LIST OF CHANGES for npg_ranger project

upgrade winston from 2.4.4 to 3.4.0
upgrade mongodb from 2.2.36 to 4.3.1
upgrade commander from 2.20.0 to 8.3.0
upgrade @prantlf/jsonlint from 8.0.2 to 10.2.0
upgrade async from 3.1.0 to 3.2.3
upgrade config-chain from 1.1.12 to 1.1.13
upgrade fs-extra from 8.1.0 to 10.0.0
upgrade http-shutdown from 1.2.1 to 1.2.2
upgrade moment from 2.24.0 to 2.29.1
upgrade semver from 6.3.0 to 7.3.5
upgrade send from 0.17.1 to 0.17.2
upgrade browserify from 16.5.0 to 17.0.0
upgrade decache from 4.5.1 to 4.6.1
upgrade grunt from 1.0.4 to 1.4.1
upgrade grunt-browserify from 5.3.0 to 6.0.0
upgrade grunt-jsdoc from 2.4.0 to 2.4.1
upgrade grunt-jsonlint from 2.0.0 to 2.1.3
upgrade pem from 1.14.3 to 1.14.4
upgrade tmp from 0.1.0 to 0.2.1
add GitHub Action and upgraded to minconda 4.10.3
add support for iRODS 4.2 clients in containers

release 3.0.0

upgrade node version to support node 10 and 12
- remove support for node 6 and 8
- update tests code to be compatible with new node versions
upgrade package dependencies and developer dependencies
modify test checking start up failure to improve test stability
added support for HTTP POST requests in server using header
- encodes regions and passes it through headers
- updated tests from GET that apply to POST
- added new tests unique to POST
add a JSON schema that POST requests query must follow
implement new module to differentiate between valid multiregion queries and invalid duplicate values in queries
- checks array of objects (valid multiregions) versus array of values (invalid)
- created test spec to check functionality
implement new module to encode and decode the multiregions headers
- gzips header and then converts to base64
- created test spec to check functionality
implement new module to validate POST request query
- checks if valid JSON first, then if fits the aforementioned JSON schema
- checks range starts and ends
- collapses any overlapping regions
- created test spec to test functionality
update Docker for openstack
- update ubuntu image to 18.04 from 14.04
- update node version to 10.16.3 from 6.11.4
- update mongo to 3.6.14 from 3.2.4
- update apache httpd image to 2.4.41 from 2.4.27
- update docker-compose version to 3 from 2
- deploy bioinformatic tools using Conda
- switch to newest versions of samtools, htslib, freebayes, biobambam
- improve documentation
change installation method for dependencies in travis to use conda
- add check for biobambam to also use cache
replace biobambam's "bamstreamingmarkduplicates" with samtools' "markdup"
- still present in dev tests
fix existing bug in ranger client for outputting and piping into file
- used to cause samtools errors in file and cause loggers to not display

release 2.0.0

upgrade async to 2.4.1 from 2.1.4
upgrade browserify to 14.4.0 from 13.3.0
upgrade fs-extra to 3.0.1 from 2.0.0
upgrade grunt-contrib-clean to 1.1.0 from 1.0.0
upgrade grunt-jasmine-nodejs to 1.6.0 from 1.5.4
upgrade http-shutdown to 1.2.0 from 1.1.0
upgrade moment to 2.18.1 from 2.17.1
upgrade mongodb to 2.2.29 from 2.2.22
upgrade pem to 1.9.7 from 1.9.4
upgrade request to 2.81.0 from 2.79.0
upgrade send to 0.15.3 from 0.14.2
update json response for server error reporting
update http error codes reported according to spec
- httperror constructor does not take verbose anymore
- trying to use unknown codes will result in 500 and log
- remove 406
- replace 409 & 422 with 400 + tailored status message
move trailer logic from error to controller
simplify url path to /ga4gh/sample (remove 'v.0.1/get')
upgrade samtools/htslib to 1.5
fix header key name for token authorisation
- client sends token under 'Authorization' header
- client formats token string as 'Bearer XXX'
- server expects token under 'authorization' header (lowercase)
- server tries to parse token string from 'Bearer XXX'
drop official support for node 4.x
update content-type to match spec
client warns on unsupported versions of json from server
set htsget as root element in JSON messages
update ranger Dockerfile to upgrade ranger docker to
- httpd@2.4.27
- npg_ranger@2.0.0
mark support for version ~1.0.0 of spec
fix complementary bugs in token use
- server returns auth header for redirection
- client only uses token from configuration for first request
remove legacy prefix/sufix code from htsget json proc
DataAccess sends access groups as array per file
don't try to suggest authurl when token missing because it may not make sense in complex configs
test with node 6.11.4 in travis matrix
support empty mediatype in data uri
switch to npm@4.5.0 in travis
set node@6.11.4 and npm@4.5.0 in package.json

release 1.4.2

fix not showing errors when next process in pipe closes
fix bug premature end of output stream when piping to output and end of stream in input (response)

