diff options
Diffstat (limited to 'topics/genenetwork')
| -rw-r--r-- | topics/genenetwork/Case_Attributes_GN2 | 2 | ||||
| -rw-r--r-- | topics/genenetwork/genenetwork-services.gmi | 122 | ||||
| -rw-r--r-- | topics/genenetwork/genenetwork-streaming-functionality.gmi | 43 | ||||
| -rw-r--r-- | topics/genenetwork/starting_gn1.gmi | 4 |
4 files changed, 168 insertions, 3 deletions
diff --git a/topics/genenetwork/Case_Attributes_GN2 b/topics/genenetwork/Case_Attributes_GN2 new file mode 100644 index 0000000..52a956f --- /dev/null +++ b/topics/genenetwork/Case_Attributes_GN2 @@ -0,0 +1,2 @@ +# Update Case Attributes to capture hierarchy info +## The following provides guidelines and insight regarding case attributes as used in GeneNetwork Webservice searches diff --git a/topics/genenetwork/genenetwork-services.gmi b/topics/genenetwork/genenetwork-services.gmi new file mode 100644 index 0000000..717fdd8 --- /dev/null +++ b/topics/genenetwork/genenetwork-services.gmi @@ -0,0 +1,122 @@ +# GeneNetwork Services + +## Tags + +* type: documentation +* keywords: documentation, docs, doc, services, genenetwork services + +## GeneNetwork Core Services + +GeneNetwork is composed of a number of different services. This document attempts to document all the services that make up GeneNetwork and document what links give access to the services. + +### GeneNetwork2 + +This is the main user-interface to the entire GeneNetwork system. + +#### Links + +=> https://github.com/genenetwork/genenetwork2 Repository +=> https://genenetwork.org/ GN2 on production +=> https://fallback.genenetwork.org/ GN2 on old production +=> https://cd.genenetwork.org/ GN2 on CI/CD +=> https://staging.genenetwork.org/ GN2 on staging + +### GeneNetwork3 + +This is the main API server for GeneNetwork. + +#### Links + +=> https://github.com/genenetwork/genenetwork3 Repository +=> https://genenetwork.org/api3/ GN3 on production +=> https://fallback.genenetwork.org/api3/ GN3 on old production +=> https://cd.genenetwork.org/api3/ GN3 on CI/CD +=> https://staging.genenetwork.org/api3/ GN3 on staging + +### Sparql Service + +The SparQL service is served from a Virtuoso-OSE service. + +=> https://issues.genenetwork.org/topics/deploy/our-virtuoso-instances We have notes on our virtuoso instances here. + + +#### Links + +=> https://github.com/genenetwork/genenetwork3 Repository +=> https://sparql.genenetwork.org/sparql/ sparql-service on production +* ??? sparql-service on old production +* ??? sparql-service on CI/CD +* ??? sparql-service on staging + +### GN-Auth + +This is the authorisation server for the GeneNetwork system. + +#### Links + +=> https://git.genenetwork.org/gn-auth/ Repository +=> https://auth.genenetwork.org/ gn-auth on production +=> https://fallback.genenetwork.org/gn-auth/ gn-auth on old production +* ??? gn-auth on CI/CD +=> https://staging-auth.genenetwork.org/ gn-auth on staging + +### GN-Uploader + +This service is to be used for uploading data to GeneNetwork. It is currently in development (best case, alpha). + +#### Links + +=> https://git.genenetwork.org/gn-uploader/ Repository +* ??? gn-uploader on production +* ??? gn-uploader on old production +* ??? gn-uploader on CI/CD +=> https://staging-uploader.genenetwork.org/ gn-uploader on staging + +### Aliases Server + +An extra server to respond with aliases for genetic (etc.) symbols. + +This is currently a project in racket, but we should probably pull in the features in this repository into one of the others (probably GeneNetwork3) and trash this repository. + +#### Links + +=> https://github.com/genenetwork/gn3 Repository +=> https://genenetwork.org/gn3/ aliases-server on production +=> https://fallback.genenetwork.org/gn3/ aliases-server on old production +=> https://cd.genenetwork.org/gn3/ aliases-server on CI/CD +=> https://staging.genenetwork.org/gn3/ aliases-server on staging + +### Markdown Editing Server + +#### Links + +=> https://git.genenetwork.org/gn-guile/ Repository +=> https://genenetwork.org/facilities/ markdown-editing-server on production +=> https://fallback.genenetwork.org/facilities/ markdown-editing-server on old production +=> https://cd.genenetwork.org/facilities/ markdown-editing-server on CI/CD +=> https://staging.genenetwork.org/facilities/ markdown-editing-server on staging + +## Support Services + +These are other services that support the development and maintenance of the core services. + +### Issue Tracker + +We use a text-based issue tracker that is accessible via +=> https://issues.genenetwork.org/ + +The repository for this service is at +=> https://github.com/genenetwork/gn-gemtext-threads/ + +### Repositories Server + +This is where a lot of the genenetwork repositories live. You can access it at +=> https://git.genenetwork.org/ + +### Continuous Integration Service + +… + +=> https://ci.genenetwork.org/ + +### … diff --git a/topics/genenetwork/genenetwork-streaming-functionality.gmi b/topics/genenetwork/genenetwork-streaming-functionality.gmi new file mode 100644 index 0000000..4f81eea --- /dev/null +++ b/topics/genenetwork/genenetwork-streaming-functionality.gmi @@ -0,0 +1,43 @@ +# Genenetwork Streaming Functionality + +## Tags +* type: documentation +* Keywords: documentation, docs, genenetwork, streaming + +### Introduction +Genenetwork implements streaming functionality that logs results from a running external process to a terminal emulator. + +The streaming functionality can be divided into several sections. + +### Streaming UI +The terminal emulator is implemented using the `xterm.js` library and +logs results from the GN3 API. + +See: +=> https://github.com/xtermjs/xterm.js + +### Streaming API +This is the main endpoint for streaming: + +See reference: +=> https://github.com/genenetwork/genenetwork3/gn3/api/streaming.py + +### How to Integrate + +#### Import the `enable_streaming` Decorator + +``` +from gn3.computations.streaming import enable_streaming +``` + +#### Apply the Decorator to Your Endpoint that Runs an External Process + +Note: To run the external process, use the `run_process` function, +which captures the `stdout` in a file identified by the `run_id`. + +``` +@app.route('/your-endpoint') +@enable_streaming +def your_endpoint(streaming_output_file): + run_process(command, streaming_output_file, run_id) +``` diff --git a/topics/genenetwork/starting_gn1.gmi b/topics/genenetwork/starting_gn1.gmi index efbfd0f..e31061f 100644 --- a/topics/genenetwork/starting_gn1.gmi +++ b/topics/genenetwork/starting_gn1.gmi @@ -51,9 +51,7 @@ On an update of guix the build may fail. Try #######################################' # Environment Variables - private ######################################### - # sql_host = '[1]tux02.uthsc.edu' - # sql_host = '128.169.4.67' - sql_host = '172.23.18.213' + sql_host = '170.23.18.213' SERVERNAME = sql_host MYSQL_SERVER = sql_host DB_NAME = 'db_webqtl' |