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Minor update
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@bherr2
bherr2 committed Jan 23, 2025
1 parent 6b002e7 commit f827276
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Showing 2 changed files with 19 additions and 18 deletions.
32 changes: 16 additions & 16 deletions src/normalization/normalize-ds-graph.js
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Original file line number Diff line number Diff line change
Expand Up @@ -126,7 +126,7 @@ function createTissueBlockObject(context, donor, block) {
.append('section_count', block.section_count)
.append('section_size', block.section_size)
.append('section_size_unit', block.section_size_unit)
.append('collision_summaries', block.rui_location?.['all_collisions'].map((collision, index) =>
.append('collision_summaries', block.rui_location?.['all_collisions']?.map((collision, index) =>
generateCollisionId(context, block, collision, index)).filter(onlyNonNull) || [])
.append('corridors', getCorridorId(context, block))
.append('links_back_to', checkDonorId(donor['@id']))
Expand Down Expand Up @@ -264,7 +264,7 @@ function normalizeCellSummaryData(context, data) {
const sampleBlockCellSummaries = donors.map((donor) => {
return donor['samples'].map((block) => {
return block['datasets']?.map((dataset) => {
return dataset['summaries']?.map((summary, index) =>
return dataset['summaries']?.map((summary, index) =>
createCellSummaryObject(context, dataset, summary, index))
}).flat();
}).flat();
Expand All @@ -273,7 +273,7 @@ function normalizeCellSummaryData(context, data) {
return donor['samples'].map((block) => {
return block['sections']?.map((section) => {
return section['datasets']?.map((dataset) => {
return dataset['summaries']?.map((summary, index) =>
return dataset['summaries']?.map((summary, index) =>
createCellSummaryObject(context, dataset, summary, index))
}).flat();
}).flat();
Expand Down Expand Up @@ -302,7 +302,7 @@ function createCellSummaryRowObject(context, dataset, summary, summaryRow, index
.append('type_of', ['CellSummaryRow'])
.append('cell_id', summaryRow.cell_id)
.append('cell_label', summaryRow.cell_label)
.append('gene_expressions', summaryRow['gene_expr']?.map((expr, itemIndex) =>
.append('gene_expressions', summaryRow['gene_expr']?.map((expr, itemIndex) =>
createGeneExpressionObject(context, dataset, summary, summaryRow, expr, itemIndex)) || [])
.append('count', summaryRow.count)
.append('percentage', summaryRow.percentage)
Expand All @@ -318,7 +318,7 @@ function createGeneExpressionObject(context, dataset, summary, summaryRow, expr,
.append('gene_label', expr.gene_label)
.append('ensembl_id', expr.ensembl_id)
.append('mean_gene_expression_value', expr.mean_gene_expr_value)
.build();
.build();
}

// ---------------------------------------------------------------------------------
Expand All @@ -333,7 +333,7 @@ function normalizeCollisionData(context, data) {
createCollisionObject(context, block, collision, index)
).filter(onlyNonNull) || []
}).flat();
}).flat();
}).flat();
}

function createCollisionObject(context, block, collision, index) {
Expand All @@ -346,9 +346,9 @@ function createCollisionObject(context, block, collision, index) {
.append('label', getCollisionLabel(block, collision, index))
.append('type_of', ['CollisionSummary'])
.append('collision_method', collision.collision_method)
.append('collision_items', collision['collisions']?.map((collisionItem, itemIndex) =>
.append('collision_items', collision['collisions']?.map((collisionItem, itemIndex) =>
createCollisionItemObject(context, block, collision, collisionItem, itemIndex)) || [])
.build();
.build();
}

function createCollisionItemObject(context, block, collision, collisionItem, index) {
Expand All @@ -359,7 +359,7 @@ function createCollisionItemObject(context, block, collision, collisionItem, ind
.append('spatial_entity_reference', collisionItem.as_3d_id)
.append('volume', collisionItem.as_volume)
.append('percentage', collisionItem.percentage)
.build();
.build();
}

// ---------------------------------------------------------------------------------
Expand All @@ -373,7 +373,7 @@ function normalizeCorridorData(context, data) {
const corridor = block['rui_location']['corridor'];
return corridor ? createCorridorObject(context, block, corridor) : null;
}).filter(onlyNonNull);
}).flat();
}).flat();
}

function createCorridorObject(context, block, corridor) {
Expand All @@ -383,7 +383,7 @@ function createCorridorObject(context, block, corridor) {
.append('type_of', ['Corridor'])
.append('file_format', corridor.file_format)
.append('file_url', corridor.file)
.build();
.build();
}

// ---------------------------------------------------------------------------------
Expand Down Expand Up @@ -411,7 +411,7 @@ function getCorridorId(context, block) {
function generateCorridorId(context, block, corridor) {
const { iri, version } = context.selectedDigitalObject;
const hashCode = getCorridorHash(block, corridor);
return `${iri}/${version}#${hashCode}`;
return `${iri}/${version}#${hashCode}`;
}

function generateCollisionId(context, block, collision, index) {
Expand All @@ -420,13 +420,13 @@ function generateCollisionId(context, block, collision, index) {
}
const { iri, version } = context.selectedDigitalObject;
const hashCode = getCollisionHash(block, collision, index);
return `${iri}/${version}#${hashCode}`;
return `${iri}/${version}#${hashCode}`;
}

function generateCollisionItemId(context, block, collision, collisionItem, index) {
const { iri, version } = context.selectedDigitalObject;
const hashCode = getCollisionItemHash(block, collision, collisionItem, index);
return `${iri}/${version}#${hashCode}`;
return `${iri}/${version}#${hashCode}`;
}

function generateCellSummaryId(context, dataset, summary, index) {
Expand Down Expand Up @@ -484,7 +484,7 @@ function getCollisionItemHash(block, collision, collisionItem, index, length=0)
function getCorridorHash(block, corridor, length=0) {
const { file } = corridor;
const primaryKey = `${block['@id']}-${file}`;
return getHashCode(primaryKey, length);
return getHashCode(primaryKey, length);
}

function getHashCode(str, length=0) {
Expand Down Expand Up @@ -550,7 +550,7 @@ function getCollisionItemLabel(block, collision, collisionItem, index) {

function getCorridorLabel(block, collision) {
const hashCode = getCorridorHash(block, collision, 5);
return `Corridor of tissue block (#${hashCode})`;
return `Corridor of tissue block (#${hashCode})`;
}

function getSexId(sex) {
Expand Down
5 changes: 3 additions & 2 deletions src/utils/logging.js
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,8 @@ export function banner(title) {
export function header(context, pipeline) {
const { type, name, version, iri } = context.selectedDigitalObject;
info('');
info(chalk.whiteBright('---') + ' ' +
chalk.green(`${type}:${version}:${name}`) + ' ' +
info(chalk.whiteBright('---') + ' ' +
chalk.green(`${type}:${version}:${name}`) + ' ' +
chalk.whiteBright(`(${pipeline})`) + ' @ ' +
chalk.cyanBright(iri) + ' ' +
chalk.whiteBright('---'));
Expand All @@ -27,6 +27,7 @@ export function warning(message) {

export function error(message) {
console.log('[' + chalk.redBright('ERROR') + '] ' + chalk.redBright(message));
console.log(message);
}

export function more(message) {
Expand Down

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