant copy number"}]},"subject":{"reference":"Patient/bc4e1aa6-cb52-40e9-8f20-594d9c84f920"},"focus":[{"reference":"DocumentReference/9ae7e542-767f-4b03-a854-7ceed17152cb"}],"specimen":{"reference":"Specimen/60c67a06-ea2d-4d24-9249-418dc77a16a9"},"component":[{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"Gene","display":"Gene"}],"text":"Gene"},"valueString":"TP53"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"Chromosome","display":"Chromosome"}],"text":"Chromosome"},"valueString":"chr17"},{"code":{"coding":[{"system":"https://my_demo.org/labA","code":"result","display":"result"}],"text":"result"},"valueString":"gain of function (GOF)"}]}
\ No newline at end of file
diff --git a/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Organization.ndjson b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Organization.ndjson
new file mode 100644
index 000000000..967445ae7
--- /dev/null
+++ b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Organization.ndjson
@@ -0,0 +1 @@
+{"resourceType":"Organization","id":"89c8dc4c-2d9c-48c7-8862-241a49a78f14","identifier":[{"use":"official","system":"https://my_demo.org/labA","value":"LabA_ORGANIZATION"}],"type":[{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/organization-type","code":"prov","display":"Healthcare Provider"}],"text":"An organization that provides healthcare services."},{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/organization-type","code":"edu","display":"Educational Institute"}],"text":"An educational institution that provides education or research facilities."}]}
\ No newline at end of file
diff --git a/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Patient.ndjson b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Patient.ndjson
new file mode 100644
index 000000000..107bf78e5
--- /dev/null
+++ b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Patient.ndjson
@@ -0,0 +1 @@
+{"resourceType":"Patient","id":"bc4e1aa6-cb52-40e9-8f20-594d9c84f920","identifier":[{"use":"official","system":"https://my_demo.org/labA","value":"patientX_1234"}],"active":true}
\ No newline at end of file
diff --git a/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/ResearchStudy.ndjson b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/ResearchStudy.ndjson
new file mode 100644
index 000000000..74cc40029
--- /dev/null
+++ b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/ResearchStudy.ndjson
@@ -0,0 +1 @@
+{"resourceType":"ResearchStudy","id":"7dacd4d0-3c8e-470b-bf61-103891627d45","identifier":[{"use":"official","system":"https://my_demo.org/labA","value":"labA"}],"name":"LabA","status":"active","description":"LabA Clinical Trial Study: FHIR Schema Chorot Integration"}
\ No newline at end of file
diff --git a/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/ResearchSubject.ndjson b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/ResearchSubject.ndjson
new file mode 100644
index 000000000..6aee6d082
--- /dev/null
+++ b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/ResearchSubject.ndjson
@@ -0,0 +1 @@
+{"resourceType":"ResearchSubject","id":"2fc448d6-a23b-4b94-974b-c66110164851","identifier":[{"use":"official","system":"https://my_demo.org/labA","value":"subjectX_1234"}],"status":"active","study":{"reference":"ResearchStudy/7dacd4d0-3c8e-470b-bf61-103891627d45"},"subject":{"reference":"Patient/bc4e1aa6-cb52-40e9-8f20-594d9c84f920"}}
\ No newline at end of file
diff --git a/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Specimen.ndjson b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Specimen.ndjson
new file mode 100644
index 000000000..b79c72cbf
--- /dev/null
+++ b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/META/Specimen.ndjson
@@ -0,0 +1 @@
+{"resourceType":"Specimen","id":"60c67a06-ea2d-4d24-9249-418dc77a16a9","identifier":[{"use":"official","system":"https://my_demo.org/labA","value":"specimen_1234_labA"}],"subject":{"reference":"Patient/bc4e1aa6-cb52-40e9-8f20-594d9c84f920"},"collection":{"collector":{"reference":"Organization/89c8dc4c-2d9c-48c7-8862-241a49a78f14"},"bodySite":{"concept":{"coding":[{"system":"http://snomed.info/sct","code":"76752008","display":"Breast"}],"text":"Breast"}}},"processing":[{"method":{"coding":[{"system":"http://snomed.info/sct","code":"117032008","display":"Spun specimen (procedure)"},{"system":"https://my_demo.org/labA","code":"Double-Spun","display":"Double-Spun"}],"text":"Spun specimen (procedure)"}}]}
\ No newline at end of file
diff --git a/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/README.md b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/README.md
new file mode 100644
index 000000000..bcad0e36e
--- /dev/null
+++ b/test/pygrip_test/fhir/fixtures/fhir-compbio-examples/README.md
@@ -0,0 +1,11 @@
+##### META folder test-data:
+
+```
+>>>> resources={'summary': {'DocumentReference': 1, 'Specimen': 1, 'Observation': 3, 'ResearchStudy': 1, 'ResearchSubject': 1, 'Organization': 1, 'Patient': 1}}
+```
+
+There are three Observations with user-defined metadata component. 
+1. Focus - reference -> Specimen
+2. Focus - reference -> DocumentReference 
+   1. The first Observation contains metadata on the file's sequencing metadata.
+   2. The second Observation includes a simple summary of a CNV analysis result computed from this file.
diff --git a/test/pygrip_test/fhir/test_load.py b/test/pygrip_test/fhir/test_load.py
new file mode 100644
index 000000000..6446749b6
--- /dev/null
+++ b/test/pygrip_test/fhir/test_load.py
@@ -0,0 +1,264 @@
+import json
+import pathlib
+import types
+from collections import defaultdict
+
+import pytest
+
+import pygrip
+from jsonpath_ng import jsonpath, parse
+
+from typing import Generator, Dict, Any
+
+
+def resources() -> Generator[Dict[str, Any], None, None]:
+    """Read a directory of ndjson files, return dictionary for each line."""
+    base = pathlib.Path(__file__).parent.absolute()
+    fixture_path = pathlib.Path(base / 'fixtures' / 'fhir-compbio-examples' / 'META')
+    assert fixture_path.exists(), f"Fixture path {fixture_path.absolute()} does not exist."
+    for file in fixture_path.glob('*.ndjson'):
+        with open(str(file)) as fp:
+            for l_ in fp.readlines():
+                yield json.loads(l_)
+
+
+@pytest.fixture
+def expected_edges() -> list[tuple]:
