Merge pull request #245 from jordan2lee/develop-0.7.0_overv-downld-gsche

Updates to files in website/content/

docs/index.xml

@@ -10,18 +10,18 @@
       <title></title>
       <link>https://bmeg.github.io/grip/docs/tutorials/pathway-commons/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/tutorials/pathway-commons/</guid>
       <description>Get Pathway Commons release
 curl -O http://www.pathwaycommons.org/archives/PC2/v10/PathwayCommons10.All.BIOPAX.owl.gz Convert to Property Graph
 grip rdf --dump --gzip pc PathwayCommons10.All.BIOPAX.owl.gz -m http://pathwaycommons.org/pc2/#=pc: -m http://www.biopax.org/release/biopax-level3.owl#=biopax: </description>
     </item>
-    
+
     <item>
       <title>Amazon Purchase Network</title>
       <link>https://bmeg.github.io/grip/docs/tutorials/amazon/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/tutorials/amazon/</guid>
       <description>Explore Amazon Product Co-Purchasing Network Metadata Download the data
 curl -O http://snap.stanford.edu/data/bigdata/amazon/amazon-meta.txt.gz Convert the data into vertices and edges
@@ -32,76 +32,76 @@ command line client
 grip query amazon &#39;O.query().V().out()&#39; python client
 pip install &amp;quot;git+https://github.com/bmeg/grip.git#egg=gripql&amp;amp;subdirectory=gripql/python/&amp;quot; import gripql conn = gripql.Connection(&amp;#34;http://localhost:8201&amp;#34;) g = conn.graph(&amp;#34;amazon&amp;#34;) # Count the Vertices print g.</description>
     </item>
-    
+
     <item>
       <title>Basic Auth</title>
       <link>https://bmeg.github.io/grip/docs/security/basic/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/security/basic/</guid>
       <description>Basic Auth By default, an GRIP server allows open access to its API endpoints, but it can be configured to require basic password authentication. To enable this, include users and passwords in your config file:
 Server: BasicAuth: - User: testuser Password: abc123 Make sure to properly protect the configuration file so that it&amp;rsquo;s not readable by everyone:
 $ chmod 600 grip.config.yml To use the password, set the GRIP_USER and GRIP_PASSWORD environment variables:</description>
     </item>
-    
+
     <item>
       <title>Developers</title>
       <link>https://bmeg.github.io/grip/docs/developers/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/developers/</guid>
       <description></description>
     </item>
-    
+
     <item>
       <title>Download</title>
       <link>https://bmeg.github.io/grip/download/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/download/</guid>
-      <description> Download 0.5.1  Linux MacOS Windows is not supported sorry!  Release History See the Releases page for release history.
+      <description> Download 0.5.1  Linux MacOS Windows is not yet supported, sorry!  Release History See the Releases page for release history.
 Docker docker pull bmeg/grip docker run bmeg/grip grip server $ git clone https://github.com/bmeg/grip.git $ cd grip $ make </description>
     </item>
-    
+
     <item>
       <title>Elasticsearch</title>
       <link>https://bmeg.github.io/grip/docs/databases/elastic/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/databases/elastic/</guid>
       <description>Elasticsearch GRIP supports storing vertices and edges in Elasticsearch.
 Config:
 Default: elastic Drivers: elastic: Elasticsearch: URL: &amp;#34;http://localhost:9200&amp;#34; DBName: &amp;#34;gripdb&amp;#34; Username: &amp;#34;&amp;#34; Password: &amp;#34;&amp;#34; </description>
     </item>
-    
+
     <item>
       <title>Embedded KV Store</title>
       <link>https://bmeg.github.io/grip/docs/databases/kvstore/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/databases/kvstore/</guid>
       <description>Embedded Key Value Stores GRIP supports storing vertices and edges in a variety of key-value stores including:
  Badger BoltDB LevelDB  Config:
 Default: kv Driver: kv: Badger: grip.db </description>
     </item>
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+
     <item>
       <title>External Resource Proxies</title>
       <link>https://bmeg.github.io/grip/docs/gripper/proxy/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/gripper/proxy/</guid>
       <description>GRIPPER GRIPPER proxy With the external resources normalized to a single data model, the graph model describes how to connect the set of collections into a graph model. Each GRIPPER is required to provide a GRPC interface that allows access to collections stored in the resource.
 The required functions include:
 rpc GetCollections(Empty) returns (stream Collection); GetCollections returns a list of all of the Collections accessible via this server.
 rpc GetCollectionInfo(Collection) returns (CollectionInfo); GetCollectionInfo provides information, such as the list of indexed fields, in a collection.</description>
     </item>
-    
+
     <item>
       <title>Getting Started</title>
       <link>https://bmeg.github.io/grip/docs/queries/getting_started/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/queries/getting_started/</guid>
       <description>Getting Started GRIP has an API for making graph queries using structured data. Queries are defined using a series of step operations.
 Install the Python Client Available on PyPI.
@@ -110,34 +110,34 @@ pip install &amp;quot;git+https://github.com/bmeg/grip.git#subdirectory=gripql/p
 First, import the client and create a connection to an GRIP server:
 import gripql G = gripql.</description>
     </item>
-    
+
     <item>
       <title>Graph Model</title>
