From fac5c378cadd027959ca7bc6358890cbc34f4efb Mon Sep 17 00:00:00 2001 From: adamstruck Date: Mon, 11 Mar 2019 15:39:03 -0700 Subject: [PATCH] update site for new release --- docs/categories/index.xml | 4 +- docs/docs/databases/elastic/index.html | 52 +++++------ docs/docs/databases/index.html | 52 +++++------ docs/docs/databases/kvstore/index.html | 52 +++++------ docs/docs/databases/mongo/index.html | 52 +++++------ docs/docs/databases/psql/index.html | 52 +++++------ docs/docs/databases/sql/index.html | 52 +++++------ docs/docs/developers/index.html | 52 +++++------ docs/docs/index.html | 54 +++++------ docs/docs/index.xml | 80 ++++++++--------- docs/docs/queries/getting_started/index.html | 54 +++++------ docs/docs/queries/graph_schemas/index.html | 52 +++++------ docs/docs/queries/graphql/index.html | 52 +++++------ docs/docs/queries/index.html | 52 +++++------ docs/docs/queries/jsonpath/index.html | 52 +++++------ docs/docs/queries/operations/index.html | 52 +++++------ docs/docs/security/basic/index.html | 52 +++++------ docs/docs/security/index.html | 52 +++++------ docs/docs/tutorials/amazon/index.html | 52 +++++------ docs/docs/tutorials/index.html | 52 +++++------ .../docs/tutorials/pathway-commons/index.html | 52 +++++------ docs/docs/tutorials/tcga-rna/index.html | 52 +++++------ docs/download/index.html | 58 ++++++------ docs/index.html | 26 +++--- docs/index.xml | 90 +++++++++---------- docs/sitemap.xml | 50 +++++------ docs/tags/index.xml | 4 +- website/config.yaml | 2 +- 28 files changed, 679 insertions(+), 679 deletions(-) diff --git a/docs/categories/index.xml b/docs/categories/index.xml index b0a071b3..ad04d5f0 100644 --- a/docs/categories/index.xml +++ b/docs/categories/index.xml @@ -2,12 +2,12 @@ Categories on GRIP - https://docs.bmeg.io/grip/categories/ + https://bmeg.github.io/grip/categories/ Recent content in Categories on GRIP Hugo -- gohugo.io en-us - + diff --git a/docs/docs/databases/elastic/index.html b/docs/docs/databases/elastic/index.html index e49aab8a..33f2fc53 100644 --- a/docs/docs/databases/elastic/index.html +++ b/docs/docs/databases/elastic/index.html @@ -12,18 +12,18 @@ - - - - - + + + + + - - + + - + @@ -32,11 +32,11 @@
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    Overview

    GRIP also provides a query API for the traversing, analyzing and manipulating your graphs. Its syntax is inspired by -Apache TinkerPop. Learn more here.

    +Apache TinkerPop. Learn more here.

    • diff --git a/docs/docs/index.xml b/docs/docs/index.xml index 5fa31105..bd0020dd 100644 --- a/docs/docs/index.xml +++ b/docs/docs/index.xml @@ -2,20 +2,20 @@ Docs on GRIP - https://docs.bmeg.io/grip/docs/ + https://bmeg.github.io/grip/docs/ Recent content in Docs on GRIP Hugo -- gohugo.io en-us - + - https://docs.bmeg.io/grip/docs/tutorials/pathway-commons/ + https://bmeg.github.io/grip/docs/tutorials/pathway-commons/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/tutorials/pathway-commons/ + https://bmeg.github.io/grip/docs/tutorials/pathway-commons/ 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: @@ -23,10 +23,10 @@ grip rdf --dump --gzip pc PathwayCommons10.All.BIOPAX.owl.gz -m http://pathwayco Amazon Purchase Network - https://docs.bmeg.io/grip/docs/tutorials/amazon/ + https://bmeg.github.io/grip/docs/tutorials/amazon/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/tutorials/amazon/ + https://bmeg.github.io/grip/docs/tutorials/amazon/ 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 python $GOPATH/src/github.com/bmeg/grip/example/amazon_convert.py amazon-meta.txt.gz amazon.data Create a graph called ‘amazon’ @@ -39,10 +39,10 @@ pip install "git+https://github.com/bmeg/grip.git#egg=gripql&su Basic Auth - https://docs.bmeg.io/grip/docs/security/basic/ + https://bmeg.github.io/grip/docs/security/basic/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/security/basic/ + https://bmeg.github.io/grip/docs/security/basic/ 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’s not readable by everyone: $ chmod 600 grip.config.yml To use the password, set the GRIP_USER and GRIP_PASSWORD environment variables: @@ -50,19 +50,19 @@ $ chmod 600 grip.config.yml To use the password, set the GRIP_USER and GRIP_PAS Developers - https://docs.bmeg.io/grip/docs/developers/ + https://bmeg.github.io/grip/docs/developers/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/developers/ + https://bmeg.github.io/grip/docs/developers/ Elasticsearch - https://docs.bmeg.io/grip/docs/databases/elastic/ + https://bmeg.github.io/grip/docs/databases/elastic/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/elastic/ + https://bmeg.github.io/grip/docs/databases/elastic/ Elasticsearch GRIP supports storing vertices and edges in Elasticsearch. Config: Database: elasticsearch Elasticsearch: URL: "http://localhost:9200" DBName: "gripdb" Username: "" Password: "" @@ -70,10 +70,10 @@ Database: elasticsearch Elasticsearch: URL: "http://localhost:9200& Embedded KV Store - https://docs.bmeg.io/grip/docs/databases/kvstore/ + https://bmeg.github.io/grip/docs/databases/kvstore/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/kvstore/ + https://bmeg.github.io/grip/docs/databases/kvstore/ Embedded Key Value Stores GRIP supports storing vertices and edges in a variety of key-value stores including: Badger BoltDB LevelDB RocksDB Config: # pick one of: badger, bolt, level, rocks Database: badger KVStorePath: grip.db @@ -81,10 +81,10 @@ Database: elasticsearch Elasticsearch: URL: "http://localhost:9200& Getting Started - https://docs.bmeg.io/grip/docs/queries/getting_started/ + https://bmeg.github.io/grip/docs/queries/getting_started/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/getting_started/ + https://bmeg.github.io/grip/docs/queries/getting_started/ 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 pip install "git+https://github.com/bmeg/grip.git#subdirectory=gripql/python" Let’s go through the features currently supported in the python client. First, import the client and create a connection to an GRIP server: @@ -93,10 +93,10 @@ import gripql G = gripql.Connection('http://bmeg.io').graph("bm Graph Schemas - https://docs.bmeg.io/grip/docs/queries/graph_schemas/ + https://bmeg.github.io/grip/docs/queries/graph_schemas/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/graph_schemas/ + https://bmeg.github.io/grip/docs/queries/graph_schemas/ 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}. @@ -105,10 +105,10 @@ Describing graph schemas There are several methods for desribing the schema of a GraphQL - https://docs.bmeg.io/grip/docs/queries/graphql/ + https://bmeg.github.io/grip/docs/queries/graphql/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/graphql/ + https://bmeg.github.io/grip/docs/queries/graphql/ 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 Load built-in example graph Loading the example data and the example schema: @@ -120,10 +120,10 @@ curl -X POST -H "Content-Type:application/graphql" -d '{__ MongoDB - https://docs.bmeg.io/grip/docs/databases/mongo/ + https://bmeg.github.io/grip/docs/databases/mongo/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/mongo/ + https://bmeg.github.io/grip/docs/databases/mongo/ MongoDB GRIP supports storing vertices and edges in MongoDB. Config: Database: mongodb MongoDB: URL: "localhost:27017" DBName: "gripdb" Username: "" Password: "" @@ -131,10 +131,10 @@ Database: mongodb MongoDB: URL: "localhost:27017" DBName: & Operations - https://docs.bmeg.io/grip/docs/queries/operations/ + https://bmeg.github.io/grip/docs/queries/operations/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/operations/ + https://bmeg.github.io/grip/docs/queries/operations/ Start a Traversal .V([ids]) Start query from Vertex G.query().V() Returns all vertices in graph G.query().V(["vertex1]") Returns: @@ -146,10 +146,10 @@ G.query().E(["edge1"]) Returns: PostgreSQL - https://docs.bmeg.io/grip/docs/databases/psql/ + https://bmeg.github.io/grip/docs/databases/psql/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/psql/ + https://bmeg.github.io/grip/docs/databases/psql/ PostgreSQL GRIP supports storing vertices and edges in PostgreSQL. Config: Database: psql PSQL: Host: localhost Port: 15432 User: "" Password: "" DBName: "" SSLMode: disable @@ -157,19 +157,19 @@ Database: psql PSQL: Host: localhost Port: 15432 User: "" Pass Query a Graph - https://docs.bmeg.io/grip/docs/queries/ + https://bmeg.github.io/grip/docs/queries/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/ + https://bmeg.github.io/grip/docs/queries/ Referencing Fields - https://docs.bmeg.io/grip/docs/queries/jsonpath/ + https://bmeg.github.io/grip/docs/queries/jsonpath/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/jsonpath/ + https://bmeg.github.io/grip/docs/queries/jsonpath/ 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(["ENSG00000012048"]).as_("gene").out("variant") Starts at vertex ENSG00000012048 and marks as gene: @@ -178,10 +178,10 @@ O.query().V(["ENSG00000012048"]).as_("gene") SQL - https://docs.bmeg.io/grip/docs/databases/sql/ + https://bmeg.github.io/grip/docs/databases/sql/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/sql/ + https://bmeg.github.io/grip/docs/databases/sql/ Connect to an existing SQL database 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’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. Configuration Notes DataSourceName is a driver-specific data source name, usually consisting of at least a database name and connection information. @@ -189,28 +189,28 @@ Configuration Notes DataSourceName is a driver-specific data source name, usual Security - https://docs.bmeg.io/grip/docs/security/ + https://bmeg.github.io/grip/docs/security/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/security/ + https://bmeg.github.io/grip/docs/security/ Setup your Database - https://docs.bmeg.io/grip/docs/databases/ + https://bmeg.github.io/grip/docs/databases/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/ + https://bmeg.github.io/grip/docs/databases/ TCGA RNA Expression - https://docs.bmeg.io/grip/docs/tutorials/tcga-rna/ + https://bmeg.github.io/grip/docs/tutorials/tcga-rna/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/tutorials/tcga-rna/ + https://bmeg.github.io/grip/docs/tutorials/tcga-rna/ Explore TCGA RNA Expression Data Create the graph grip create tcga-rna Get the data curl -O http://download.cbioportal.org/gbm_tcga_pub2013.tar.gz tar xvzf gbm_tcga_pub2013.tar.gz Load clinical data @@ -221,10 +221,10 @@ curl -O http://download.cbioportal.org/gbm_tcga_pub2013.tar.gz tar xvzf gbm_tcga Tutorials - https://docs.bmeg.io/grip/docs/tutorials/ + https://bmeg.github.io/grip/docs/tutorials/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/tutorials/ + https://bmeg.github.io/grip/docs/tutorials/ diff --git a/docs/docs/queries/getting_started/index.html b/docs/docs/queries/getting_started/index.html index 898bc20d..70a49a5a 100644 --- a/docs/docs/queries/getting_started/index.html +++ b/docs/docs/queries/getting_started/index.html @@ -12,18 +12,18 @@ - - - - - + + + + + - - + + - + @@ -32,11 +32,11 @@
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    Getting Started

    -

    GRIP has an API for making graph queries using structured data. Queries are defined using a series of step operations).

    +

    GRIP has an API for making graph queries using structured data. Queries are defined using a series of step operations).