+    """Return the expected edges for the resources."""
+    return [('21f3411d-89a4-4bcc-9ce7-b76edb1c745f', '60c67a06-ea2d-4d24-9249-418dc77a16a9', 'specimen'),
+            ('21f3411d-89a4-4bcc-9ce7-b76edb1c745f', '9ae7e542-767f-4b03-a854-7ceed17152cb', 'focus'),
+            ('21f3411d-89a4-4bcc-9ce7-b76edb1c745f', 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920', 'subject'),
+            ('2fc448d6-a23b-4b94-974b-c66110164851', '7dacd4d0-3c8e-470b-bf61-103891627d45', 'study'),
+            ('2fc448d6-a23b-4b94-974b-c66110164851', 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920', 'subject'),
+            ('4e3c6b59-b1fd-5c26-a611-da4cde9fd061', '60c67a06-ea2d-4d24-9249-418dc77a16a9', 'focus'),
+            ('4e3c6b59-b1fd-5c26-a611-da4cde9fd061', 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920', 'subject'),
+            ('60c67a06-ea2d-4d24-9249-418dc77a16a9', '89c8dc4c-2d9c-48c7-8862-241a49a78f14', 'collection_collector'),
+            ('60c67a06-ea2d-4d24-9249-418dc77a16a9', 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920', 'subject'),
+            ('9ae7e542-767f-4b03-a854-7ceed17152cb', '60c67a06-ea2d-4d24-9249-418dc77a16a9', 'subject'),
+            ('cec32723-9ede-5f24-ba63-63cb8c6a02cf', '60c67a06-ea2d-4d24-9249-418dc77a16a9', 'specimen'),
+            ('cec32723-9ede-5f24-ba63-63cb8c6a02cf', '9ae7e542-767f-4b03-a854-7ceed17152cb', 'focus'),
+            ('cec32723-9ede-5f24-ba63-63cb8c6a02cf', 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920', 'subject')]
+
+
+@pytest.fixture
+def expected_vertices() -> list[tuple]:
+    """Return the expected vertices (only id, label) for the resources."""
+    return [('21f3411d-89a4-4bcc-9ce7-b76edb1c745f', 'Observation'),
+            ('2fc448d6-a23b-4b94-974b-c66110164851', 'ResearchSubject'),
+            ('4e3c6b59-b1fd-5c26-a611-da4cde9fd061', 'Observation'),
+            ('60c67a06-ea2d-4d24-9249-418dc77a16a9', 'Specimen'),
+            ('7dacd4d0-3c8e-470b-bf61-103891627d45', 'ResearchStudy'),
+            ('89c8dc4c-2d9c-48c7-8862-241a49a78f14', 'Organization'),
+            ('9ae7e542-767f-4b03-a854-7ceed17152cb', 'DocumentReference'),
+            ('bc4e1aa6-cb52-40e9-8f20-594d9c84f920', 'Patient'),
+            ('cec32723-9ede-5f24-ba63-63cb8c6a02cf', 'Observation')]
+
+
+@pytest.fixture
+def expected_dataframe_associations():
+    return {
+        ('ResearchSubject', '2fc448d6-a23b-4b94-974b-c66110164851'): [
+            ('ResearchStudy', '7dacd4d0-3c8e-470b-bf61-103891627d45'),
+            ('Patient', 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920'),
+            ('Specimen', '60c67a06-ea2d-4d24-9249-418dc77a16a9')],
+        ('Specimen', '60c67a06-ea2d-4d24-9249-418dc77a16a9'): [
+            ('ResearchStudy', '7dacd4d0-3c8e-470b-bf61-103891627d45'),
+            ('ResearchSubject', '2fc448d6-a23b-4b94-974b-c66110164851'),
+            ('Patient', 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920'),
+            ('Observation', '4e3c6b59-b1fd-5c26-a611-da4cde9fd061')],
+        ('ResearchStudy', '7dacd4d0-3c8e-470b-bf61-103891627d45'): [
+            ('ResearchSubject', '2fc448d6-a23b-4b94-974b-c66110164851')],
+        ('Organization', '89c8dc4c-2d9c-48c7-8862-241a49a78f14'): [
+            ('ResearchStudy', '7dacd4d0-3c8e-470b-bf61-103891627d45'),
+            ('ResearchSubject', '2fc448d6-a23b-4b94-974b-c66110164851'),
+            ('Patient', 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920'),
+            ('Specimen', '60c67a06-ea2d-4d24-9249-418dc77a16a9'),
+            ('DocumentReference', '9ae7e542-767f-4b03-a854-7ceed17152cb')],
+        ('DocumentReference', '9ae7e542-767f-4b03-a854-7ceed17152cb'): [
+            ('ResearchStudy', '7dacd4d0-3c8e-470b-bf61-103891627d45'),
+            ('ResearchSubject', '2fc448d6-a23b-4b94-974b-c66110164851'),
+            ('Patient', 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920'),
+            ('Specimen', '60c67a06-ea2d-4d24-9249-418dc77a16a9'),
+            ('Observation', '21f3411d-89a4-4bcc-9ce7-b76edb1c745f'),
+            ('Observation', 'cec32723-9ede-5f24-ba63-63cb8c6a02cf')],
+        ('Patient', 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920'): [
+            ('ResearchStudy', '7dacd4d0-3c8e-470b-bf61-103891627d45'),
+            ('ResearchSubject', '2fc448d6-a23b-4b94-974b-c66110164851'),
+            ('Specimen', '60c67a06-ea2d-4d24-9249-418dc77a16a9'),
+            ('Observation', '21f3411d-89a4-4bcc-9ce7-b76edb1c745f'),
+            ('Observation', '4e3c6b59-b1fd-5c26-a611-da4cde9fd061'),
+            ('Observation', 'cec32723-9ede-5f24-ba63-63cb8c6a02cf')]
+    }
+
+
+def match_label(self, vertex_gid, label, seen_already=None) -> dict:
+    """Recursively find the first vertex of a given label, starting traversals from vertex_gid."""
+
+    # check params
+    assert vertex_gid is not None, "Expected vertex_gid to be not None."
+    assert label is not None, "Expected label to be not None."
+    # mutable default arguments are evil
+    # See https://florimond.dev/en/posts/2018/08/python-mutable-defaults-are-the-source-of-all-evil
+    if seen_already is None:
+        seen_already = []
+
+    # get all edges for vertex
+    q = self.V(vertex_gid).both()
+
+    # get all vertices for edges
+    # TODO - consider if this should be a vertices_of_label() -> generator[dict] instead
+    for _ in q:
+        if _['vertex']['label'] == label:
+            return _
+        else:
+            if _['vertex']['gid'] in seen_already:
+                continue
+            seen_already.append(_['vertex']['gid'])
+            return self.match_label(_['vertex']['gid'], label, seen_already=seen_already)
+
+
+def dataframe_associations(self, vertex_gid, vertex_label, labels=('ResearchStudy', 'ResearchSubject', 'Patient', 'Specimen', 'DocumentReference', 'Observation')) -> list[dict]:
+    """Return all objects associated with vertex_gid."""
+    associations = []
+    for label in labels:
+        if label == 'Observation':
+            continue
+        if vertex_label == label:
+            continue
+        _ = self.match_label(vertex_gid, label)
+        if _ is not None:
+            associations.append(_['vertex']['data'])
+    if 'Observation' in labels:
+        q = self.V(vertex_gid).in_(["focus", "subject"]).hasLabel("Observation")
