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Have open/closed dataset details section #13

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Aug 12, 2024
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Have open/closed dataset details section #13

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313 changes: 313 additions & 0 deletions src/data/bia-export-test.json
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@@ -0,0 +1,313 @@
{
"uuid": "a2fdbd58-ee11-4cd9-bc6a-f3d3da7fff71",
"version": 1,
"model": {
"type_name": "Study",
"version": 1
},
"accession_id": "S-BIADTEST",
"licence": "CC0",
"author": [
{
"rorid": null,
"address": null,
"website": null,
"orcid": "0000-0000-0000-0000",
"display_name": "Test Author1",
"affiliation": [
{
"rorid": null,
"address": null,
"website": null,
"display_name": "Test College 1"
}
],
"contact_email": "[email protected]",
"role": "corresponding author"
},
{
"rorid": null,
"address": null,
"website": null,
"orcid": "1111-1111-1111-1111",
"display_name": "Test Author2",
"affiliation": [
{
"rorid": null,
"address": null,
"website": null,
"display_name": "Test College 2"
}
],
"contact_email": "[email protected]",
"role": "first author"
}
],
"title": "A test submission with title greater than 25 characters",
"release_date": "2024-02-13",
"description": "A test submission to allow testing without retrieving from bia server",
"keyword": [
"Test keyword1",
"Test keyword2",
"Test keyword3"
],
"acknowledgement": "We thank you",
"see_also": [],
"related_publication": [],
"grant": [
{
"id": "TESTFUNDS1",
"funder": [
{
"display_name": "Test funding body1",
"id": null
}
]
},
{
"id": "TESTFUNDS2",
"funder": [
{
"display_name": "Test funding body2",
"id": null
}
]
}
],
"funding_statement": "This work was funded by the EBI",
"attribute": {},
"experimental_imaging_component": [
{
"title_id": "Study Component 1",
"uuid": "47a4ab60-c76d-4424-bfaa-c2a024de720c",
"version": 1,
"model": {
"type_name": "ExperimentalImagingDataset",
"version": 1
},
"description": "Description of study component 1",
"attribute": {
"associations": [
{
"biosample": "Test Biosample 1",
"image_acquisition": "Test Primary Screen Image Acquisition",
"specimen": "Test specimen 1"
},
{
"biosample": "Test Biosample 2",
"image_acquisition": "Test Primary Screen Image Acquisition",
"specimen": "Test specimen 1"
}
]
},
"analysis_method": [
{
"protocol_description": "Test image analysis",
"features_analysed": "Test image analysis overview"
}
],
"correlation_method": [],
"example_image_uri": [],
"submitted_in_study_uuid": "a2fdbd58-ee11-4cd9-bc6a-f3d3da7fff71",
"acquisition_process": [
{
"title_id": "Test Primary Screen Image Acquisition",
"uuid": "c2e44a1b-a43c-476e-8ddf-8587f4c955b3",
"version": 1,
"model": {
"type_name": "ImageAcquisition",
"version": 1
},
"protocol_description": "Test image acquisition parameters 1",
"imaging_instrument_description": "Test imaging instrument 1",
"fbbi_id": [],
"imaging_method_name": "confocal microscopy"
}
],
"specimen_imaging_preparation_protocol": [
{
"title_id": "Test specimen 1",
"uuid": "7199d730-29f1-4ad8-b599-e9089cbb2d7b",
"version": 1,
"model": {
"type_name": "SpecimenImagingPrepartionProtocol",
"version": 1
},
"protocol_description": "Test sample preparation protocol 1",
"signal_channel_information": []
}
],
"biological_entity": [
{
"title_id": "Test Biosample 1",
"uuid": "64a67727-4e7c-469a-91c4-6219ae072e99",
"version": 1,
"model": {
"type_name": "BioSample",
"version": 1
},
"organism_classification": [
{
"common_name": "human",
"scientific_name": "Homo sapiens",
"ncbi_id": null
}
],
"biological_entity_description": "Test biological entity 1",
"experimental_variable_description": [
"Test experimental entity 1"
],
"extrinsic_variable_description": [
"Test extrinsic variable 1"
],
"intrinsic_variable_description": [
"Test intrinsic variable 1\\nwith escaped character"
]
},
{
"title_id": "Test Biosample 2",
"uuid": "6950718c-4917-47a1-a807-11b874e80a23",
"version": 1,
"model": {
"type_name": "BioSample",
