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revision of issue #3
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@feserm
feserm committed Feb 22, 2024
1 parent 3c57499 commit 2af6b3c
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6 changes: 3 additions & 3 deletions src/components/isa/generic/TableLoader.svelte
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Expand Up @@ -59,7 +59,7 @@
{#if !fileUploaded}
<p style="margin: 0 0 20px 0;">
Please download the template file and fill it with your materials as rows according to the column names:
&nbsp; <button on:click={handleDownload} class="add">Download Template</button>
&nbsp; <button on:click={handleDownload} class="btn btn-secondary">Download Template</button>

<p>
Please then upload the list of materials by clicking the upload area below or by dragging and dropping the file onto the upload area.
Expand Down Expand Up @@ -95,8 +95,8 @@
Only the first {previewSize} rows are shown here.
</p>
{/if}
<button class="add" style="float: right" on:click={createEvent}>Approve and Load</button>
<button class="add" style="float: left" on:click={()=>{fileUploaded=false;}}>Go back</button>
<button class="btn btn-secondary" style="float: right" on:click={createEvent}>Approve and Load</button>
<button class="btn btn-secondary" style="float: left" on:click={()=>{fileUploaded=false;}}>Go back</button>
<br/>
{/if}
</section>
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212 changes: 114 additions & 98 deletions src/components/isa/generic/Uploader.svelte
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Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,30 @@
import Schema from "@/lib/schemas.js";
import String from "./String.svelte";
import { split } from "@nfdi4plants/arctrl/fable_modules/fable-library.4.5.0/String";
import { onMount } from "svelte";
let study;
export { study as value };
export let jsonPath;
//FIXME: In Expert mode this is not working as it only checks on component creation, but not if the parameter value is changed later
//FIXME: Value is not updated directly in the isa-json when the component loads
onMount(()=>{
let growth_protocol = study.protocols.find(protocol => protocol.name === 'Growth');
if (study.processSequence.length > 0) {
let growth_process = study.processSequence.find(process => {
return process.executesProtocol.name === 'Growth'
})
if (growth_process) {
for (let parameterValue of growth_process.parameterValues) {
let protocol_parameter = growth_protocol.parameters.find(parameter => parameter.parameterName.annotationValue === parameterValue.category.parameterName.annotationValue)
if (protocol_parameter) {
parameterValue.value = protocol_parameter.comments[0].value;
}
}
}
}
})
//TODO: Add to config
let template = new Blob(["Art_calc,Jahr_calc,Sortiment_calc,BKR_Nr,BKR_Bezeichnung,Anbaugebiet_Nr,Anbaugebiete,Standort_calc,Bundeslandkuerzel,DATUM,BBCH_VON,BBCH,BBCH_BIS,Termin,Merkmal,MerkmalsBez,StufenNrFak1,StufenNrFak2,Wdh,Sorte,Status,KennNr,Wert"], { type: 'text/csv;charset=utf-8,' });
Expand All @@ -19,107 +38,92 @@
let characterisitcs = 'Anbaugebiete,Standort_calc,Jahr_calc,Art_calc';
let previewSize = 5;
function writeStudy(groupedDF){
function writeStudy(df){
let groupedDF = df
.groupBy(...source_key.split(','))
.toCollection();
study.materials.sources = [];
study.materials.samples = [];
study.processSequence = [];
groupedDF.forEach((group) => {
groupedDF.forEach((source_group) => {
let source = Schema.getSource(
group.group.select(source_key).toArray()[0][0],
group.group.select(...characterisitcs.split(',')).toCollection()[0]
Object.values(source_group.groupKey),
source_group.group.select(...characterisitcs.split(',')).toCollection()[0]
);
if (!study.materials.sources.find(s => s.name === source.name)) {
study.materials.sources = [...study.materials.sources, source];
}
let sample = Schema.getObjectFromSchema('sample');
sample.name = Object.values(group.groupKey).join('-');
study.materials.samples = [...study.materials.samples, sample];
//FIXME: if the comment is removed the double binding is not working for the parameter declaration.
