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Merged
HMS17 merged 2 commits into from
Feb 4, 2026
Merged

[BI-2716] Exp preview observation variable count is wrong #456

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86186dd
[BI-2716] When counting Observation Variables, excluding Time Stamps
Feb 2, 2026
3af85de
Merge branch 'develop' into bug/BI-2716
HMS17 Feb 4, 2026
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276 changes: 185 additions & 91 deletions src/views/import/ImportExperiment.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -18,25 +18,26 @@
<template>
<div id="import-experiment">
<ImportTemplate
v-bind:abort-msg="'No records will be added, and the import in progress will be completely removed.'"
v-bind:system-import-template-name="experimentImportTemplateName"
v-bind:confirm-msg="'Preview Experimental Upload'"
v-bind:import-type-name="'Experiments & Observations'"
v-bind:confirm-import-state="confirmImportState"
v-bind:user-input="experimentUserInput"
v-bind:show-proceed-warning="showProceedDialog"
v-on="$listeners"
v-on:finished="importFinished"
v-on:preview-data-loaded="previewDataLoaded"
v-on:statistics-loaded="statisticsLoaded"
v-bind:abort-msg="'No records will be added, and the import in progress will be completely removed.'"
v-bind:system-import-template-name="experimentImportTemplateName"
v-bind:confirm-msg="'Preview Experimental Upload'"
v-bind:import-type-name="'Experiments & Observations'"
v-bind:confirm-import-state="confirmImportState"
v-bind:user-input="experimentUserInput"
v-bind:show-proceed-warning="showProceedDialog"
v-on="$listeners"
v-on:finished="importFinished"
v-on:preview-data-loaded="previewDataLoaded"
v-on:statistics-loaded="statisticsLoaded"
>

<template v-slot:importInfoTemplateMessageBox>
<ImportInfoTemplateMessageBox v-bind:import-type-name="'Experiments & Observations'"
v-bind:template-url="'https://www.dropbox.com/scl/fi/5abbq8cxuxwepstlr3www/Experimental_Template_V08.xls?rlkey=ny3zavzqv4jyu0bl95hnpi7fz&st=3002jr3s&dl=1'"
class="mb-5">
<ImportInfoTemplateMessageBox
v-bind:import-type-name="'Experiments & Observations'"
v-bind:template-url="'https://www.dropbox.com/scl/fi/5abbq8cxuxwepstlr3www/Experimental_Template_V08.xls?rlkey=ny3zavzqv4jyu0bl95hnpi7fz&st=3002jr3s&dl=1'"
class="mb-5"
>
<strong>Before You Import...</strong>
<br/>
<br>
Experimental germplasm and ontology terms must be created in the system before experiments can be created via import.
See the import template for more information about data requirements. Importing phenotypic
observations into existing experiments requires only Observation Unit IDs
Expand All @@ -45,145 +46,239 @@
</template>

<template v-slot:confirmImportMessageBox="{ statistics, dynamicColumns, abort, confirm, rows }">
<ConfirmImportMessageBox v-bind:num-records="getNumNewExperimentRecords(statistics)"
v-bind:import-type-name="'Experiments & Observations'"
v-bind:confirm-import-state="confirmImportState"
v-bind:show-loading-on-confirm="!showProceedDialog"
v-on:abort="abort"
v-on:confirm="confirm"
class="mb-4">
<ConfirmImportMessageBox
v-bind:num-records="getNumNewExperimentRecords(statistics)"
v-bind:import-type-name="'Experiments & Observations'"
v-bind:confirm-import-state="confirmImportState"
v-bind:show-loading-on-confirm="!showProceedDialog"
class="mb-4"
v-on:abort="abort"
v-on:confirm="confirm"
>
<div>
<p>Review your experimental data import before committing to the database.</p>
<div class = "left-confirm-column">
<p class="is-size-5 mb-2"><strong>Experiment</strong></p>
<template v-if="rows && rows.length > 0">
Title: {{ rows[0].trial.brAPIObject.trialName }}
<br>Description: {{ rows[0].trial.brAPIObject.trialDescription }}
<br>Experimental Unit: {{ rows[0].trial.brAPIObject.additionalInfo.defaultObservationLevel }}
<br>Type: {{ rows[0].trial.brAPIObject.additionalInfo.experimentType }}
<br>Experimental Design: Externally generated
</template>
<template v-if="isExisting(rows)"><br>User: {{ rows[0].trial.brAPIObject.additionalInfo.createdBy.userName }}</template>
<template v-if="isExisting(rows)"><br>Creation Date: {{ rows[0].trial.brAPIObject.additionalInfo.createdDate | dmy}}</template>
</div>
<div id="experiment-summary" class ="right-confirm-column">
<p class="is-size-5 mb-2"><strong>Import Summary</strong></p>
<br>Observation Variables: {{ dynamicColumns.length }}