"version": 1
},
"organism_classification": [
{
"common_name": "mouse",
"scientific_name": "Mus musculus",
"ncbi_id": null
}
],
"biological_entity_description": "Test biological entity 2",
"experimental_variable_description": [
"Test experimental entity 2"
],
"extrinsic_variable_description": [
"Test extrinsic variable 2"
],
"intrinsic_variable_description": [
"Test intrinsic variable 2"
]
}
],
"specimen_growth_protocol": []
},
{
"title_id": "Study Component 2",
"uuid": "47a4ab60-c76d-4424-bfaa-c2a024de720c",
"version": 1,
"model": {
"type_name": "ExperimentalImagingDataset",
"version": 1
},
"description": "Description of study component 1",
"attribute": {
"associations": [
{
"biosample": "Test Biosample 1",
"image_acquisition": "Test Primary Screen Image Acquisition",
"specimen": "Test specimen 1"
},
{
"biosample": "Test Biosample 2",
"image_acquisition": "Test Primary Screen Image Acquisition",
"specimen": "Test specimen 1"
}
]
},
"analysis_method": [
{
"protocol_description": "Test image analysis",
"features_analysed": "Test image analysis overview"
}
],
"correlation_method": [],
"example_image_uri": [],
"submitted_in_study_uuid": "a2fdbd58-ee11-4cd9-bc6a-f3d3da7fff71",
"acquisition_process": [
{
"title_id": "Test Primary Screen Image Acquisition",
"uuid": "c2e44a1b-a43c-476e-8ddf-8587f4c955b3",
"version": 1,
"model": {
"type_name": "ImageAcquisition",
"version": 1
},
"protocol_description": "Test image acquisition parameters 1",
"imaging_instrument_description": "Test imaging instrument 1",
"fbbi_id": [],
"imaging_method_name": "confocal microscopy"
}
],
"specimen_imaging_preparation_protocol": [
{
"title_id": "Test specimen 1",
"uuid": "7199d730-29f1-4ad8-b599-e9089cbb2d7b",
"version": 1,
"model": {
"type_name": "SpecimenImagingPrepartionProtocol",
"version": 1
},
"protocol_description": "Test sample preparation protocol 1",
"signal_channel_information": []
}
],
"biological_entity": [
{
"title_id": "Test Biosample 1",
"uuid": "64a67727-4e7c-469a-91c4-6219ae072e99",
"version": 1,
"model": {
"type_name": "BioSample",
"version": 1
},
"organism_classification": [
{
"common_name": "human",
"scientific_name": "Homo sapiens",
"ncbi_id": null
}
],
"biological_entity_description": "Test biological entity 1",
"experimental_variable_description": [
"Test experimental entity 1"
],
"extrinsic_variable_description": [
"Test extrinsic variable 1"
],
"intrinsic_variable_description": [
"Test intrinsic variable 1\\nwith escaped character"
]
},
{
"title_id": "Test Biosample 3",
"uuid": "6950718c-4917-47a1-a807-11b874e80a23",
"version": 1,
"model": {
"type_name": "BioSample",
"version": 1
},
"organism_classification": [
{
"common_name": "mouse",
"scientific_name": "Mus musculus",
"ncbi_id": null
}
],
"biological_entity_description": "Test biological entity 2",
"experimental_variable_description": [
"Test experimental entity 2"
],
"extrinsic_variable_description": [
"Test extrinsic variable 2"
],
"intrinsic_variable_description": [
"Test intrinsic variable 2"
]
}
],
"specimen_growth_protocol": []
}
]
}
10 changes: 9 additions & 1 deletion src/data/output_modified.json
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Expand Up @@ -44,6 +44,7 @@
"submitted_in_study": "UUID-study-1",
"specimen_imaging_preparation_protocol": [
{
"default_open": true,
"uuid": "UUID-specimen-preparation-protocol-1",
"title_id": "Pycnogonum litorale amputees",
"protocol_description": "All specimens were fixed and stored in Bouin’s fluid (10% formaldehyde, 5% glacial acetic acid in saturated aqueous picric acid) at room temperature (RT). Specimens were briefly rinsed in phosphate-buffered saline (PBS; 1.86 mM NaH2PO4, 8.41 mM Na2HPO4, 175 mM NaCl, pH 7.4; at least 3× 5 min), transferred into deionized water, dehydrated via an ascending ethanol series, incubated in a tissue contrasting solution of 2% iodine (resublimated; Carl Roth; #X864.1) in 99.5% ethanol for 48 h at RT, rinsed in 99.5% ethanol (3 to 4× 10 min), and critical point-dried with a Leica EM CPD300.",