//TODO: Switch to @id use for less repetition?
let growth_protocol = study.protocols.find(protocol => protocol.name === 'Growth');
let process = Schema.getObjectFromSchema('process')
process.inputs = [source];
process.executesProtocol = growth_protocol;
process.parameterValues = growth_protocol.parameters.map(parameter => {
let value = parameter.comments[0].value;
let process_parameter_value = Schema.getObjectFromSchema('process_parameter_value');
process_parameter_value.category = parameter;
process_parameter_value.value = value
return process_parameter_value;
});
process.outputs = [sample];
study.processSequence = [...study.processSequence, process];
study.materials.sources = [...study.materials.sources, source];
source_group.group.groupBy(...sample_key.split(',')).toCollection().forEach((sample_group) => {
let sample = Schema.getObjectFromSchema('sample');
sample.name = Object.values(sample_group.groupKey).join('-');
sample.derivesFrom = source;
study.materials.samples = [...study.materials.samples, sample];
});
});
let growth_protocol = study.protocols.find(protocol => protocol.name === 'Growth');
let process = Schema.getObjectFromSchema('process');
process.inputs = study.materials.sources;
process.executesProtocol = growth_protocol;
process.parameterValues = growth_protocol.parameters.map(parameter => {
let value = parameter.comments[0].value;
let process_parameter_value = Schema.getObjectFromSchema('process_parameter_value');
process_parameter_value.category = parameter;
process_parameter_value.value = value
return process_parameter_value;
});
process.outputs = study.materials.samples;
study.processSequence = [...study.processSequence, process];
}
function writeAssay(groupedDF) {
study.protocols = [study.protocols[0]];
groupedDF[0].group.unique('Merkmal').toCollection().map(obj=>obj['Merkmal']).forEach(
variable => {
let protocol = Schema.getObjectFromSchema('protocol');
protocol.name = variable;
study.protocols = [...study.protocols, protocol];
}
);
function writeAssay(df) {
let phenotyping_protocol = Schema.getObjectFromSchema('protocol');
phenotyping_protocol.name = 'Phenotyping';
study.protocols = [study.protocols[0], phenotyping_protocol];
//TODO: Streamline
let tmp = [];
groupedDF.forEach(group => {
tmp = [...tmp, group.group.select(...sample_key.split(','),...dataframe_keys.split(',')).toCollection()];
});
let df = new DataFrame(tmp.flat(),[...sample_key.split(','),...dataframe_keys.split(',')]).toCollection();
const addSampleNameKey = (objects, keysString) => {
const keysArray = keysString.split(',');
return objects.map(obj => {
let sampleNameValue = '';
keysArray.forEach((key, index) => {
if (obj.hasOwnProperty(key)) {
sampleNameValue += obj[key];
if (index < keysArray.length - 1) {
sampleNameValue += '-';
}
}
});
obj['Sample Name'] = sampleNameValue;
return obj;
});
};
df = addSampleNameKey(df, sample_key);
df = new DataFrame(df).select('Sample Name', ...dataframe_keys.split(',')).toCollection();
study.assays = [];
let assay = Schema.getObjectFromSchema('assay');
assay.materials.samples = study.materials.samples;
assay.dataFiles = [];
let datafileContent = Schema.getObjectFromSchema('comment');
datafileContent.name = 'Content';
datafileContent.value = JSON.stringify(
df.select(...sample_key.split(','), ...dataframe_keys.split(','))
.withColumn(
'Sample Name',
row => sample_key.split(',').map(key => row.get(key)).join('-')
)
.select('Sample Name', ...dataframe_keys.split(','))
.toCollection()
);
let dataFile = Schema.getObjectFromSchema('data');
dataFile.name = 'phenotyping-results.csv';
dataFile.type = 'Raw Data File';
dataFile.name = 'datasets/phenotyping-results.csv';
dataFile.comments = [{
name: 'Content',
value: JSON.stringify(df)
}];
assay.dataFiles = [dataFile];
