mitre/fusera issues and pull requests

#173 - Any way to mount dbGaP folder outside of AWS?

Issue - State: open - Opened by osowiecki over 1 year ago

#172 - is ngc file still a valid way to copy over controlled files within aws?

Issue - State: open - Opened by mirahan about 4 years ago

#171 - Mounting fastq files when available

Issue - State: open - Opened by AntonS-bio over 4 years ago

#170 - Instructions broken on install page

Issue - State: open - Opened by outpaddling over 4 years ago

#169 - Access from compute node to the fusera instance mount at master

Issue - State: open - Opened by duanjingqi over 4 years ago

#168 - Local and AWS dbGaP key not found using docker image

Issue - State: open - Opened by BrenKenna over 4 years ago - 1 comment

#167 - SDL API v2 returned a file without indicating what region it's in

Issue - State: open - Opened by cloudbroken over 4 years ago

#165 - Getting 'failed to decode response' error while running sracp

Issue - State: open - Opened by kjamrog about 5 years ago - 1 comment

#164 - Transport endpoint is not connected

Issue - State: open - Opened by ericweinberg about 5 years ago

#163 - Develop

Pull Request - State: closed - Opened by mattrbianchi about 5 years ago

#162 - Remove urfave/cli from listed pkg deps

Pull Request - State: closed - Opened by mattrbianchi about 5 years ago

#161 - Update master with version 2 code now that v1 is in a branch

Pull Request - State: closed - Opened by mattrbianchi about 5 years ago

#160 - Update for new changes in SDL API. Dubbed version 2

Pull Request - State: closed - Opened by mattrbianchi about 5 years ago

#159 - Change requester-pays param to fit SDL API's new accept-charges param

Issue - State: closed - Opened by mattrbianchi over 5 years ago - 1 comment

#158 - Provide `location-type` parameter to SDL API

Issue - State: closed - Opened by mattrbianchi over 5 years ago - 1 comment

#157 - Adapt Fusera to the possibility of getting new "redirect" links from API

Issue - State: closed - Opened by mattrbianchi over 5 years ago - 1 comment

#156 - Add AWS instance token functionality

Issue - State: closed - Opened by mattrbianchi over 5 years ago - 1 comment

#155 - "fusera mount" will fail if SSH terminal / session is closed ?

Issue - State: closed - Opened by fulxie over 5 years ago - 1 comment

#154 - Develop

Pull Request - State: closed - Opened by mattrbianchi over 5 years ago

#153 - Differentiate between API error and API being down

Issue - State: open - Opened by mattrbianchi over 5 years ago

#152 - 136/check root

Pull Request - State: closed - Opened by mattrbianchi over 5 years ago

#151 - Unable to install on Mac

Issue - State: closed - Opened by jcgrenier over 5 years ago - 3 comments

#150 - Change User-Agent to binary name and version for sdl req

Pull Request - State: closed - Opened by mattrbianchi over 5 years ago

#149 - Corrected passing of platform for sracp

Pull Request - State: closed - Opened by mattrbianchi over 5 years ago

#148 - sracp v0.0.17 on an AWS EC2 instance: DEBUG 2019/05/03 20:26:04 root.go:134: location given contained more than one "." which means it cannot be parsed according to expected cloud.region

Issue - State: closed - Opened by saulakravitz over 5 years ago - 1 comment
Labels: bug

#147 - allow_other FUSE option

Issue - State: closed - Opened by jonathonl over 5 years ago - 2 comments

#146 - Invalid location with sracp V0.0.17 on GCP

Issue - State: closed - Opened by jonathonl over 5 years ago - 1 comment
Labels: bug

#145 - Make fusera and sracp installable through package managers like apt-get.

