Ecosyste.ms: Issues

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GitHub / nmdp-bioinformatics/phycus issues and pull requests

#127 - Bump gson from 2.8.1 to 2.8.9 in /client/java/freq-client

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#126 - phycus shiny app

Pull Request - State: open - Opened by csexton-nmdp about 2 years ago

#125 - Doc

Pull Request - State: closed - Opened by mmaiers-nmdp over 2 years ago

#124 - Adhikasp feature/swagger version

Pull Request - State: closed - Opened by mmaiers-nmdp over 2 years ago
Labels: enhancement

#123 - error when starting db

Issue - State: closed - Opened by mmaiers-nmdp over 2 years ago - 1 comment

#122 - docker-compose error

Issue - State: closed - Opened by mmaiers-nmdp over 2 years ago - 1 comment

#121 - Docker build on Windows

Issue - State: open - Opened by mmaiers-nmdp over 2 years ago

#120 - README.md needs to be updated to reflect running via docker

Issue - State: open - Opened by mmaiers-nmdp over 2 years ago - 1 comment

#119 - The python module in the client needs to be renamed

Issue - State: open - Opened by mmaiers-nmdp over 2 years ago - 1 comment
Labels: enhancement

#118 - javaGui is not in master

Issue - State: closed - Opened by mmaiers-nmdp over 2 years ago - 2 comments

#117 - Swagger-codegen can't make api/bin #2

Issue - State: closed - Opened by dpratt3 over 2 years ago - 2 comments

#116 - add population ID to import client

Pull Request - State: closed - Opened by mmaiers-nmdp about 3 years ago

#115 - Bump commons-io from 2.6 to 2.7 in /client/java/freq-tools

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#114 - Bump junit from 4.12 to 4.13.1 in /client/java/freq-client

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#113 - Bump junit from 3.8.1 to 4.13.1 in /client/java/freq-tools

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#112 - Bump junit from 4.12 to 4.13.1 in /client/java

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#111 - Final commit Java client

Pull Request - State: closed - Opened by kaeaton almost 4 years ago - 1 comment

#110 - updated docs

Pull Request - State: closed - Opened by mmaiers-nmdp about 4 years ago

#109 - [WIP] Feature KeyCloak - M01

Pull Request - State: open - Opened by scout23DF over 4 years ago

#108 - Swagger config: add build version

Pull Request - State: closed - Opened by adhikasp over 4 years ago - 1 comment

#107 - Add minimum value for haplotype frequency total

Pull Request - State: closed - Opened by kaeaton almost 5 years ago

#106 - Ion

Pull Request - State: closed - Opened by kaeaton almost 5 years ago

#105 - Test issue

Issue - State: closed - Opened by mmaiers-nmdp almost 5 years ago

#104 - Pop search

Pull Request - State: closed - Opened by kaeaton almost 5 years ago

#103 - Phycus files (as opposed to csv files)

Pull Request - State: closed - Opened by kaeaton almost 5 years ago

#102 - Error fixes

Pull Request - State: closed - Opened by kaeaton almost 5 years ago

#101 - Gui receipts

Pull Request - State: closed - Opened by kaeaton almost 5 years ago

#100 - Display build version in Swagger UI

Issue - State: closed - Opened by jbrelsf2-nmdp about 5 years ago - 2 comments

#99 - have the Java UI present the list of label types

Issue - State: open - Opened by mmaiers-nmdp about 5 years ago

#98 - Add constraints to labels

Issue - State: open - Opened by mmaiers-nmdp about 5 years ago - 4 comments

#97 - Updating README.md

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

#96 - Fix the Java CLI

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

#95 - Adding the GUI

Pull Request - State: closed - Opened by kaeaton about 5 years ago - 4 comments

#94 - Fix bad merge between quality calculator and spring boot 2 branches

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

#93 - Migrate to spring boot2

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

#92 - Remove label list usage from java client

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

#91 - Remove LabelList usage from the Java client

Pull Request - State: closed - Opened by kaeaton over 5 years ago - 9 comments

#90 - Update the Java client to accommodate new LabelData structure

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

#89 - Add quality metric calculation

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

#88 - SAM_POP should be an attribute of the population not an HFC

Issue - State: open - Opened by mmaiers-nmdp over 5 years ago
Labels: swagger-spec

#87 - the return structure from post /hfc contains ids that don't have their own endpoints

Issue - State: open - Opened by mmaiers-nmdp over 5 years ago
Labels: swagger-spec

#86 - Update SwaggerDocumentationConfig.java

Pull Request - State: closed - Opened by sauter over 5 years ago - 1 comment

#85 - Remove unnecessary definition of list only types

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

#84 - Lambda

Pull Request - State: closed - Opened by mhalagan over 5 years ago - 1 comment

#83 - Perlclient

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

#82 - Added the new repository for pull access

Pull Request - State: closed - Opened by jbrelsf2-nmdp over 5 years ago

#81 - Create maven build when creating docker image

Pull Request - State: closed - Opened by fscheel almost 6 years ago
Labels: hackathon

#80 - Change "Contact" URL to github project

Issue - State: closed - Opened by fscheel almost 6 years ago - 1 comment
Labels: hackathon

#79 - Quality Tags

Issue - State: open - Opened by mmaiers-nmdp almost 6 years ago - 5 comments
Labels: hackathon

#78 - Push docker image to docker hub

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

#77 - Flyway database migration

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

#76 - Add building of docker image to circle ci

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

#75 - How to handle database migrations?

