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brapi-pedigree-viewer's Introduction

solgenomics

The mason components needed to run the solgenomics.net website

brapi-pedigree-viewer's People

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jxtreehouse nahuel-soldevilla kyrazhang777 breeding-insight

brapi-pedigree-viewer's Issues

Add color coded tiles to each nodes for representing genotypic (and other) information

Add color coded tiles to each nodes for representing genotypic information. Maximum 10 tiles / accession. Should be able to represent any color value, but for most genotyping apps, 3 should be enough. Position under node? For marker data, the markers to represent in the tiles could be read from a MarkerSet (chosen from a select box of available MarkerSets)

Convert to Angular

Hi,
I am going to convert the pedigree viewer into an Angular based tool, and I am new to this area. Would you like to give some hints? Like where should I start and which part should I be aware of?

Thank you!

Kyra Zhang

Use pedigree viewer with Angular applications

Hello @dauglyon ,

I am trying to import and use this tool inside Angular 7 application. In browser console, I have this error message concerning the use of "PedigreeViewer()" function:

ERROR TypeError: "Object(...) is not a function"
    ngOnInit genealogic-tree.component.ts:23
    Angular 5
        checkAndUpdateDirectiveInline
        checkAndUpdateNodeInline
        checkAndUpdateNode
        debugCheckAndUpdateNode
        debugCheckDirectivesFn
    View_GermplasmCardComponent_1 GermplasmCardComponent.html:778
    Angular 27
    RxJS 5
    Angular 11
GermplasmCardComponent.html:750:2
    View_GermplasmCardComponent_1 GermplasmCardComponent.html:750
    Angular 15
    RxJS 5
    Angular 11

I created a component genealogic-tree with the following file genealogic-tree.component.ts:

import { Component, Input, OnInit } from '@angular/core';
import { BrAPI } from '@solgenomics/brapijs';
import { PedigreeViewer } from '@solgenomics/brapi-pedigree-viewer';

import { BrapiGermplasm } from '../models/brapi.model';
import { BrapiService } from '../brapi.service';

@Component({
    selector: 'faidare-genealogic-tree',
    templateUrl: './genealogic-tree.component.html',
    styleUrls: ['./genealogic-tree.component.scss']
})
export class GenealogicTreeComponent implements OnInit {

    @Input() germplasmId: String;

    constructor(private brapiService: BrapiService) {
        this.germplasmId = 'aHR0cHM6Ly9kb2kub3JnLzEwLjE1NDU0L01FQVJBUw%3D%3D';
    }

    ngOnInit() {
        const pdg = PedigreeViewer(
            /*REQUIRED Server: BrAPI.js handle for target endpoint*/
            BrAPI('http://localhost:8380/faidare-dev/brapi/v1'),
            // this.brapiService,
            /*OPTIONAL a function which returns a link to a germplasm information page,*/
            function() {
                return 'http://localhost:4200/faidare-dev/germplasm?id=aHR0cHM6Ly9kb2kub3JnLzEwLjE1NDU0L01FQVJBUw%3D%3D';
            }
        );
        if (pdg != null) {
            pdg.newTree(
                // REQUIRED root germplasmDbId of germplasm which should be displayed on start (highlighted in pink)
                this.germplasmId
            );

            pdg.drawViewer(
                // REQUIRED selector for the parent node of the new viewer SVG element.
                'div#pdgv-wrap',
                // OPTIONAL width of viewer
                800,
                // OPTIONAL height of viewer
                400
            );
        }
    }
}

In genealogic-tree.component.html':

<div id="pdgv-wrap"></div>

And in the germplasm-card.component.html, I added a selector:

<div>
  <faidare-genealogic-tree [germplasmId]="germplasmGnpis.germplasmDbId"></faidare-genealogic-tree>
</div>

Thanks for your attention

Mélanie Buy

Commands not working in Windows 10

Hi,
When I was trying to install BrAPI pedigree viewer in visual studio code environment in windows 10, the "rm", "-rf", "cp" commands did not work and they were not recognized in windows.
Error shown like this:
'cp' is not recognized as an internal or external command,

Thank you for your attention!
Kyra Zhang

Make nodes selectable

Make nodes selectable so that actions can be run on a group of nodes, such as a link to a haplotype viewer

Loading progeny of many-progeny germplasm is too slow.

See solgenomics/sgn#1839 and plantbreeding/BrAPI#239

Question about required calls

Hi @dauglyon ,

This is a very promising BrAPP! I'm very keen in replacing in replacing the BMS current pedigree viewer with this.

One question: I see in your demo gif that you're traversing the tree in both directions, so it seems to me like the code must be relying on the Pedigree call to get parents and the yet to be brapified Progeny call to get the progenies. Am I right?

If that's the case I'll can forward with implementing the Pedigree call in BMS as it is defined now and wait for the progeny spec to to be Merged.

Once again, thanks so much for sharing this high quality tools with the community!

make compatible with brapi v1.2

main problem to fix is use parent1DbId and parent2DbId instead of parent1Id and parent2Id in the pedigree call. also use germplasmDbId and defaultDisplayName instead of progenyGermplasmDbId in the progeny call.

https://brapi.docs.apiary.io/#reference/germplasm/germplasm-pedigree/germplasm-pedigree-by-id
https://brapi.docs.apiary.io/#reference/germplasm/germplasm-progeny/germplasm-progeny-by-id

for future implementation: brapi pedigree call now includes "siblings" as an array in the response

Type "null" for progeny field in progeny object instead of empty array

Hi,

In our BrAPI endpoint at URGI, the germplasm without progeny have this sort of result:

{
"result":
{"germplasmDbId": "aHR0cHM6Ly9kb2kub3JnLzEwLjE1NDU0L0ZLSEFZSA==",
"defaultDisplayName": "662200176",
"progeny":null
}"

Theses cases cause problems with pedigree viewer:

TypeError: "ped_pro_germId[1].progeny is null"

Thank you for your attention,

Mélanie Buy

Version Not Defined in PedigreeViewer.js

Utilizing the latest commit of BrAPI-Pedigree-Viewer (as opposed to pulling from NPM) results in a version is not defined error.

It seems the PedigreeViewer.js in BrAPI-Pedigree-Viewer is out of sync with the version on sgn. The BrAPI-Pedigree-Viewer received the update to retrieve parent nodes differently depending on BrAPI version but the version is not passed in.

PedigreeViewer.js?fda6:147 Uncaught (in promise) ReferenceError: version is not defined
    at eval (PedigreeViewer.js?fda6:147:1)
    at eval (BrAPI.js?f10b:833:1)
    at eval (BrAPI.js?f10b:675:1)
    at Array.forEach (<anonymous>)
    at Filter_Node.publishResult (BrAPI.js?f10b:674:1)
    at eval (BrAPI.js?f10b:805:1)
    at eval (BrAPI.js?f10b:675:1)
    at Array.forEach (<anonymous>)
    at Join_Node.publishResult (BrAPI.js?f10b:674:1)
    at eval (BrAPI.js?f10b:900:1)