release 1.4.1

update database entries in docker for public data
update ranger Dockerfile to upgrade ranger docker to

release 1.4.0

add options to enable https communication between npg_ranger and npg_sentry

release 1.3.0

parameter in CLI for CA
parameter in CLI for token configuration
use request library to support proxy env variables for CLI client
switch to streaming for CLI client
upgrade mongodb to 2.2.22 from 2.2.21
upgrade js-md5 to 0.4.2 from 0.4.1
upgrade winston to 2.3.1 from 2.3.0
upgrade send to 0.14.2 from 0.14.1
add new authorisation strategy; make authorisation requests to npg_sentry via tokens

release 1.2.0

remove directly logging to file due to winston bug
add flags to change logging level
all logging output is now sent to stderr
upgrade mongodb to 2.2.21 from 2.2.12
upgrade browserify to 13.3.0 from 13.1.1
upgrade moment to 2.17.1 from 2.17.0
upgrade pem to 1.9.4 from 1.9.2
upgrade fs-extra to 2.0.0 from 1.0.0

release 1.1.0

cwd before executing pipelines and cleaning after pipeline finishes
added more filters for /sample url
switch to htslib@1.3.2 with curl support and samtools@1.3.1-npg-Sep2016 in Travis
remove forwarding protocol from proxy, use protocol only from conf
upgrade moment to 2.17.0 from 2.16.0
upgrade mongodb to 2.2.12 from 2.2.11
upgrade pem to 1.9.2 from 1.8.3
upgrade tmp to 0.0.31 from 0.0.30
do not allow query strings containing multiple attribute-value pairs for the same attribute
upgrade Freebayes to 1.1.0 from 1.0.2-npg-Aug2016 in TravisCI and docs
include docker configuration to deploy with containers

release 1.0.0

show error in log when controller tests fail to cleanup
bring back test for unknown server, keep external servers as pending tests
security option for server start (TLS)
/file url now serves files of all formats without processing

release 0.7.0

use npg_ranger server for roundtrip tests
add prototype for reference resolve
upgrade moment to 2.16.0 from 2.15.2
upgrade tmp to 0.0.30 from 0.0.29
upgrade fs-extra to 1.0.0 from ^0.30.0
upgrade winston to 2.3.0 from 2.2.0

release 0.6.0

example apache.conf in docs
badges in README.md
add cluster support
faster server shutdown with http-shutdown

release 0.5.0

allow for email in the remote user value
server/client version from package.json
updated docs for 0.5.0
increase timouts for some tests
remove assert for process.env.USER in bin/server
upgrade browserify to 13.1.1 from 13.1.0
upgrade moment to 2.15.2 from 2.15.1
upgrade mongodb to 2.2.11 from 2.2.10

release 0.4.0

set node recomended to >= 4.5.0 in package.json
add config-chain 1.1.11
upgrade moment to 2.15.1 from 2.14.1
upgrade mongodb to 2.2.10 from 2.2.8
upgrade tmp to 0.0.29 from 0.0.28
use npm 3.10.7 in travis
use node 4.5.0 in travis
kill all processes after -g seconds after client disconnection
Provide VCF files using freebayes
add new module to handle config options
fix error in interpreting the end range value in the user query
client library - an option to accept trailers and failing the overall request if data is truncated
client script - exit with error code if the request is unsuccessful
server - only set trailers if the client declared that it accepts them
restrict request types handled by the server to GET and OPTIONS
add a separate handler for OPTIONS request, set CORS headers
read-only configuration when options are read from a command line
proxy-aware server configuration
validation for reference name user input
full cycle tests using bioinf tools, compiled tools cached in travis

release 0.3.0

publish as npm package
expand docs for installing and running client/server
upgrade mongodb from 2.2.4 to 2.2.8
upgrade grunt-jasmine-nodejs from 1.5.3 to 1.5.4
upgrade load-grunt-tasks from 'latest' to 3.5.2
fix wrongly reporting error while closing fd in client
compliance with the GA4GH API: redirection urls as objects
restructure documentation
upgrading moment to 2.14.1 from 2.13.0
upgrading grunt-jscs to 3.0.1 from 3.0.0
new client code to comply with GA4GH API
client code fit to use with browserify

release 0.2.1

compliance with the GA4GH API: use upper case for format

release 0.2.0

application model and controller as separate modules
GA4GH API url and redirection
logging with Winston

release 0.1.1

HTTP errors compliant with GA4GH API.

release 0.1

Initial version: a node.js server running on a socket or on a port serving either individual files or merging all available files for a sample, a range to serve and data format to serve can be specified, mongodb is used to find file locations, authorization is switched on by default (can be disabled), relies on authentication done elsewhere (the incoming request should have X-Remote-User header set), so this server should be run behind a reverse proxy that will perform authentication and set the header, 'data_truncated' trailer header is set to 'false' if the data processing pipeline completed successfully, in case of an error in the pipeline it is set to 'true'.

Package detail

@absanger/npg_ranger

readme

changelog