       <link>https://bmeg.github.io/grip/docs/gripper/graphmodel/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/gripper/graphmodel/</guid>
       <description>GRIPPER Graph Model The graph model describes how GRIP will access multiple gripper servers. The graph is described using three sections, sources, vertices and edges.
 The sources section describes all of the GRIPPER resources that GRIP will use to build the graph. The vertices section describes how different collections found in these sources will be turned into Vertex found in the graph. Finally, the edges section describes the different kinds of rules that can be used build the edges in the graph.</description>
     </item>
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+
     <item>
       <title>Graph Schemas</title>
       <link>https://bmeg.github.io/grip/graph_schemas/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/graph_schemas/</guid>
       <description>Graph Schemas Graph schemas are themselves an instance of a graph. As such, they can be traversed like any other graph. The schemas are automatically added to the database following the naming pattern {graph-name}__schema__.
 Get the schema of a graph The schema of a graph can be accessed via a GET request to /v1/graph/{graph-name}/schema.
 Alternatively, you can use the grip CLI: grip schema get {graph-name}.
 Describing graph schemas There are several methods for describing the schema of a graph.</description>
     </item>
-    
+
     <item>
       <title>GraphQL</title>
       <link>https://bmeg.github.io/grip/docs/queries/graphql/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/queries/graphql/</guid>
       <description>GraphQL GRIP supports GraphQL access of the property graphs. Currently this is read-only access to the graph.
 GraphQL access is only supported when using the MongoDB driver
@@ -147,54 +147,54 @@ grip dump example-graph --vertex --edge See the example graph schema
 grip schema example-graph Example queries Get Types:
 curl -X POST -H &amp;quot;Content-Type:application/graphql&amp;quot; -d &#39;{__schema{types{name}}}&#39; http://localhost:8201/graphql/example-graph Get Info about Human object</description>
     </item>
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+
     <item>
       <title>GRIP Plugable External Resources</title>
       <link>https://bmeg.github.io/grip/docs/gripper/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/gripper/</guid>
       <description></description>
     </item>
-    
+
     <item>
       <title>GRIPPER</title>
       <link>https://bmeg.github.io/grip/docs/databases/gripper/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/databases/gripper/</guid>
       <description>GRIPPER GRIP Plugable External Resources are data systems that GRIP can combine together to create graphs.
 Example:
 Drivers: swapi-driver: Gripper: ConfigFile: ./swapi.yaml Graph: swapi ConfigFile - Path to GRIPPER graph map
 Graph - Name of the graph for the mapped external resources.</description>
     </item>
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+
     <item>
       <title>Intro</title>
       <link>https://bmeg.github.io/grip/docs/gripper/gripper/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/gripper/gripper/</guid>
       <description>GRIPPER GRIP Plugin External Resources GRIP Plugin External Resources (GRIPPERs) are GRIP drivers that take external resources and allow GRIP to access them are part of a unified graph. To integrate new resources into the graph, you first deploy griper proxies that plug into the external resources. They are unique and configured to access specific resources. These provide a view into external resources as a series of document collections. For example, an SQL gripper would plug into an SQL server and provide the tables as a set of collections with each every row a document.</description>
     </item>
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     <item>
       <title>MongoDB</title>
       <link>https://bmeg.github.io/grip/docs/databases/mongo/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/databases/mongo/</guid>
       <description>MongoDB GRIP supports storing vertices and edges in MongoDB.
 Config:
 Default: mongo Drivers: mongo: MongoDB: URL: &amp;#34;mongodb://localhost:27000&amp;#34; DBName: &amp;#34;gripdb&amp;#34; Username: &amp;#34;&amp;#34; Password: &amp;#34;&amp;#34; UseCorePipeline: False BatchSize: 0 UseCorePipeline - Default is to use Mongo pipeline API to do graph traversals. By enabling UseCorePipeline, GRIP will do the traversal logic itself, only using Mongo for graph storage.
 BatchSize - For core engine operations, GRIP dispatches element lookups in batches to minimize query overhead.</description>
     </item>
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     <item>
       <title>Operations</title>
       <link>https://bmeg.github.io/grip/docs/queries/operations/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/queries/operations/</guid>
       <description>Start a Traversal .V([ids]) Start query from Vertex
 G.query().V() Returns all vertices in graph
@@ -204,84 +204,84 @@ G.query().E() Returns all edges in graph
 G.query().E([&amp;#34;edge1&amp;#34;]) Returns:
 {&amp;#34;gid&amp;#34; : &amp;#34;edge1&amp;#34;, &amp;#34;label&amp;#34;:&amp;#34;TestEdge&amp;#34;, From: &amp;#34;vertex1&amp;#34;, To: &amp;#34;vertex2&amp;#34;, data&amp;#34;:{}} Traverse the graph .in_(), inV() Following incoming edges. Optional argument is the edge label (or list of labels) that should be followed. If no argument is provided, all incoming edges.</description>