dataFile.comments = [datafileContent];
assay.dataFiles = [...assay.dataFiles, dataFile];
assay.processSequence = [];
for (let i=1; i<study.protocols.length; i++) {
study.materials.samples.forEach( sample => {
let process = Schema.getObjectFromSchema('process');
process.executesProtocol = study.protocols[i];
process.inputs = sample;
process.outputs = [dataFile];
assay.processSequence = [...assay.processSequence, process];
});
}
let process = Schema.getObjectFromSchema('process');
process.inputs = study.materials.samples;
process.executesProtocol = phenotyping_protocol;
process.outputs = [dataFile];
assay.processSequence = [...assay.processSequence, process];
study.assays = [...study.assays, assay];
}
function handleApprove(event) {
let groupedDF = new DataFrame(event.detail.detail.rows, event.detail.detail.columns).groupBy(...sample_key.split(',')).toCollection();
let df = new DataFrame(event.detail.detail.rows, event.detail.detail.columns)
writeStudy(groupedDF);
writeAssay(groupedDF);
writeStudy(df);
writeAssay(df);
}
</script>

<section>
Expand All @@ -133,31 +137,40 @@
{#each study.materials.sources[0].characteristics as characteristic}
<th>{characteristic.category.characteristicType.annotationValue}</th>
{/each}
{#each study.protocols[0].parameters as parameter}
<th>{parameter.parameterName.annotationValue}</th>
{/each}
<!-- Uncomment, if the growth protocol parameter values defined previously should be displayed-->
<!--
{#each study.protocols[0].parameters as parameter}
<th>{parameter.parameterName.annotationValue}</th>
{/each}
-->
<th>Sample Name</th>
</thead>
<tbody>
{#each study.processSequence.slice(0,previewSize) as process}
{#each study.processSequence as process}
{#each process.outputs.slice(0,previewSize) as output, j}
<tr>
<td>{process.inputs[0].name}</td>
{#each process.inputs[0].characteristics as characteristic}
<td>{output.derivesFrom.name}</td>
{#each output.derivesFrom.characteristics as characteristic}
<td>{characteristic.value}</td>
{/each}
{#each process.parameterValues as process_parameter_value}
<td>{process_parameter_value.value}</td>
{/each}
<td>{process.outputs[0].name}</td>
<!-- Uncomment, if the growth protocol parameter values defined previously should be displayed-->
<!--
{#each process.parameterValues as process_parameter_value}
<td>{process_parameter_value.value}</td>
{/each}
-->
<td>{output.name}</td>
</tr>
{/each}
{/each}
</tbody>
</table>
{#if study.processSequence.length > previewSize}
{#if study.processSequence[0].outputs.length > previewSize}
<p class="info-box">
Only the first {previewSize} of {study.processSequence.length} rows are shown here.
Only the first {previewSize} of {study.processSequence[0].outputs.length} rows are shown here.
</p>
{/if}
{#if study.assays[0].processSequence.length > 0}
<h3>Samples</h3>
<table>
<thead>
Expand All @@ -166,19 +179,22 @@
<th>Data File</th>
</thead>
<tbody>
{#each study.assays[0].materials.samples.slice(0,previewSize) as _,idx}
{#each study.assays[0].processSequence as process}
{#each process.inputs.slice(0,previewSize) as input}
<tr>
<td>{study.assays[0].materials.samples[idx].name}</td>
<td>D_GREI1</td>
<td>datasets/phenotyping-results.csv</td>
<td>{input.name}</td>
<td>{process.executesProtocol.name}</td>
<td>{process.outputs[0].name}</td>
</tr>
{/each}
{/each}
</tbody>
</table>
{#if study.assays[0].processSequence.length > previewSize}
{#if study.assays[0].processSequence[0].inputs.length > previewSize}
<p class="info-box">
Only the first {previewSize} of {study.assays[0].processSequence.length} rows are shown here.
Only the first {previewSize} of {study.assays[0].processSequence[0].inputs.length} rows are shown here.
</p>
{/if}
{/if}
{/if}
</div>
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