Issue - State: closed - Opened by fscheel about 6 years ago - 1 comment
Labels: question

#74 - Save enums as strings in the database

Pull Request - State: closed - Opened by fscheel about 6 years ago - 1 comment

#73 - Update curation-swagger-spec.yaml

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

#72 - Add a .gitattributes file

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

#71 - Add instructions about local development with Windows

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

#70 - How to run PHYCUS locally?

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

#69 - Make perl client usable

Pull Request - State: closed - Opened by fscheel about 6 years ago - 2 comments

#68 - PHYCUS instance currenty returns error 500

Issue - State: closed - Opened by fscheel about 6 years ago - 3 comments

#67 - Repairing merge mess

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

#66 - Merge pull request #7 from mpresteg/cohort-name

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

#65 - Remove "CohortData" from HFCurationRequest and make CohortID(integer) required

Issue - State: closed - Opened by mmaiers-nmdp over 6 years ago - 1 comment
Labels: swagger-spec

#64 - Make PopulationRequest.name a required field

Issue - State: closed - Opened by mmaiers-nmdp over 6 years ago - 1 comment
Labels: swagger-spec

#63 - Create Cohort API in the same pattern of Population API

Issue - State: closed - Opened by mmaiers-nmdp over 6 years ago - 1 comment
Labels: swagger-spec

#62 - Reorg docs

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

#61 - Update Swagger Codegen

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

#60 - Socket timeout when pushing large frequency sets

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

#59 - Fix Python client

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

#58 - Use Swagger Codegen Maven Plugin

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

#57 - Connect an actual consuming client

Issue - State: open - Opened by mpresteg over 6 years ago - 1 comment

#56 - Dockerization of application

Pull Request - State: closed - Opened by jbrelsf2-nmdp over 6 years ago - 1 comment

#55 - Removed unnecessary maven dependencies and added to .gitignore

Pull Request - State: closed - Opened by mpresteg over 6 years ago - 2 comments

#54 - added Java client

Pull Request - State: closed - Opened by mpresteg over 6 years ago - 3 comments

#53 - Manually create error 400

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

#52 - Phycus and local

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

#51 - Delete Submission included

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

#50 - Label and method list modeling is inconvenient

Issue - State: closed - Opened by fscheel over 6 years ago
Labels: swagger-spec

#49 - Make java automatically validate required elements

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

#48 - TypeOfAccess is marked required but comment says there will be a default, if no provided

Issue - State: open - Opened by fscheel over 6 years ago - 2 comments
Labels: swagger-spec

#47 - Should the clients be checked in with the service?

Issue - State: closed - Opened by mpresteg over 6 years ago - 3 comments
Labels: question

#46 - added cohort name

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

#45 - Do we need a more general mechanism for selecting / identifying frequency sets

Issue - State: open - Opened by mpresteg over 6 years ago - 6 comments
Labels: question

#44 - Add name and descriptor to Cohort

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

#43 - Delete based on submission ID

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

#42 - Fix error500 on non existing entities

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

#41 - Allow additional information in error responses

Issue - State: open - Opened by fscheel over 6 years ago - 1 comment
Labels: swagger-spec

#40 - Consider / implement a strategy for avoiding duplicate entities

Issue - State: open - Opened by mpresteg over 6 years ago - 3 comments
Labels: defer

#39 - Create a delete endpoint

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

#37 - Check correct data member for null

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

#21 - perl client

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

#20 - Add Perl client

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

#19 - HFCurationRequest PopulationID required

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

#18 - Error 500 when retrieving non-existing detail data

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

#17 - Submitting new data with an existing cohort ID ignores the data

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

#15 - Missing input validation

Issue - State: open - Opened by fscheel almost 7 years ago - 4 comments

#14 - Missing Access Control

Issue - State: open - Opened by fscheel almost 7 years ago - 2 comments

#13 - Use a relational persistance layer and other things

Pull Request - State: closed - Opened by fscheel about 7 years ago

#11 - Include SubmitterID in response /{submissionID}/Haplotypes

Issue - State: open - Opened by Rozemuller about 7 years ago - 1 comment
Labels: swagger-spec

#4 - Working version

Pull Request - State: closed - Opened by mhalagan over 7 years ago