+        for _ in q:
+            associations.append(_['vertex']['data'])
+    return associations
+
+
+@pytest.fixture
+def graph() -> pygrip.GraphDBWrapper:
+    """Load the resources into the graph."""
+    graph = pygrip.NewMemServer()
+    jsonpath_expr = parse('*..reference')
+    for _ in resources():
+        graph.addVertex(_['id'], _['resourceType'], _)
+        for match in jsonpath_expr.find(_):
+            # value will be something like "Specimen/60c67a06-ea2d-4d24-9249-418dc77a16a9"
+            # full_path will be something like "specimen.reference" or "focus.[0].reference"
+            type_, dst_id = match.value.split('/')
+            path_parts = str(match.full_path).split('.')
+            path_parts = [part for part in path_parts if '[' not in part and part != 'reference']
+            label = '_'.join(path_parts)
+            graph.addEdge(_['id'], dst_id, label)
+
+    # monkey patch the graph object with our methods
+    graph.match_label = types.MethodType(match_label, graph)
+    graph.dataframe_associations = types.MethodType(dataframe_associations, graph)
+
+    yield graph
+
+
+def test_graph_vertices(graph, expected_vertices):
+    """Test the graph vertices."""
+
+    actual_vertices = []
+    for _ in graph.V():
+        assert 'vertex' in _, f"Expected 'vertex' in {_}"
+        vertex = _['vertex']
+        assert 'data' in vertex, f"Expected 'data' in {vertex}"
+        assert 'gid' in vertex, f"Expected 'gid' in {vertex}"
+        assert 'label' in vertex, f"Expected 'label' in {vertex}"
+        assert 'data' in vertex, f"Expected 'data' in {vertex}"
+        resource = _['vertex']['data']
+        actual_vertices.append((resource['id'], resource['resourceType']))
+
+    print(actual_vertices)
+    assert actual_vertices == expected_vertices, f"Expected {expected_vertices} but got {actual_vertices}."
+
+
+def test_graph_edges(graph, expected_edges):
+    """Test the graph vertices."""
+
+    # check edges all edges
+    actual_edges = []
+    for _ in graph.V().outE():
+        assert 'edge' in _, f"Expected 'edge' in {_}"
+        edge = _['edge']
+        assert 'gid' in edge, f"Expected 'gid' in {edge}"
+        assert 'label' in edge, f"Expected 'label' in {edge}"
+        assert 'from' in edge, f"Expected 'from' in {edge}"
+        assert 'to' in edge, f"Expected 'to' in {edge}"
+        assert 'data' in edge, f"Expected 'data' in {edge}"
+
+        actual_edges.append((edge['from'], edge['to'], edge['label']))
+
+    print(actual_edges)
+    assert actual_edges == expected_edges, f"Expected {expected_edges} but got {actual_edges}."
+
+
+def test_graph_methods(graph):
+    """Test the methods we expect in a graph object."""
+    assert 'V' in dir(graph), f"Expected 'V' in {type(graph)}"
+    assert 'match_label' in dir(graph), f"Expected 'match_label' in {type(graph)}"
+    assert 'dataframe_associations' in dir(graph), f"Expected 'dataframe_associations' in {type(graph)}"
+
+
+def test_traversals(graph):
+    """Test basic traversals"""
+
+    # specimen -> patient
+    q = graph.V().hasLabel("Specimen").out("subject")
+    actual_specimen_patient_count = len(list(q))
+    assert actual_specimen_patient_count == 1, f"Expected 1 but got {actual_specimen_patient_count}."
+    assert list(q)[0]['vertex']['data']['resourceType'] == 'Patient'
+
+    q = graph.V().hasLabel("DocumentReference").outV().hasLabel("Specimen").outV().hasLabel("Patient")
+    assert len(list(q)) == 1, f"Expected 1 but got {len(list(q))}."
+    actual_document_reference_patient_count = len(list(q))
+    assert actual_document_reference_patient_count == 1, f"Expected 1 but got {actual_document_reference_patient_count}."
+    assert list(q)[0]['vertex']['data']['resourceType'] == 'Patient'
+
+    # follow edges by edge label
+    q = graph.V().hasLabel("DocumentReference").out("subject")
+    assert len(list(q)) == 1, f"Expected 1 but got {len(list(q))}."
+    for subject in q:
+        subject = subject['vertex']['data']
+        assert subject['resourceType'] == 'Specimen', f"Expected Specimen but got {subject['resourceType']}."
+
+    # follow all out all edges recursively to a vertex of type X
+
+    q = graph.V().hasLabel("DocumentReference")
+    assert len(list(q)) == 1, f"Expected 1 but got {len(list(q))}."
+    document_reference_gid = list(q)[0]['vertex']['gid']
+
+    # 1 hop
+    specimen = graph.match_label(document_reference_gid, 'Specimen')
+    assert specimen is not None, "Expected Specimen"
+    assert specimen['vertex']['gid'] == '60c67a06-ea2d-4d24-9249-418dc77a16a9', f"Expected 60c67a06-ea2d-4d24-9249-418dc77a16a9 but got {specimen}."
+
+    # 2 hops
+    patient = graph.match_label(document_reference_gid, 'Patient')
+    assert patient is not None, "Expected Patient"
+    assert patient['vertex']['gid'] == 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920', f"Expected bc4e1aa6-cb52-40e9-8f20-594d9c84f920 but got {patient}."
+
+    # 4 hops
+    research_study = graph.match_label(document_reference_gid, 'ResearchStudy')
+    assert research_study is not None, "Expected ResearchStudy"
+    assert research_study['vertex']['gid'] == '7dacd4d0-3c8e-470b-bf61-103891627d45', f"Expected 7dacd4d0-3c8e-470b-bf61-103891627d45 but got {research_study}."
+
+    # Observations
+    q = graph.V(document_reference_gid).in_(["focus", "subject"]).hasLabel("Observation")
+    assert len(list(q)) == 2, f"Expected 2 but got {len(list(q))} for {document_reference_gid}."
+
+
+def test_dataframe_associations(graph, expected_vertices, expected_dataframe_associations):
+    """Test the dataframe associations."""
+
+    actual_dataframe_associations = defaultdict(list)
+    # for all objects in the graph except Observations, retrieve the associated objects useful for a dataframe
+    for vertex_gid, vertex_label in expected_vertices:
+        if vertex_label == 'Observation':
+            continue
+        df = graph.dataframe_associations(vertex_gid, vertex_label)
+        actual_dataframe_associations[(vertex_label, vertex_gid)] = [(_['resourceType'], _['id']) for _ in df]
+    assert actual_dataframe_associations == expected_dataframe_associations, f"Expected {expected_dataframe_associations} but got {actual_dataframe_associations}."