<span v-if="isExisting(rows)" >
<br>New Observations: {{ statistics.Observations.newObjectCount }}
<br>Existing Observations: {{ statistics.Existing_Observations.newObjectCount }}
<br>Overwritten Observations: {{ statistics.Mutated_Observations.newObjectCount }}
</span>
<span v-else>
<br>Observations: {{ statistics.Observations.newObjectCount }}
</span>


</div>
<div class="left-confirm-column">
<p class="is-size-5 mb-2">
<strong>Experiment</strong>
</p>
<template v-if="rows && rows.length > 0">
Title: {{ rows[0].trial.brAPIObject.trialName }}
<br>Description: {{ rows[0].trial.brAPIObject.trialDescription }}
<br>Experimental Unit: {{ rows[0].trial.brAPIObject.additionalInfo.defaultObservationLevel }}
<br>Type: {{ rows[0].trial.brAPIObject.additionalInfo.experimentType }}
<br>Experimental Design: Externally generated
</template>
<template v-if="isExisting(rows)">
<br>User: {{ rows[0].trial.brAPIObject.additionalInfo.createdBy.userName }}
</template>
<template v-if="isExisting(rows)">
<br>Creation Date: {{ rows[0].trial.brAPIObject.additionalInfo.createdDate | dmy }}
</template>
</div>
<div
id="experiment-summary"
class="right-confirm-column"
>
<p class="is-size-5 mb-2">
<strong>Import Summary</strong>
</p>
<!-- just count the observation variables in dynamicColumns that do not start with "TS:"-->
<br>Observation Variables: {{ dynamicColumns.filter( obsVar => !obsVar.startsWith("TS:") ).length }}
<span v-if="isExisting(rows)">
<br>New Observations: {{ statistics.Observations.newObjectCount }}
<br>Existing Observations: {{ statistics.Existing_Observations.newObjectCount }}
<br>Overwritten Observations: {{ statistics.Mutated_Observations.newObjectCount }}
</span>
<span v-else>
<br>Observations: {{ statistics.Observations.newObjectCount }}
</span>
</div>
</div>
</ConfirmImportMessageBox>
</template>

<template v-slot:userInput>
<!-- TODO: change to use mutated observations count when api ready -->
<form v-if="experimentUserInput.overwrite"
class="new-form"
novalidate="true"
<form
v-if="experimentUserInput.overwrite"
class="new-form"
novalidate="true"
>
<p class="is-size-5 has-text-weight-bold mb-0">Overwrite Request</p>
{{ repeatObservationsCount }} values detected that repeat observations already saved to the system. If you
do not want to overwrite existing observations you will need to edit the import file.
<BasicInputField
class="pb-2"
<p class="is-size-5 has-text-weight-bold mb-0">
Overwrite Request
</p>
{{ repeatObservationsCount }} values detected that repeat observations already saved to the system. If you
do not want to overwrite existing observations you will need to edit the import file.
<BasicInputField
v-model="experimentUserInput.overwriteReason"
class="pb-2"
v-bind:field-name="'Reason for overwrite:'"
v-bind:placeholder="'Reason'"
v-bind:show-label="true"
/>
/>
</form>
</template>