     </item>
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     <item>
       <title>Overview</title>
       <link>https://bmeg.github.io/grip/docs/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/</guid>
       <description>Overview GRIP stands for GRaph Integration Platform. It provides a graph interface on top of a variety of existing database technologies including: MongoDB, Elasticsearch, PostgreSQL, MySQL, MariaDB, Badger, and LevelDB.
 Properties of an GRIP graph:
  Both vertices and edges in a graph can have any number of properties associated with them. There are many types of vertices and edges in a graph. Thus two vertices may have myriad types of edges connecting them reflecting myriad types of relationships.</description>
     </item>
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     <item>
       <title>PostgreSQL</title>
       <link>https://bmeg.github.io/grip/docs/databases/psql/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/databases/psql/</guid>
       <description>PostgreSQL GRIP supports storing vertices and edges in PostgreSQL.
 Config:
 Default: psql Drivers: psql: PSQL: Host: localhost Port: 15432 User: &amp;#34;&amp;#34; Password: &amp;#34;&amp;#34; DBName: &amp;#34;grip&amp;#34; SSLMode: disable </description>
     </item>
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     <item>
       <title>Query a Graph</title>
       <link>https://bmeg.github.io/grip/docs/queries/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/queries/</guid>
       <description></description>
     </item>
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     <item>
       <title>Referencing Fields</title>
       <link>https://bmeg.github.io/grip/docs/queries/jsonpath/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/queries/jsonpath/</guid>
       <description>Referencing Vertex/Edge Properties Several operations (where, fields, render, etc.) reference properties of the vertices/edges during the traversal. GRIP uses a variation on JSONPath syntax as described in http://goessner.net/articles/ to reference fields during traversals.
 The following query:
 O.query().V([&amp;quot;ENSG00000012048&amp;quot;]).as_(&amp;quot;gene&amp;quot;).out(&amp;quot;variant&amp;quot;) Starts at vertex ENSG00000012048 and marks as gene:
 { &amp;quot;gid&amp;quot;: &amp;quot;ENSG00000012048&amp;quot;, &amp;quot;label&amp;quot;: &amp;quot;gene&amp;quot;, &amp;quot;data&amp;quot;: { &amp;quot;symbol&amp;quot;: { &amp;quot;ensembl&amp;quot;: &amp;quot;ENSG00000012048&amp;quot;, &amp;quot;hgnc&amp;quot;: 1100, &amp;quot;entrez&amp;quot;: 672, &amp;quot;hugo&amp;quot;: &amp;quot;BRCA1&amp;quot; } &amp;quot;transcipts&amp;quot;: [&amp;quot;ENST00000471181.7&amp;quot;, &amp;quot;ENST00000357654.8&amp;quot;, &amp;quot;ENST00000493795.5&amp;quot;] } } as &amp;ldquo;gene&amp;rdquo; and traverses the graph to:</description>
     </item>
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     <item>
       <title>Security</title>
       <link>https://bmeg.github.io/grip/docs/security/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/security/</guid>
       <description></description>
     </item>
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     <item>
       <title>Setup your Database</title>
       <link>https://bmeg.github.io/grip/docs/databases/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/databases/</guid>
       <description></description>
     </item>
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     <item>
       <title>SQL</title>
       <link>https://bmeg.github.io/grip/docs/databases/sql/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/databases/sql/</guid>
       <description>Connect to an existing SQL database Note: This driver is being superseded by the GRIPPER engine
 GRIP supports modeling an existing SQL database as a graph. GRIP has been tested against PostgreSQL, but should work with MySQL (4.1+) and MariaDB.
 Since GRIP uses Go&amp;rsquo;s database/sql package, we could (in thoery) support any SQL databases listed on: https://github.com/golang/go/wiki/SQLDrivers. Open an issue if you would like to request support for your favorite SQL database.</description>
     </item>
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     <item>
       <title>TCGA RNA Expression</title>
       <link>https://bmeg.github.io/grip/docs/tutorials/tcga-rna/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/tutorials/tcga-rna/</guid>
       <description>Explore TCGA RNA Expression Data Create the graph
 grip create tcga-rna Get the data
@@ -291,15 +291,15 @@ curl -O http://download.cbioportal.org/gbm_tcga_pub2013.tar.gz tar xvzf gbm_tcga
 ./example/load_matrix.py tcga-rna gbm_tcga_pub2013/data_RNA_Seq_v2_expression_median.txt -t --index-col 1 --no-vertex --edge &#39;RNA:{_gid}&#39; rna Connect Clinical data to subtypes
 ./example/load_matrix.py tcga-rna gbm_tcga_pub2013/data_clinical.txt --no-vertex -e &amp;quot;{EXPRESSION_SUBTYPE}&amp;quot; subtype --dst-vertex &amp;quot;{EXPRESSION_SUBTYPE}&amp;quot; Subtype Load Hugo Symbol to EntrezID translation table from RNA matrix annotations</description>
     </item>
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     <item>
       <title>Tutorials</title>
       <link>https://bmeg.github.io/grip/docs/tutorials/</link>
       <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
-      
+
       <guid>https://bmeg.github.io/grip/docs/tutorials/</guid>
       <description></description>
     </item>
-    
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   </channel>
 </rss>