From 9770579dc9116a329c22b66665f1d684adb7d60d Mon Sep 17 00:00:00 2001
From: Brian Walsh <brian@bwalsh.com>
Date: Thu, 5 Sep 2024 13:02:31 -0700
Subject: [PATCH 14/17] adds comments and TODO

---
 test/pygrip_test/fhir/test_load.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/test/pygrip_test/fhir/test_load.py b/test/pygrip_test/fhir/test_load.py
index 6446749b6..4b32d0b84 100644
--- a/test/pygrip_test/fhir/test_load.py
+++ b/test/pygrip_test/fhir/test_load.py
@@ -24,7 +24,7 @@ def resources() -> Generator[Dict[str, Any], None, None]:
 
 @pytest.fixture
 def expected_edges() -> list[tuple]:
-    """Return the expected edges for the resources."""
+    """Return the expected edges for the resources [(src, dst, label)]."""
     return [('21f3411d-89a4-4bcc-9ce7-b76edb1c745f', '60c67a06-ea2d-4d24-9249-418dc77a16a9', 'specimen'),
             ('21f3411d-89a4-4bcc-9ce7-b76edb1c745f', '9ae7e542-767f-4b03-a854-7ceed17152cb', 'focus'),
             ('21f3411d-89a4-4bcc-9ce7-b76edb1c745f', 'bc4e1aa6-cb52-40e9-8f20-594d9c84f920', 'subject'),
@@ -42,7 +42,7 @@ def expected_edges() -> list[tuple]:
 
 @pytest.fixture
 def expected_vertices() -> list[tuple]:
-    """Return the expected vertices (only id, label) for the resources."""
+    """Return the expected vertices [(id, label)] for the resources."""
     return [('21f3411d-89a4-4bcc-9ce7-b76edb1c745f', 'Observation'),
             ('2fc448d6-a23b-4b94-974b-c66110164851', 'ResearchSubject'),
             ('4e3c6b59-b1fd-5c26-a611-da4cde9fd061', 'Observation'),
@@ -56,6 +56,7 @@ def expected_vertices() -> list[tuple]:
 
 @pytest.fixture
 def expected_dataframe_associations():
+    """Return the expected dataframe associations for the resources. { (resource_type, resource_id): [(association_resource_type, association_resource_id)]."""
     return {
         ('ResearchSubject', '2fc448d6-a23b-4b94-974b-c66110164851'): [
             ('ResearchStudy', '7dacd4d0-3c8e-470b-bf61-103891627d45'),
@@ -137,8 +138,10 @@ def dataframe_associations(self, vertex_gid, vertex_label, labels=('ResearchStud
 
 @pytest.fixture
 def graph() -> pygrip.GraphDBWrapper:
-    """Load the resources into the graph."""
+    """Load the resources into the graph. Note: this does _not_ consider iceberg schema."""
+    # TODO - add parameter or test environment variable to switch between in-memory and remote graph
     graph = pygrip.NewMemServer()
+    # use jsonpath to find all references with a resource
     jsonpath_expr = parse('*..reference')
     for _ in resources():
         graph.addVertex(_['id'], _['resourceType'], _)
@@ -146,12 +149,16 @@ def graph() -> pygrip.GraphDBWrapper:
             # value will be something like "Specimen/60c67a06-ea2d-4d24-9249-418dc77a16a9"
             # full_path will be something like "specimen.reference" or "focus.[0].reference"
             type_, dst_id = match.value.split('/')
+            # determine label from full path
             path_parts = str(match.full_path).split('.')
+            # strip out array indices and reference
             path_parts = [part for part in path_parts if '[' not in part and part != 'reference']
+            # make it a label
             label = '_'.join(path_parts)
             graph.addEdge(_['id'], dst_id, label)
 
     # monkey patch the graph object with our methods
+    # TODO - consider a more formal subclass of pygrip.GraphDBWrapper
     graph.match_label = types.MethodType(match_label, graph)
     graph.dataframe_associations = types.MethodType(dataframe_associations, graph)
 

From 24f21102f54b04dec20dcd618c258a44b9591549 Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Tue, 4 Feb 2025 13:43:23 -0800
Subject: [PATCH 15/17] Adding python dependencies to unit tests

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 910dedc48..8d4787049 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -238,7 +238,7 @@ jobs:
       - name: Check out code
         uses: actions/checkout@v2
       - name: Python Dependencies for Conformance
-        run: pip install requests numpy PyYAML
+        run: pip install requests numpy PyYAML pytest jsonpath-ng
       - name: install gripql
         run: |
           cd gripql/python

From 6f0c8a12928cba40a66662022f43ca3f1fe29b20 Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Fri, 4 Apr 2025 08:54:24 -0700
Subject: [PATCH 16/17] Eliminating debugging Printf statements

---
 accounts/basic.go                  |  6 ++-
 accounts/casbin.go                 |  9 ++--
 accounts/util.go                   | 10 ++--
 engine/core/util.go                |  8 ----
 grids/new.go                       |  5 +-
 gripper/server.go                  |  8 ++--
 gripql/marshal_flattened.go        |  4 +-
 main.go                            |  3 +-
 mongo/compile.go                   |  6 +--
 mongo/has_evaluator.go             |  4 +-
 pygrip/__init__.py                 | 74 ------------------------------
 pygrip/wrapper.go                  | 13 ++++++
 server/api.go                      |  2 +-
 server/endpoints.go                |  2 +-
 server/server.go                   |  2 +-
 test/pygrip_test/fhir/test_load.py |  2 +-
 16 files changed, 45 insertions(+), 113 deletions(-)
 delete mode 100644 pygrip/__init__.py

diff --git a/accounts/basic.go b/accounts/basic.go
index ffbf6b119..01c74761a 100644
--- a/accounts/basic.go
+++ b/accounts/basic.go
@@ -4,6 +4,8 @@ import (
 	"encoding/base64"
 	"fmt"
 	"strings"
+
+	"github.com/bmeg/grip/log"
 )
 
 // BasicCredential describes a username and password for use with Funnel's basic auth.
@@ -18,7 +20,7 @@ func (ba BasicAuth) Validate(md MetaData) (string, error) {
 	var auth []string
 	var ok bool
 
-	fmt.Printf("Running BasicAuth: %#v\n", md)
+	log.Infof("Running BasicAuth: %#v\n", md)
 
 	if auth, ok = md["Authorization"]; !ok {
 		if auth, ok = md["authorization"]; !ok {
@@ -28,7 +30,7 @@ func (ba BasicAuth) Validate(md MetaData) (string, error) {
 
 	if len(auth) > 0 {
 		user, password, ok := parseBasicAuth(auth[0])
-		fmt.Printf("User: %s Password: %s OK: %s\n", user, password, ok)
+		log.Debugf("User: %s Password: %s OK: %#v\n", user, password, ok)
 		for _, c := range ba {
 			if c.User == user && c.Password == password {
 				return user, nil
diff --git a/accounts/casbin.go b/accounts/casbin.go
index ce4a576bd..d953857a1 100644
--- a/accounts/casbin.go
+++ b/accounts/casbin.go
@@ -3,6 +3,7 @@ package accounts
 import (
 	"fmt"
 
+	"github.com/bmeg/grip/log"
 	"github.com/casbin/casbin/v2"
 )
 
@@ -17,19 +18,19 @@ func (ce *CasbinAccess) init() {
 		if e, err := casbin.NewEnforcer(ce.Model, ce.Policy); err == nil {
 			ce.encforcer = e
 		} else {
-			fmt.Printf("Casbin Error: %s", err)
+			log.Errorf("Casbin Error: %s", err)
 		}
 	}
 }
 
 func (ce *CasbinAccess) Enforce(user string, graph string, operation Operation) error {
 	ce.init()
-	fmt.Printf("Casbin request '%s' '%s' '%s'\n", user, graph, operation)
+	log.Infof("Casbin request '%s' '%s' '%s'\n", user, graph, operation)
 	if res, err := ce.encforcer.Enforce(user, graph, string(operation)); res {
 		return nil
 	} else if err != nil {
-		fmt.Printf("casbin error: %s\n", err)
+		log.Errorf("casbin error: %s\n", err)
 	}
-	fmt.Printf("Not allowed: '%s' '%s' '%s'\n", user, graph, operation)
+	log.Errorf("Not allowed: '%s' '%s' '%s'\n", user, graph, operation)
 	return fmt.Errorf("action restricted")
 }
diff --git a/accounts/util.go b/accounts/util.go
index c70a5afd7..b93377264 100644
--- a/accounts/util.go
+++ b/accounts/util.go
@@ -54,11 +54,11 @@ func (c *Config) StreamInterceptor() grpc.StreamServerInterceptor {
 // using a password stored in the config.
 func unaryAuthInterceptor(auth Authenticate, access Access) grpc.UnaryServerInterceptor {
 	return func(ctx context.Context, req interface{}, info *grpc.UnaryServerInfo, handler grpc.UnaryHandler) (interface{}, error) {
-		//fmt.Printf("AuthInt: %#v\n", ctx)
+		//log.Infof("AuthInt: %#v\n", ctx)
 		md, _ := metadata.FromIncomingContext(ctx)
-		//fmt.Printf("Metadata: %#v\n", md)
+		//log.Infof("Metadata: %#v\n", md)
 		//omd, _ := metadata.FromOutgoingContext(ctx)
-		//fmt.Printf("Raw: %#v\n", omd)
+		//log.Infof("Raw: %#v\n", omd)
 