Expand All @@ -52,6 +53,7 @@
],
"acquisition_process": [
{
"default_open": true,
"uuid": "UUID-image-acquisition-1",
"title_id": "Pycnogonum litorale µCT",
"protocol_description": "Dried specimens were placed in plastic tubes for overview scans. For higher resolution scans of the posterior body region with the regenerates, they were subsequently attached to plastic welding rods with hot glue. Scans were performed under 40 kV/200 μA/8 W or 30 kV/200 μA/6 W settings. Depending on the specimen size and region of interest, a 4×, 10×, or 20× objective was chosen. Exposure times were individually adjusted for each scan, ranging from 0.75 to 6.5 s. To reduce noise, binning 2 was applied during data acquisition. Tomography projections were reconstructed with the XMReconstructor software (Carl Zeiss Microscopy) with binning 1 (= full resolution) and TIFF format image stacks as output.",
Expand All @@ -62,6 +64,7 @@
]
},
{
"default_open": true,
"uuid": "UUID-image-acquisition-2",
"title_id": "Pycnogonum litorale 1",
"imaging_instrument_description": "Xradia MicroXCT-200 (Carl Zeiss Microscopy)",
Expand All @@ -73,6 +76,7 @@
],
"biological_entity": [
{
"default_open": true,
"uuid": "UUID-biosample-1",
"title_id": "Pycnogonida (sea spiders)",
"organism_classification": [
Expand All @@ -89,7 +93,8 @@
"biological_entity_description": "Complete specimens and selected ROIs"
},
{
"uuid": "UUID-biosample-1",
"default_open": true,
"uuid": "UUID-biosample-2",
"title_id": "Pycnogonida (sea spiders) - 2",
"organism_classification": [
{
Expand Down Expand Up @@ -120,6 +125,7 @@
"submitted_in_study": "UUID-study-1",
"specimen_imaging_preparation_protocol": [
{
"default_open": false,
"uuid": "UUID-specimen-preparation-protocol-1",
"title_id": "Pycnogonum litorale amputees",
"protocol_description": "All specimens were fixed and stored in Bouin’s fluid (10% formaldehyde, 5% glacial acetic acid in saturated aqueous picric acid) at room temperature (RT). Specimens were briefly rinsed in phosphate-buffered saline (PBS; 1.86 mM NaH2PO4, 8.41 mM Na2HPO4, 175 mM NaCl, pH 7.4; at least 3× 5 min), transferred into deionized water, dehydrated via an ascending ethanol series, incubated in a tissue contrasting solution of 2% iodine (resublimated; Carl Roth; #X864.1) in 99.5% ethanol for 48 h at RT, rinsed in 99.5% ethanol (3 to 4× 10 min), and critical point-dried with a Leica EM CPD300.",
Expand All @@ -128,6 +134,7 @@
],
"acquisition_process": [
{
"default_open": false,
"uuid": "UUID-image-acquisition-1",
"title_id": "Pycnogonum litorale µCT",
"protocol_description": "Dried specimens were placed in plastic tubes for overview scans. For higher resolution scans of the posterior body region with the regenerates, they were subsequently attached to plastic welding rods with hot glue. Scans were performed under 40 kV/200 μA/8 W or 30 kV/200 μA/6 W settings. Depending on the specimen size and region of interest, a 4×, 10×, or 20× objective was chosen. Exposure times were individually adjusted for each scan, ranging from 0.75 to 6.5 s. To reduce noise, binning 2 was applied during data acquisition. Tomography projections were reconstructed with the XMReconstructor software (Carl Zeiss Microscopy) with binning 1 (= full resolution) and TIFF format image stacks as output.",
Expand All @@ -140,6 +147,7 @@
],
"biological_entity": [
{
"default_open": true,
"uuid": "UUID-biosample-2",
"title_id": "Cambropycnogon klausmuelleri (sea spiders)",
"organism_classification": [
Expand Down
7 changes: 3 additions & 4 deletions src/layouts/DatasetDetailLayout.astro
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Expand Up @@ -23,13 +23,12 @@ const render_field = Object.keys(data).map((key) => {
}
});

//TODO: set this on a per-section basis
const is_open = "True"

---

<details open={is_open}>
<details open={data.default_open}>
<summary>
<b>{data.title_id}</b>
<b>{data.title_id}</b> {data.default_open? ' ':'(as above)'}
</summary>

<ul>
Expand Down
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