<template v-slot:importPreviewTable="previewData">


<ExpandableTable
v-bind:records="previewData.import"
v-bind:loading="false"
v-bind:pagination="previewData.pagination"
v-on:show-error-notification="$emit('show-error-notification', $event)"
scrollable
v-bind:records="previewData.import"
v-bind:loading="false"
v-bind:pagination="previewData.pagination"
scrollable
v-on:show-error-notification="$emit('show-error-notification', $event)"
>
<!-- Germplasm Name -->
<b-table-column field="germplasmName" label="Germplasm Name" v-slot="props" :th-attrs="(column) => ({scope:'col'})"
:td-attrs="(row, column) => ({class: 'db-filled'})">
<b-table-column
v-slot="props"
field="germplasmName"
label="Germplasm Name"
:th-attrs="(column) => ({scope:'col'})"
:td-attrs="(row, column) => ({class: 'db-filled'})"
>
{{ getField(props.row.data.germplasm, 'germplasmName') }}
</b-table-column>
<!-- Germplasm GID -->
<b-table-column field="germplasmGID" label="Germplasm GID" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="germplasmGID"
label="Germplasm GID"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getField(props.row.data.germplasm, 'accessionNumber') }}
</b-table-column>
<!-- Test or Check -->
<b-table-column field="testOrCheck" label="Test (T) or Check (C)" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="testOrCheck"
label="Test (T) or Check (C)"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getField(props.row.data.observationUnit, 'observationUnitPosition.entryType') }}
</b-table-column>
<!-- Env -->
<b-table-column field="env" label="Env" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="env"
label="Env"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getField(props.row.data.study, 'studyName', true) }}
</b-table-column>
<!-- Env Location -->
<b-table-column field="envLocation" label="Env Location" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="envLocation"
label="Env Location"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getField(props.row.data.location, 'name') }}
</b-table-column>
<!-- Env year -->
<b-table-column field="envYear" label="Env Year" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="envYear"
label="Env Year"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getField(props.row.data.study, 'additionalInfo.envYear') }}
</b-table-column>
<!-- Exp Unit ID -->
<b-table-column field="expUnitID" label="Exp Unit ID" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="expUnitID"
label="Exp Unit ID"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getField(props.row.data.observationUnit, 'observationUnitName', true) }}
</b-table-column>
<!-- Exp Replicate # -->
<b-table-column field="expRepNo" label="Exp Replicate #" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="expRepNo"
label="Exp Replicate #"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getObservationLevelRelationships(props.row.data.observationUnit, 'rep') }}
</b-table-column>
<!-- Exp Block # -->
<b-table-column field="expBlockNo" label="Exp Block #" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="expBlockNo"
label="Exp Block #"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getObservationLevelRelationships(props.row.data.observationUnit, 'block') }}
</b-table-column>
<!-- Row -->
<b-table-column field="row" label="Row" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="row"
label="Row"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getField(props.row.data.observationUnit, 'observationUnitPosition.positionCoordinateX') }}
</b-table-column>
<!-- Column -->
<b-table-column field="column" label="Column" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="column"
label="Column"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getField(props.row.data.observationUnit, 'observationUnitPosition.positionCoordinateY') }}
</b-table-column>
<!-- Geocoordinates -->
<b-table-column field="lat" label="Lat" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="lat"
label="Lat"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getGeoCoordinates(props.row.data.observationUnit).lat }}
</b-table-column>
<b-table-column field="long" label="Long" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="long"
label="Long"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getGeoCoordinates(props.row.data.observationUnit).lon }}
</b-table-column>
<b-table-column field="elevation" label="Elevation" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="elevation"
label="Elevation"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getGeoCoordinates(props.row.data.observationUnit).elevation }}
</b-table-column>
<b-table-column field="rtk" label="RTK" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="rtk"
label="RTK"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getField(props.row.data.observationUnit, 'additionalInfo.rtk') }}
</b-table-column>
<!-- Treatment Factors -->
<b-table-column field="expTreatmentFactorName" label="Treatment Factors" v-slot="props" :th-attrs="(column) => ({scope:'col'})">
<b-table-column
v-slot="props"
field="expTreatmentFactorName"
label="Treatment Factors"
:th-attrs="(column) => ({scope:'col'})"
>
{{ getTreatment(props.row.data.observationUnit) }}
</b-table-column>
<!-- Dynamic Phenotype and Timestamp Columns -->
<b-table-column v-for="(variable, index) in phenotypeColumns"
v-slot="props"
:key="variable"
:label="variable"
:th-attrs="(column) => ({scope:'col'})"
:td-attrs="cellClassIfExisting"
:meta="{'index': index}">
<b-table-column
v-for="(variable, index) in phenotypeColumns"
:key="variable"
v-slot="props"
:label="variable"
:th-attrs="(column) => ({scope:'col'})"
:td-attrs="cellClassIfExisting"
:meta="{'index': index}"
>
<p> {{ retrieveDynamicColVal(props.row.data.observations, variable) }}</p>
</b-table-column>

Expand All @@ -194,7 +289,6 @@
</template>
</ExpandableTable>
</template>

</ImportTemplate>
</div>
</template>
Expand Down