    Install the Python Client

    diff --git a/docs/docs/queries/graph_schemas/index.html b/docs/docs/queries/graph_schemas/index.html index 40d935b3..769af6f1 100644 --- a/docs/docs/queries/graph_schemas/index.html +++ b/docs/docs/queries/graph_schemas/index.html @@ -12,18 +12,18 @@ - - - - - + + + + + - - + + - + @@ -32,11 +32,11 @@
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    GRaph Integration Platform (GRIP)

    - Download - Documentation + Download + Documentation
    diff --git a/docs/index.xml b/docs/index.xml index 91d3200e..cb3ea07b 100644 --- a/docs/index.xml +++ b/docs/index.xml @@ -2,20 +2,20 @@ GRIP - https://docs.bmeg.io/grip/ + https://bmeg.github.io/grip/ Recent content on GRIP Hugo -- gohugo.io en-us - + - https://docs.bmeg.io/grip/docs/tutorials/pathway-commons/ + https://bmeg.github.io/grip/docs/tutorials/pathway-commons/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/tutorials/pathway-commons/ + https://bmeg.github.io/grip/docs/tutorials/pathway-commons/ 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: @@ -23,10 +23,10 @@ grip rdf --dump --gzip pc PathwayCommons10.All.BIOPAX.owl.gz -m http://pathwayco Amazon Purchase Network - https://docs.bmeg.io/grip/docs/tutorials/amazon/ + https://bmeg.github.io/grip/docs/tutorials/amazon/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/tutorials/amazon/ + https://bmeg.github.io/grip/docs/tutorials/amazon/ 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 python $GOPATH/src/github.com/bmeg/grip/example/amazon_convert.py amazon-meta.txt.gz amazon.data Create a graph called ‘amazon’ @@ -39,10 +39,10 @@ pip install "git+https://github.com/bmeg/grip.git#egg=gripql&su Basic Auth - https://docs.bmeg.io/grip/docs/security/basic/ + https://bmeg.github.io/grip/docs/security/basic/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/security/basic/ + https://bmeg.github.io/grip/docs/security/basic/ 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’s not readable by everyone: $ chmod 600 grip.config.yml To use the password, set the GRIP_USER and GRIP_PASSWORD environment variables: @@ -50,29 +50,29 @@ $ chmod 600 grip.config.yml To use the password, set the GRIP_USER and GRIP_PAS Developers - https://docs.bmeg.io/grip/docs/developers/ + https://bmeg.github.io/grip/docs/developers/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/developers/ + https://bmeg.github.io/grip/docs/developers/ Download - https://docs.bmeg.io/grip/download/ + https://bmeg.github.io/grip/download/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/download/ - Download 0.4.0 Linux MacOS Windows is not supported sorry! Release History See the Releases page for release history. + https://bmeg.github.io/grip/download/ + Download 0.5.0 Linux MacOS Windows is not supported sorry! Release History See the Releases page for release history. Build From Source $ mkdir -p $GOPATH/src/github.com/bmeg $ cd $GOPATH/src/github.com/bmeg $ git clone https://github.com/bmeg/grip.git $ cd grip $ make Elasticsearch - https://docs.bmeg.io/grip/docs/databases/elastic/ + https://bmeg.github.io/grip/docs/databases/elastic/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/elastic/ + https://bmeg.github.io/grip/docs/databases/elastic/ Elasticsearch GRIP supports storing vertices and edges in Elasticsearch. Config: Database: elasticsearch Elasticsearch: URL: "http://localhost:9200" DBName: "gripdb" Username: "" Password: "" @@ -80,10 +80,10 @@ Database: elasticsearch Elasticsearch: URL: "http://localhost:9200& Embedded KV Store - https://docs.bmeg.io/grip/docs/databases/kvstore/ + https://bmeg.github.io/grip/docs/databases/kvstore/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/kvstore/ + https://bmeg.github.io/grip/docs/databases/kvstore/ Embedded Key Value Stores GRIP supports storing vertices and edges in a variety of key-value stores including: Badger BoltDB LevelDB RocksDB Config: # pick one of: badger, bolt, level, rocks Database: badger KVStorePath: grip.db @@ -91,10 +91,10 @@ Database: elasticsearch Elasticsearch: URL: "http://localhost:9200& Getting Started - https://docs.bmeg.io/grip/docs/queries/getting_started/ + https://bmeg.github.io/grip/docs/queries/getting_started/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/getting_started/ + https://bmeg.github.io/grip/docs/queries/getting_started/ 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 pip install "git+https://github.com/bmeg/grip.git#subdirectory=gripql/python" Let’s go through the features currently supported in the python client. First, import the client and create a connection to an GRIP server: @@ -103,10 +103,10 @@ import gripql G = gripql.Connection('http://bmeg.io').graph("bm Graph Schemas - https://docs.bmeg.io/grip/docs/queries/graph_schemas/ + https://bmeg.github.io/grip/docs/queries/graph_schemas/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/graph_schemas/ + https://bmeg.github.io/grip/docs/queries/graph_schemas/ 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}. @@ -115,10 +115,10 @@ Describing graph schemas There are several methods for desribing the schema of a GraphQL - https://docs.bmeg.io/grip/docs/queries/graphql/ + https://bmeg.github.io/grip/docs/queries/graphql/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/graphql/ + https://bmeg.github.io/grip/docs/queries/graphql/ 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 Load built-in example graph Loading the example data and the example schema: @@ -130,10 +130,10 @@ curl -X POST -H "Content-Type:application/graphql" -d '{__ MongoDB - https://docs.bmeg.io/grip/docs/databases/mongo/ + https://bmeg.github.io/grip/docs/databases/mongo/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/mongo/ + https://bmeg.github.io/grip/docs/databases/mongo/ MongoDB GRIP supports storing vertices and edges in MongoDB. Config: Database: mongodb MongoDB: URL: "localhost:27017" DBName: "gripdb" Username: "" Password: "" @@ -141,10 +141,10 @@ Database: mongodb MongoDB: URL: "localhost:27017" DBName: & Operations - https://docs.bmeg.io/grip/docs/queries/operations/ + https://bmeg.github.io/grip/docs/queries/operations/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/operations/ + https://bmeg.github.io/grip/docs/queries/operations/ Start a Traversal .V([ids]) Start query from Vertex G.query().V() Returns all vertices in graph G.query().V(["vertex1]") Returns: @@ -156,10 +156,10 @@ G.query().E(["edge1"]) Returns: Overview - https://docs.bmeg.io/grip/docs/ + https://bmeg.github.io/grip/docs/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/ + https://bmeg.github.io/grip/docs/ 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. @@ -167,10 +167,10 @@ Properties of an GRIP graph: PostgreSQL - https://docs.bmeg.io/grip/docs/databases/psql/ + https://bmeg.github.io/grip/docs/databases/psql/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/psql/ + https://bmeg.github.io/grip/docs/databases/psql/ PostgreSQL GRIP supports storing vertices and edges in PostgreSQL. Config: Database: psql PSQL: Host: localhost Port: 15432 User: "" Password: "" DBName: "" SSLMode: disable @@ -178,19 +178,19 @@ Database: psql PSQL: Host: localhost Port: 15432 User: "" Pass Query a Graph - https://docs.bmeg.io/grip/docs/queries/ + https://bmeg.github.io/grip/docs/queries/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/ + https://bmeg.github.io/grip/docs/queries/ Referencing Fields - https://docs.bmeg.io/grip/docs/queries/jsonpath/ + https://bmeg.github.io/grip/docs/queries/jsonpath/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/queries/jsonpath/ + https://bmeg.github.io/grip/docs/queries/jsonpath/ 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(["ENSG00000012048"]).as_("gene").out("variant") Starts at vertex ENSG00000012048 and marks as gene: @@ -199,10 +199,10 @@ O.query().V(["ENSG00000012048"]).as_("gene") SQL - https://docs.bmeg.io/grip/docs/databases/sql/ + https://bmeg.github.io/grip/docs/databases/sql/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/sql/ + https://bmeg.github.io/grip/docs/databases/sql/ Connect to an existing SQL database 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’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. Configuration Notes DataSourceName is a driver-specific data source name, usually consisting of at least a database name and connection information. @@ -210,28 +210,28 @@ Configuration Notes DataSourceName is a driver-specific data source name, usual Security - https://docs.bmeg.io/grip/docs/security/ + https://bmeg.github.io/grip/docs/security/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/security/ + https://bmeg.github.io/grip/docs/security/ Setup your Database - https://docs.bmeg.io/grip/docs/databases/ + https://bmeg.github.io/grip/docs/databases/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/databases/ + https://bmeg.github.io/grip/docs/databases/ TCGA RNA Expression - https://docs.bmeg.io/grip/docs/tutorials/tcga-rna/ + https://bmeg.github.io/grip/docs/tutorials/tcga-rna/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/tutorials/tcga-rna/ + https://bmeg.github.io/grip/docs/tutorials/tcga-rna/ Explore TCGA RNA Expression Data Create the graph grip create tcga-rna Get the data curl -O http://download.cbioportal.org/gbm_tcga_pub2013.tar.gz tar xvzf gbm_tcga_pub2013.tar.gz Load clinical data @@ -242,10 +242,10 @@ curl -O http://download.cbioportal.org/gbm_tcga_pub2013.tar.gz tar xvzf gbm_tcga Tutorials - https://docs.bmeg.io/grip/docs/tutorials/ + https://bmeg.github.io/grip/docs/tutorials/ Mon, 01 Jan 0001 00:00:00 +0000 - https://docs.bmeg.io/grip/docs/tutorials/ + https://bmeg.github.io/grip/docs/tutorials/ diff --git a/docs/sitemap.xml b/docs/sitemap.xml index efb0e8e2..2e83e76e 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -3,107 +3,107 @@ xmlns:xhtml="http://www.w3.org/1999/xhtml"> - https://docs.bmeg.io/grip/docs/tutorials/pathway-commons/ + https://bmeg.github.io/grip/docs/tutorials/pathway-commons/ - https://docs.bmeg.io/grip/docs/tutorials/amazon/ + https://bmeg.github.io/grip/docs/tutorials/amazon/ - https://docs.bmeg.io/grip/docs/security/basic/ + https://bmeg.github.io/grip/docs/security/basic/ - https://docs.bmeg.io/grip/categories/ + https://bmeg.github.io/grip/categories/ 0 - https://docs.bmeg.io/grip/docs/developers/ + https://bmeg.github.io/grip/docs/developers/ - https://docs.bmeg.io/grip/docs/ + https://bmeg.github.io/grip/docs/ 0 - https://docs.bmeg.io/grip/download/ + https://bmeg.github.io/grip/download/ - https://docs.bmeg.io/grip/docs/databases/elastic/ + https://bmeg.github.io/grip/docs/databases/elastic/ - https://docs.bmeg.io/grip/docs/databases/kvstore/ + https://bmeg.github.io/grip/docs/databases/kvstore/ - https://docs.bmeg.io/grip/ + https://bmeg.github.io/grip/ 0 - https://docs.bmeg.io/grip/docs/queries/getting_started/ + https://bmeg.github.io/grip/docs/queries/getting_started/ - https://docs.bmeg.io/grip/docs/queries/graph_schemas/ + https://bmeg.github.io/grip/docs/queries/graph_schemas/ - https://docs.bmeg.io/grip/docs/queries/graphql/ + https://bmeg.github.io/grip/docs/queries/graphql/ - https://docs.bmeg.io/grip/docs/databases/mongo/ + https://bmeg.github.io/grip/docs/databases/mongo/ - https://docs.bmeg.io/grip/docs/queries/operations/ + https://bmeg.github.io/grip/docs/queries/operations/ - https://docs.bmeg.io/grip/docs/ + https://bmeg.github.io/grip/docs/ - https://docs.bmeg.io/grip/docs/databases/psql/ + https://bmeg.github.io/grip/docs/databases/psql/ - https://docs.bmeg.io/grip/docs/queries/ + https://bmeg.github.io/grip/docs/queries/ - https://docs.bmeg.io/grip/docs/queries/jsonpath/ + https://bmeg.github.io/grip/docs/queries/jsonpath/ - https://docs.bmeg.io/grip/docs/databases/sql/ + https://bmeg.github.io/grip/docs/databases/sql/ - https://docs.bmeg.io/grip/docs/security/ + https://bmeg.github.io/grip/docs/security/ - https://docs.bmeg.io/grip/docs/databases/ + https://bmeg.github.io/grip/docs/databases/ - https://docs.bmeg.io/grip/docs/tutorials/tcga-rna/ + https://bmeg.github.io/grip/docs/tutorials/tcga-rna/ - https://docs.bmeg.io/grip/tags/ + https://bmeg.github.io/grip/tags/ 0 - https://docs.bmeg.io/grip/docs/tutorials/ + https://bmeg.github.io/grip/docs/tutorials/ \ No newline at end of file diff --git a/docs/tags/index.xml b/docs/tags/index.xml index 512103ae..05c0931e 100644 --- a/docs/tags/index.xml +++ b/docs/tags/index.xml @@ -2,12 +2,12 @@ Tags on GRIP - https://docs.bmeg.io/grip/tags/ + https://bmeg.github.io/grip/tags/ Recent content in Tags on GRIP Hugo -- gohugo.io en-us - + diff --git a/website/config.yaml b/website/config.yaml index c7a47241..3376963a 100644 --- a/website/config.yaml +++ b/website/config.yaml @@ -1,4 +1,4 @@ -baseURL: https://docs.bmeg.io/grip +baseURL: https://bmeg.github.io/grip canonifyURLs: true languageCode: en-us title: GRIP