website/content/docs.md

@@ -14,9 +14,9 @@ MongoDB, Elasticsearch, PostgreSQL, MySQL, MariaDB, Badger, and LevelDB.
 Properties of an GRIP graph:
 
 * Both vertices and edges in a graph can have any number of properties associated with them.
-* There are many types of vertices and edges in a graph. Thus two vertices may have myriad types of edges
-  connecting them reflecting myriad types of relationships.
+* There are many types of vertices and edges in a graph. Two vertices may have many types of edges
+  connecting them, thus reflecting a myriad of relationship types.
 * Edges in the graph are directed, meaning they have a source and destination.
 
 GRIP also provides a query API for the traversing, analyzing and manipulating your graphs. Its syntax is inspired by
-[Apache TinkerPop](http://tinkerpop.apache.org/). Learn more [here](/docs/queries/getting_started).
+[Apache TinkerPop](http://tinkerpop.apache.org/). Learn more [here](/docs/queries/getting_started) about GRIP and its application for querying the Bio Medical Evidence Graph ([BMEG](https://bmeg.io)).

website/content/download.md

@@ -19,7 +19,7 @@ docker run bmeg/grip grip server
 ```
 
 <h3>Build From Source</h3>
-Go 1.12 or above suggested
+Recommended [Go](https://golang.org/) version 1.12 or later.
 
 ```shell
 $ git clone https://github.com/bmeg/grip.git

website/content/graph_schemas.md

@@ -8,20 +8,20 @@ menu:
 # Graph Schemas
 
 Graph schemas are themselves an instance of a graph. As such, they can be traversed like any other graph.
-The schemas are automatically added to the database following the naming pattern `{graph-name}__schema__`.
+The schemas are automatically added to the database following the naming pattern. `{graph-name}__schema__`
 
-## Get the schema of a graph
+## Get the Schema of a Graph
 
-The schema of a graph can be accessed via a GET request to `/v1/graph/{graph-name}/schema`.
+The schema of a graph can be accessed via a GET request to `/v1/graph/{graph-name}/schema`
 
-Alternatively, you can use the grip CLI: `grip schema get {graph-name}`.
+Alternatively, you can use the grip CLI. `grip schema get {graph-name}`
 
-## Describing graph schemas
+## Describing Graph Schemas
 There are several methods for describing the schema of a graph.
 
 - Provide the schema (as a YAML file) to the server at runtime. `grip server --schema {schema-file}`
-- POST the schema `/v1/graph/{graph-name}/schema` via curl or use the CLI `grip schema post --yaml {file} --json {file}`.
-- Configure Grip to build the schema by sampling the data in each graph.
+- POST the schema `/v1/graph/{graph-name}/schema` via curl or use the CLI. `grip schema post --yaml {file} --json {file}`
+- Configure GRIP to build the schema by sampling the data in each graph.
 
 ```yaml
 Server: