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[BI-1230] Truly Unknown Germplasm #260

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Merged
HMS17 merged 3 commits into from
Sep 21, 2022
Merged

[BI-1230] Truly Unknown Germplasm #260

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9452a5e
[BI-1230] Unknown Germplasm, saving, display, start of pedigree work
HMS17 Aug 17, 2022
13d0243
Unknown germplasm displays minus 10+ progeny
HMS17 Sep 6, 2022
1f0473f
Merge branch 'develop' into feature/BI-1230
HMS17 Sep 21, 2022
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14 changes: 14 additions & 0 deletions src/breeding-insight/model/import/germplasm/Pedigree.ts
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Expand Up @@ -44,4 +44,18 @@ export class Pedigree {
}
}

/**
* Wrapper of parsePedigreeString that handles female/male parent unknown cases.
*
* @param pedigreeString
* @param femaleParentUnknown
* @param maleParentUnknown
*/
public static parsePedigreeStringWithUnknowns(pedigreeString: string, femaleParentUnknown: string, maleParentUnknown: string, gid: string) : Pedigree {
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@timparsons timparsons Sep 15, 2022

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It looks like the femaleParentUnknown and maleParentUnknown additionalInfo fields are booleans. Can the types of the parameters in this method can be updated to reflect this?

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@HMS17 HMS17 Sep 16, 2022

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Vue yells at me if I change the parameter type to boolean despite it being very clearly processed as a boolean in the method. It is strange.

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@timparsons timparsons Sep 16, 2022

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Ok, thanks for looking into this!

let parsedPedigree = this.parsePedigreeString(pedigreeString);
if (femaleParentUnknown) parsedPedigree.femaleParent = "Unknown";
if (maleParentUnknown) parsedPedigree.maleParent = "Unknown";
return parsedPedigree;
}