Issue - State: open - Opened by mattrbianchi over 5 years ago

#144 - Fusera and scarp should include binary name and version in http requests to SDL

Issue - State: closed - Opened by mattrbianchi over 5 years ago

#143 - Add version to help message

Pull Request - State: closed - Opened by mattrbianchi over 5 years ago

#142 - Platform now set when using manual location

Pull Request - State: closed - Opened by mattrbianchi over 5 years ago

#141 - Issue 135/loc flag seg fault

Pull Request - State: closed - Opened by mattrbianchi over 5 years ago

#140 - Amazon Machine Image for fusera?

Issue - State: closed - Opened by ramoya over 5 years ago - 1 comment

#139 - fusera help should print version number

Issue - State: closed - Opened by saulakravitz over 5 years ago - 1 comment
Labels: enhancement

#138 - fusera and sracp should have diagnostic mode

Issue - State: open - Opened by saulakravitz over 5 years ago - 1 comment
Labels: enhancement

#137 - sracp should check that target location is writeable, and fail with error if not

Issue - State: closed - Opened by saulakravitz over 5 years ago
Labels: enhancement

#136 - fusera (and sracp?) should issue warning if run as 'root'

Issue - State: closed - Opened by saulakravitz over 5 years ago
Labels: enhancement

#135 - fusera 0.0.15 Segementation Violation

Issue - State: closed - Opened by saulakravitz over 5 years ago - 5 comments
Labels: bug

#134 - sracp 0.0.15 segmentation violation

Issue - State: closed - Opened by saulakravitz over 5 years ago - 1 comment
Labels: bug

#133 - Add ngc flag back for backwards compatibility

Pull Request - State: closed - Opened by mattrbianchi almost 6 years ago

#132 - Feature/ngc now token

Pull Request - State: closed - Opened by mattrbianchi almost 6 years ago

#131 - Add comparison to SRA toolkit to documentation

Issue - State: open - Opened by seandavi about 6 years ago - 3 comments

#130 - Add details of what data are available via fusera to documentation?

Issue - State: closed - Opened by seandavi about 6 years ago - 1 comment

#129 - Change location resolution to read the location from a file on GCP

Issue - State: closed - Opened by mattrbianchi about 6 years ago - 1 comment

#128 - Rm location

Pull Request - State: closed - Opened by mattrbianchi about 6 years ago

#127 - Better user experience with fusera's output

Issue - State: closed - Opened by mattrbianchi about 6 years ago

#126 - Better sdl printout

Pull Request - State: closed - Opened by mattrbianchi about 6 years ago

#125 - Add ability to read requester pays buckets

Pull Request - State: closed - Opened by mattrbianchi about 6 years ago

#124 - Add mock sdl api app for testing purposes

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago

#123 - Add live error logs for file read errors

Issue - State: open - Opened by mattrbianchi over 6 years ago

#122 - sracp progress printout is some times inaccurate

Issue - State: open - Opened by mattrbianchi over 6 years ago
Labels: bug

#121 - Fix metadata batch

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago

#120 - Add batch of 2k to metadata calls

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago

#119 - Fusera still mounts if all accessions fail

Issue - State: closed - Opened by mattrbianchi over 6 years ago
Labels: bug

#118 - Fusera shows no folders when location is faulty

Issue - State: closed - Opened by mattrbianchi over 6 years ago - 1 comment
Labels: bug

#117 - failed to locate accessions: API returned no accessions

Issue - State: closed - Opened by gversmee over 6 years ago

#116 - fusera with native URLs

Issue - State: closed - Opened by saulakravitz over 6 years ago
Labels: enhancement

#115 - fusera 0.0.8 and CWL

Issue - State: closed - Opened by saulakravitz over 6 years ago - 1 comment
Labels: bug

#114 - running with -a and a large list of accessions (5077) doesn't work

Issue - State: closed - Opened by saulakravitz over 6 years ago - 2 comments
Labels: bug

#113 - -ngc does not work (-n works)

Issue - State: closed - Opened by saulakravitz over 6 years ago - 1 comment

#112 - Simplify dockerfile

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago

#111 - Refactor nr pkg to become sdl pkg

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago

#110 - Long list of Accessions in command line --> error

Issue - State: closed - Opened by saulakravitz over 6 years ago

#109 - document how to launch fusera through vm orchestration on GCP and AWS

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#108 - Fusera in Daemon Mode