 		metaData := MetaData{}
 		for i := range md {
@@ -89,10 +89,10 @@ func unaryAuthInterceptor(auth Authenticate, access Access) grpc.UnaryServerInte
 // using a password stored in the config.
 func streamAuthInterceptor(auth Authenticate, access Access) grpc.StreamServerInterceptor {
 	return func(srv interface{}, ss grpc.ServerStream, info *grpc.StreamServerInfo, handler grpc.StreamHandler) error {
-		//fmt.Printf("Streaming query: %#v\n", info)
+		//log.Infof("Streaming query: %#v\n", info)
 		md, _ := metadata.FromIncomingContext(ss.Context())
 
-		//fmt.Printf("Metadata: %#v\n", md)
+		//log.Infof("Metadata: %#v\n", md)
 		metaData := MetaData{}
 		for i := range md {
 			metaData[i] = md[i]
diff --git a/engine/core/util.go b/engine/core/util.go
index 2cc616ef3..03a6ff036 100644
--- a/engine/core/util.go
+++ b/engine/core/util.go
@@ -1,13 +1,5 @@
 package core
 
-import (
-	"github.com/kr/pretty"
-)
-
-func debug(i ...interface{}) {
-	pretty.Println(i...)
-}
-
 func dedupStringSlice(s []string) []string {
 	seen := make(map[string]struct{}, len(s))
 	j := 0
diff --git a/grids/new.go b/grids/new.go
index 42c52441b..a5f8e6e93 100644
--- a/grids/new.go
+++ b/grids/new.go
@@ -9,6 +9,7 @@ import (
 
 	"github.com/bmeg/benchtop/bsontable"
 	"github.com/bmeg/grip/gripql"
+	"github.com/bmeg/grip/log"
 	"github.com/bmeg/grip/timestamp"
 )
 
@@ -42,7 +43,7 @@ func (kgraph *GDB) AddGraph(graph string) error {
 }
 func newGraph(baseDir, name string) (*Graph, error) {
 	dbPath := filepath.Join(baseDir, name)
-	fmt.Printf("Creating new GRIDS graph %s\n", name)
+	log.Infof("Creating new GRIDS graph %s\n", name)
 
 	// Create directory if it doesn't exist
 	if _, err := os.Stat(dbPath); os.IsNotExist(err) {
@@ -78,7 +79,7 @@ func newGraph(baseDir, name string) (*Graph, error) {
 
 func getGraph(baseDir, name string) (*Graph, error) {
 	dbPath := filepath.Join(baseDir, name)
-	fmt.Printf("fetching GRIDS graph %s\n", name)
+	log.Infof("fetching GRIDS graph %s\n", name)
 
 	versionPath := filepath.Join(dbPath, "VERSION")
 	file, err := os.Open(versionPath)
diff --git a/gripper/server.go b/gripper/server.go
index 6feaa2cd4..0f28ff23a 100644
--- a/gripper/server.go
+++ b/gripper/server.go
@@ -3,9 +3,9 @@ package gripper
 import (
 	"context"
 	"fmt"
-	"log"
 	"net"
 
+	"github.com/bmeg/grip/log"
 	"google.golang.org/grpc"
 	"google.golang.org/protobuf/types/known/structpb"
 )
@@ -36,13 +36,13 @@ func NewSimpleTableServer(dr map[string]Driver) *SimpleTableServicer {
 func StartServer(port int, serv GRIPSourceServer) {
 	lis, err := net.Listen("tcp", fmt.Sprintf("localhost:%d", port))
 	if err != nil {
-		log.Fatalf("failed to listen: %v", err)
+		log.Errorf("failed to listen: %v", err)
 	}
 	var opts []grpc.ServerOption
 	grpcServer := grpc.NewServer(opts...)
 
 	RegisterGRIPSourceServer(grpcServer, serv)
-	fmt.Printf("Starting: %d\n", port)
+	log.Infof("Starting: %d\n", port)
 	grpcServer.Serve(lis)
 }
 
@@ -97,7 +97,7 @@ func (st *SimpleTableServicer) GetRowsByID(srv GRIPSource_GetRowsByIDServer) err
 		if err != nil {
 			break
 		}
-		log.Printf("Request: %s %s", err, req)
+		log.Debugf("Request: %s %s", err, req)
 		if dr, ok := st.drivers[req.Collection]; ok {
 			if row, err := dr.FetchRow(req.Id); err == nil {
 				data, _ := structpb.NewStruct(row.Value)
diff --git a/gripql/marshal_flattened.go b/gripql/marshal_flattened.go
index da2ab6bc0..6a285a3ea 100644
--- a/gripql/marshal_flattened.go
+++ b/gripql/marshal_flattened.go
@@ -2,8 +2,8 @@ package gripql
 
 import (
 	"encoding/json"
-	"fmt"
 
