From 1bd705860add20da992f1ac648f235f82cce8cd6 Mon Sep 17 00:00:00 2001
From: Kirsten Winther <winther@stanford.edu>
Date: Fri, 11 Jan 2019 09:46:21 -0800
Subject: [PATCH 1/3] log interface

---
 api.py    | 10 +++++++++-
 models.py | 17 ++++++++++++++++-
 2 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/api.py b/api.py
index 2a81edb3..7851fc5a 100644
--- a/api.py
+++ b/api.py
@@ -240,6 +240,12 @@ class Meta:
     # name = graphene.InputField()
     # systems = graphene.List('api.Systems')
 
+class Log(CustomSQLAlchemyObjectType):
+
+    class Meta:
+        model = models.Log
+        interfaces = (graphene.relay.Node, )
+
 
 class System(CustomSQLAlchemyObjectType):
 
@@ -613,8 +619,10 @@ class Query(graphene.ObjectType):
         ReactionSystem, **get_filter_fields(models.ReactionSystem))
     publications = FilteringConnectionField(
         Publication, **get_filter_fields(models.Publication))
+    logs = FilteringConnectionField(
+        Log, **get_filter_fields(models.Log))
 
 
 schema = graphene.Schema(
-    query=Query, types=[System, Species, TextKeyValue, NumberKeyValue, Key, Reaction, ReactionSystem, Publication
+    query=Query, types=[System, Species, TextKeyValue, NumberKeyValue, Key, Reaction, ReactionSystem, Publication, Log
     ])
diff --git a/models.py b/models.py
index c63f6a40..6c21e1ff 100644
--- a/models.py
+++ b/models.py
@@ -5,7 +5,7 @@
 import sqlalchemy.types
 import sqlalchemy.ext.declarative
 from sqlalchemy import or_
-from sqlalchemy.dialects.postgresql import JSONB, TSVECTOR
+from sqlalchemy.dialects.postgresql import JSONB, TSVECTOR, BYTEA
 from sqlalchemy import String, Float, Integer
 from sqlalchemy.types import ARRAY
 from sqlalchemy.ext.associationproxy import association_proxy
@@ -97,6 +97,16 @@ class ReactionSystem(Base):
     id = sqlalchemy.Column(sqlalchemy.Integer,
                            sqlalchemy.ForeignKey('{}.reaction.id'.format(SCHEMA)),
                            primary_key=True)
+
+class Log(Base):
+    __tablename__ = 'log'
+    __table_args__ = ({'schema': SCHEMA})
+
+    ase_id = sqlalchemy.Column(sqlalchemy.String,
+                               sqlalchemy.ForeignKey('{}.systems.unique_id'.format(SCHEMA)),
+                               primary_key=True)
+    logfile = sqlalchemy.Column(BYTEA, )
+
     
 class Reaction(Base):
     __tablename__ = 'reaction'
@@ -222,6 +232,11 @@ class System(Base):
         backref="systems",
         uselist=True)
 
+    log = sqlalchemy.orm.relationship(
+        "Log",
+        backref="systems",
+        uselist=True)
+
     #reaction = sqlalchemy.orm.relationship("ReactionSystems", backref='systems', uselist=True)
     
     publication = sqlalchemy.orm.relationship("Publication",

From 1e90ea29c4f13bc9ebe73f4f840108e21ac445da Mon Sep 17 00:00:00 2001
From: Kirsten Winther <winther@stanford.edu>
Date: Fri, 11 Jan 2019 11:12:46 -0800
Subject: [PATCH 2/3] decoded Logtext

---
 models.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/models.py b/models.py
index 6c21e1ff..bfc51552 100644
--- a/models.py
+++ b/models.py
@@ -105,7 +105,11 @@ class Log(Base):
     ase_id = sqlalchemy.Column(sqlalchemy.String,
                                sqlalchemy.ForeignKey('{}.systems.unique_id'.format(SCHEMA)),
                                primary_key=True)
-    logfile = sqlalchemy.Column(BYTEA, )
+    logfile = sqlalchemy.Column(sqlalchemy.String, )
+
+    @hybrid_property
+    def _logtext(self):
+        return bytes(self.logfile).decode('utf-8')
 
     
 class Reaction(Base):
@@ -408,7 +412,8 @@ def hybrid_prop_parameters(key):
                     'Ctime': ['id', 'ctime'],
                     'Mtime': ['id', 'mtime'],
                     'Pbc': ['id', 'pbc'],
-                    'Trajdata': ['all']}
+                    'Trajdata': ['all'],
+                    'Logtext': ['logfile']}
 
     if key not in h_parameters:
         return ['id', 'key_value_pairs']

From c886a5c5ddd9d94ce3342cfccfef3248c64bab80 Mon Sep 17 00:00:00 2001
From: Kirsten Winther <winther@stanford.edu>
Date: Fri, 11 Jan 2019 11:22:00 -0800
Subject: [PATCH 3/3] log list under systems

---
 api.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/api.py b/api.py
index 7851fc5a..0739896c 100644
--- a/api.py
+++ b/api.py
@@ -256,6 +256,7 @@ class Meta:
         interfaces = (graphene.relay.Node, )
 
     publication = graphene.List('api.Publication')
+    log = graphene.List('api.Log')
 
     @staticmethod
     def resolve__input_file(self, info, format="py"):