Issue - State: closed - Opened by saulakravitz over 6 years ago

#107 - Add a fusera docker image to docker hub

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#106 - have unmount command only attempt to unmount fusera by checking for .initialized file

Issue - State: open - Opened by mattrbianchi over 6 years ago

#105 - Use cobra

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago

#104 - Conduct a refactoring of fusera

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#103 - Add eager flag that signs urls on start up

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#102 - Make an easy one step way of installing fusera and sracp

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#101 - update fusera and sracp to use type query argument with the Name Resolver API

Issue - State: closed - Opened by mattrbianchi over 6 years ago - 1 comment

#100 - document issues with docker and fuse

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#99 - Ask for identity when dealing with ftp urls to avoid gzipping

Issue - State: closed - Opened by mattrbianchi over 6 years ago - 1 comment

#98 - Update fusera to use the new Name Resolver API features

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#97 - Combine acc-file and acc flags into one accession flag

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#96 - Fusera should stop attempting to validate cloud regions in loc flag, as these could change.

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#95 - Fusera doesn't allow urls to s3 or gcp for acc-file location

Issue - State: closed - Opened by mattrbianchi over 6 years ago
Labels: bug

#94 - Documentation: Room for confusion about fusera startup

Issue - State: closed - Opened by saulakravitz over 6 years ago - 1 comment

#93 - Add tests around fusera to encourage contributing and code quality

Issue - State: open - Opened by mattrbianchi over 6 years ago

#92 - Correct comparison of location prefix

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago
Labels: bug

#91 - customizing batch not actually working

Issue - State: closed - Opened by mattrbianchi over 6 years ago
Labels: bug

#90 - Add a single retry request to failed batch calls

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago

#89 - Change help to reflect proper defaults for batch

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago
Labels: bug

#88 - correct the help printout where it incorrectly states the batch defaults are 0

Issue - State: closed - Opened by mattrbianchi over 6 years ago
Labels: bug

#87 - Create a .stat file that contains the statistics of the mounted file system

Issue - State: closed - Opened by mattrbianchi over 6 years ago
Labels: enhancement

#86 - Fusera still mounts when there is an issue with the folder it's trying to mount to

Issue - State: closed - Opened by mattrbianchi over 6 years ago
Labels: bug

#85 - Add a retry to the batch requests in the nr package

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#84 - Include the accessions that failed in a batch request when getting a 500 internal server error

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#83 - Check that file urls are valid by using them to perform HTTP HEAD calls

Issue - State: closed - Opened by mattrbianchi over 6 years ago

#82 - Swap the use of urfave/cli with cobra for parsing command line flags/args and env vars

Issue - State: closed - Opened by mattrbianchi over 6 years ago
Labels: enhancement

#81 - fusera and sracp need to both understand and handle gzipped data appropriately

Issue - State: closed - Opened by mattrbianchi over 6 years ago
Labels: enhancement

#80 - sracp needs to stop using the external cURL tool to download files

Issue - State: closed - Opened by mattrbianchi over 6 years ago - 1 comment
Labels: enhancement

#79 - Update API endpoint

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago

#78 - Gracefully handle a failure to resolve location

Pull Request - State: closed - Opened by gkelly over 6 years ago

#77 - Add Dockerfile

Pull Request - State: closed - Opened by gkelly over 6 years ago - 1 comment

#76 - Behave like cp by copying over existing files

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago

#75 - Batch requests to the Name Resolver API

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago

#74 - error log files for errors in accessions

Pull Request - State: closed - Opened by mattrbianchi over 6 years ago

#73 - fusera does not account for the expiration date after the first expiration happens

Issue - State: closed - Opened by hatimkhan over 6 years ago - 3 comments

GitHub / mitre/fusera issues and pull requests