+	"github.com/bmeg/grip/log"
 	"google.golang.org/protobuf/encoding/protojson"
 	"google.golang.org/protobuf/proto"
 	"google.golang.org/protobuf/types/known/structpb"
@@ -80,7 +80,7 @@ func (mflat *MarshalFlatten) Unmarshal(data []byte, v interface{}) error {
 			}
 			s, err := structpb.NewStruct(data)
 			if err != nil {
-				fmt.Printf("NewStruct error: %s", err)
+				log.Errorf("NewStruct error: %s", err)
 			}
 			if err == nil {
 				y.Data = s
diff --git a/main.go b/main.go
index df320e840..53fa06cea 100644
--- a/main.go
+++ b/main.go
@@ -1,7 +1,6 @@
 package main
 
 import (
-	"fmt"
 	"os"
 
 	"github.com/bmeg/grip/cmd"
@@ -11,7 +10,7 @@ import (
 func main() {
 	log.ConfigureLogger(log.DefaultLoggerConfig())
 	if err := cmd.RootCmd.Execute(); err != nil {
-		fmt.Println("Error:", err.Error())
+		log.Errorf("Error:", err.Error())
 		os.Exit(1)
 	}
 }
diff --git a/mongo/compile.go b/mongo/compile.go
index 2d2eb382a..29391fe17 100644
--- a/mongo/compile.go
+++ b/mongo/compile.go
@@ -528,10 +528,10 @@ func (comp *Compiler) Compile(stmts []*gripql.GraphStatement, opts *gdbi.Compile
 			keys := protoutil.AsStringList(stmt.HasKey)
 			for _, key := range keys {
 				lKey := ToPipelinePath(key)
-				fmt.Printf("Key: %s -> %s\n", key, lKey)
+				//log.Debugf("Key: %s -> %s\n", key, lKey)
 				hasKeys[lKey] = bson.M{"$exists": true}
 			}
-			fmt.Printf("hasKey: %#v\n", hasKeys)
+			//log.Debugf("hasKey: %#v\n", hasKeys)
 			query = append(query, bson.D{primitive.E{Key: "$match", Value: hasKeys}})
 
 		case *gripql.GraphStatement_Limit:
@@ -581,7 +581,7 @@ func (comp *Compiler) Compile(stmts []*gripql.GraphStatement, opts *gdbi.Compile
 				},
 			},
 			})
-			fmt.Printf("Distinct: %s\n", query)
+			//log.Debugf("Distinct: %s\n", query)
 			switch lastType {
 			case gdbi.VertexData:
 				query = append(query, bson.D{primitive.E{Key: "$project", Value: bson.M{
diff --git a/mongo/has_evaluator.go b/mongo/has_evaluator.go
index 5e08af15f..c4f644c57 100644
--- a/mongo/has_evaluator.go
+++ b/mongo/has_evaluator.go
@@ -1,8 +1,6 @@
 package mongo
 
 import (
-	"fmt"
-
 	"github.com/bmeg/grip/gripql"
 	"github.com/bmeg/grip/log"
 	"go.mongodb.org/mongo-driver/bson"
@@ -22,7 +20,7 @@ func convertHasExpression(stmt *gripql.HasExpression, not bool) bson.M {
 			} else {
 				key := cond.Key
 				output = convertHasExpression(gripql.And(gripql.Gt(key, lims[0]), gripql.Lt(key, lims[1])), not)
-				fmt.Printf("inside: %#v\n", output)
+				//log.Debugf("inside: %#v\n", output)
 			}
 
 		case gripql.Condition_OUTSIDE:
diff --git a/pygrip/__init__.py b/pygrip/__init__.py
deleted file mode 100644
index 33964bf1a..000000000
--- a/pygrip/__init__.py
+++ /dev/null
@@ -1,74 +0,0 @@
-
-
-from __future__ import print_function
-from ctypes import *
-from ctypes.util import find_library
-import os, inspect, sysconfig
-import random, string
-import json
-from gripql.query import QueryBuilder
-
-cwd = os.getcwd()
-currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
-#print("frame: %s" % (inspect.getfile(inspect.currentframe())))
-#print("cd to %s" % (currentdir))
-os.chdir(currentdir)
-_lib = cdll.LoadLibrary("./_pygrip" + sysconfig.get_config_vars()["EXT_SUFFIX"])
-os.chdir(cwd)
-
-_lib.ReaderNext.restype = c_char_p
-
-class GoString(Structure):
-    _fields_ = [("p", c_char_p), ("n", c_longlong)]
-
-def NewMemServer():
-    return GraphDBWrapper( _lib.NewMemServer() )
-
-def getGoString(s):
-    return GoString(bytes(s, encoding="raw_unicode_escape"), len(s))
-
-def id_generator(size=6, chars=string.ascii_uppercase + string.digits):
-    return ''.join(random.choice(chars) for _ in range(size))
-
-class QueryWrapper(QueryBuilder):
-    def __init__(self, wrapper):
-        super(QueryBuilder, self).__init__()
-        self.query = []
-        self.wrapper = wrapper
-
-    def __iter__(self):
-        jquery = json.dumps({ "graph" : "default", "query" : self.query })
-        reader = _lib.Query( self.wrapper._handle, getGoString(jquery) )
-        while not _lib.ReaderDone(reader):
-            j = _lib.ReaderNext(reader)
-            yield json.loads(j)
-
-    def _builder(self):
-        return QueryWrapper(self.wrapper)
-
-class GraphDBWrapper:
-    def __init__(self, handle) -> None:
-        self._handle = handle
-
-    def addVertex(self, gid, label, data={}):
-        """
-        Add vertex to a graph.
-        """
-        _lib.AddVertex(self._handle, getGoString(gid), getGoString(label), 
-                       getGoString(json.dumps(data)))
-    
-    def addEdge(self, src, dst, label, data={}, gid=None):
-        """
-        Add edge to a graph.
-        """
-        if gid is None:
-            gid = id_generator(10)
-
-        _lib.AddEdge(self._handle, getGoString(gid), 
-                     getGoString(src), getGoString(dst), getGoString(label), 
-                     getGoString(json.dumps(data)))
-        
-
-
-    def V(self, *ids):
-        return QueryWrapper(self).V(*ids)
\ No newline at end of file
diff --git a/pygrip/wrapper.go b/pygrip/wrapper.go
index 0657f2c81..de9f7bbaa 100644
--- a/pygrip/wrapper.go
+++ b/pygrip/wrapper.go
@@ -16,6 +16,7 @@ import (
 	"github.com/bmeg/grip/engine/core"
 	"github.com/bmeg/grip/engine/pipeline"
 	"github.com/bmeg/grip/gdbi"
+	"github.com/bmeg/grip/grids"
 	"github.com/bmeg/grip/gripql"
 	"github.com/bmeg/grip/kvgraph"
 	"github.com/bmeg/grip/kvi"
@@ -49,6 +50,18 @@ func NewMemServer() GraphHandle {
 	return GraphHandle(cgo.NewHandle(g))
 }
 