}
3 changes: 3 additions & 0 deletions src/components/germplasm/GermplasmPedigreesView.vue
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Expand Up @@ -126,6 +126,9 @@ export default class GermplasmPedigreesView extends GermplasmBase {
let pedigree = PedigreeViewer(`${process.env.VUE_APP_BI_API_V1_PATH}/programs/${this.activeProgram!.id}/brapi/v2`, undefined, 'v2.0',
function (dbId: any, germplasm: any) {
const parsedName = parseGermplasmName(germplasm.value.name);
if (parsedName.gid === "0") {
return null;
}
return `${germplasmDetailsUrl}/gid-${parsedName.gid}`;
},
{
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4 changes: 2 additions & 2 deletions src/views/germplasm/GermplasmDetails.vue
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Expand Up @@ -39,12 +39,12 @@
<GermplasmLink
v-if="germplasm.pedigree"
v-bind:germplasmUUID="Pedigree.parsePedigreeString(germplasm.additionalInfo.pedigreeByUUID).femaleParent"
v-bind:germplasmGID="Pedigree.parsePedigreeString(germplasm.pedigree).femaleParent"
v-bind:germplasmGID="Pedigree.parsePedigreeStringWithUnknowns(germplasm.pedigree,germplasm.additionalInfo.femaleParentUnknown,germplasm.additionalInfo.maleParentUnknown, germplasm.germplasmDbId).femaleParent"
> </GermplasmLink>
<template v-if="Pedigree.parsePedigreeString(germplasm.pedigree).maleParent">
/ <GermplasmLink
v-bind:germplasmUUID="Pedigree.parsePedigreeString(germplasm.additionalInfo.pedigreeByUUID).maleParent"
v-bind:germplasmGID="Pedigree.parsePedigreeString(germplasm.pedigree).maleParent"
v-bind:germplasmGID="Pedigree.parsePedigreeStringWithUnknowns(germplasm.pedigree,germplasm.additionalInfo.femaleParentUnknown,germplasm.additionalInfo.maleParentUnknown, germplasm.germplasmDbId).maleParent"
> </GermplasmLink></template>
</li>
<li><b>Synonyms: </b> {{ GermplasmUtils.formatSynonyms(germplasm.synonyms) }}</li>
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4 changes: 2 additions & 2 deletions src/views/germplasm/GermplasmTable.vue
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Expand Up @@ -36,13 +36,13 @@
<b-table-column field="femaleParentGID" label="Female Parent GID" sortable v-slot="props" :th-attrs="(column) => ({scope:'col'})" searchable>
<GermplasmLink
v-bind:germplasmUUID="Pedigree.parsePedigreeString(props.row.data.additionalInfo.pedigreeByUUID).femaleParent"
v-bind:germplasmGID="Pedigree.parsePedigreeString(props.row.data.pedigree).femaleParent"
v-bind:germplasmGID="Pedigree.parsePedigreeStringWithUnknowns(props.row.data.pedigree, props.row.data.additionalInfo.femaleParentUnknown, props.row.data.additionalInfo.maleParentUnknown, props.row.data.accessionNumber).femaleParent"
> </GermplasmLink>
</b-table-column>
<b-table-column field="maleParentGID" label="Male Parent GID" sortable v-slot="props" :th-attrs="(column) => ({scope:'col'})" searchable>
<GermplasmLink
v-bind:germplasmUUID="Pedigree.parsePedigreeString(props.row.data.additionalInfo.pedigreeByUUID).maleParent"
v-bind:germplasmGID="Pedigree.parsePedigreeString(props.row.data.pedigree).maleParent"
v-bind:germplasmGID="Pedigree.parsePedigreeStringWithUnknowns(props.row.data.pedigree,props.row.data.additionalInfo.femaleParentUnknown,props.row.data.additionalInfo.maleParentUnknown, props.row.data.accessionNumber).maleParent"
> </GermplasmLink>
</b-table-column>
<b-table-column field="createdDate" label="Created Date" sortable v-slot="props" :th-attrs="(column) => ({scope:'col'})" searchable>
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24 changes: 23 additions & 1 deletion src/views/import/ImportGermplasm.vue
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Expand Up @@ -112,7 +112,7 @@
{{ props.row.data.brAPIObject.seedSource }}
</b-table-column>
<b-table-column field="pedigree" label="Pedigree" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
{{ props.row.data.brAPIObject.pedigree }}
{{ getPedigree(props.row.data.brAPIObject) }}
</b-table-column>
<b-table-column field="femaleParentGid" label="Female Parent GID" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
{{ props.row.data.brAPIObject.additionalInfo.femaleParentGid }}
Expand Down Expand Up @@ -162,6 +162,7 @@ import ExpandableTable from "@/components/tables/expandableTable/ExpandableTable
import {ImportObjectState} from "@/breeding-insight/model/import/ImportObjectState";
import {ExternalUID} from "@/breeding-insight/model/import/germplasm/ExternalUID";
import {GermplasmUtils} from "@/breeding-insight/utils/GermplasmUtils";
import {Germplasm} from "@/breeding-insight/brapi/model/germplasm";

@Component({
components: {
Expand Down Expand Up @@ -217,5 +218,26 @@ export default class ImportGermplasm extends ProgramsBase {
importFinished() {
this.germplasmList = new GermplasmList();
}

getPedigree(germplasm: Germplasm) {
//return germplasm.pedigree;
let originalPedigree = germplasm.pedigree ? germplasm.pedigree.split('/') : [""];
let displayPedigree = "";
if (germplasm.additionalInfo && germplasm.additionalInfo.femaleParentUnknown){
displayPedigree = "Unknown";
} else {
displayPedigree = originalPedigree[0];
}
if (germplasm.additionalInfo && germplasm.additionalInfo.maleParentUnknown){
displayPedigree += "/Unknown";
} else if (originalPedigree.length == 2) {
displayPedigree +=`/${originalPedigree[1]}`;
}
//todo future card, handle case of unknown female/known male, which currently has null pedigree posted

return displayPedigree;

}

}
</script>