+func NewGRIDServer(path string) GraphHandle {
+	graphDB, err := grids.NewGraphDB(path)
+	if err != nil {
+		log.Errorf("Graph init error: %s\n", err)
+	}
+	g, err := graphDB.Graph("default")
+	if err != nil {
+		log.Errorf("Graph init error: %s\n", err)
+	}
+	return GraphHandle(cgo.NewHandle(g))
+}
+
 func CloseServer(graph GraphHandle) {
 	cgo.Handle(graph).Delete()
 }
diff --git a/server/api.go b/server/api.go
index 44d548523..4c7a9cff2 100644
--- a/server/api.go
+++ b/server/api.go
@@ -663,7 +663,7 @@ func (server *GripServer) AddSchema(ctx context.Context, req *gripql.Graph) (*gr
 func (server *GripServer) AddJsonSchema(ctx context.Context, rawjson *gripql.RawJson) (*gripql.EditResult, error) {
 	bytes, err := protojson.Marshal(rawjson.Data)
 	if err != nil {
-		fmt.Printf("Failed to marshal data to bytes: %v\n", err)
+		log.Errorf("Failed to marshal data to bytes: %v\n", err)
 		return nil, err
 	}
 	req, err := schema.ParseJSchema(bytes, rawjson.Graph)
diff --git a/server/endpoints.go b/server/endpoints.go
index 4adff8840..490e3d5ee 100644
--- a/server/endpoints.go
+++ b/server/endpoints.go
@@ -25,7 +25,7 @@ func (server *GripServer) AddEndpoint(name string, path string, config map[strin
 	if err != nil {
 		return err
 	}
-	fmt.Printf("Method: %#v\n", gen)
+	log.Infof("Method: %#v\n", gen)
 	if x, ok := (gen).(func(client gripql.Client, config map[string]string) (http.Handler, error)); ok {
 		log.Infof("Plugin %s loaded", path)
 		endpointMap[name] = x
diff --git a/server/server.go b/server/server.go
index 02a191655..fa2c61309 100644
--- a/server/server.go
+++ b/server/server.go
@@ -122,7 +122,7 @@ func NewGripServer(conf *config.Config, baseDir string, drivers map[string]gdbi.
 	if _, ok := gdbs[conf.Default]; !ok {
 		return nil, fmt.Errorf("default driver '%s' does not exist", conf.Default)
 	}
-	fmt.Printf("Default graph driver: %s\n", conf.Default)
+	log.Infof("Default graph driver: %s\n", conf.Default)
 	return server, nil
 }
 
diff --git a/test/pygrip_test/fhir/test_load.py b/test/pygrip_test/fhir/test_load.py
index 4b32d0b84..8ce6e087c 100644
--- a/test/pygrip_test/fhir/test_load.py
+++ b/test/pygrip_test/fhir/test_load.py
@@ -5,7 +5,7 @@
 
 import pytest
 
-import pygrip
+import pygrip.pygrip as pygrip
 from jsonpath_ng import jsonpath, parse
 
 from typing import Generator, Dict, Any

From e99e76f752f60fabed97ae935822dec6ab2850be Mon Sep 17 00:00:00 2001
From: Kyle Ellrott <kellrott@gmail.com>
Date: Wed, 9 Apr 2025 14:39:08 -0700
Subject: [PATCH 17/17] Trying to put togeather a grpc based embedded grip

---
 cmd/root.go     | 2 ++
 pygrip/Makefile | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/cmd/root.go b/cmd/root.go
index b2a85c8d4..d2cacc389 100644
--- a/cmd/root.go
+++ b/cmd/root.go
@@ -10,6 +10,7 @@ import (
 	"github.com/bmeg/grip/cmd/delete"
 	"github.com/bmeg/grip/cmd/drop"
 	"github.com/bmeg/grip/cmd/dump"
+	"github.com/bmeg/grip/cmd/embedded"
 	"github.com/bmeg/grip/cmd/erclient"
 	"github.com/bmeg/grip/cmd/info"
 	"github.com/bmeg/grip/cmd/job"
@@ -73,6 +74,7 @@ func init() {
 	RootCmd.AddCommand(version.Cmd)
 	RootCmd.AddCommand(kvload.Cmd)
 	RootCmd.AddCommand(delete.Cmd)
+	RootCmd.AddCommand(embedded.Cmd)
 
 }
 
diff --git a/pygrip/Makefile b/pygrip/Makefile
index e3d2cad19..dbe3ccf27 100644
--- a/pygrip/Makefile
+++ b/pygrip/Makefile
@@ -1,4 +1,4 @@
 
 
-pygrip.so: wrapper.go
-	go build -o pygrip.so -buildmode=c-shared wrapper.go
+pygrip/gripql_pb2.py: ../gripql/gripql.proto
+	protoc --proto_path=../gripql/ --python_out=./pygrip -I ../googleapis/ ../gripql/gripql.proto
\ No newline at end of file