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Tests for 'Add sample type, model organ to project detail page'. Resolves #805. #899

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merged 1 commit into from
Sep 26, 2019
Merged

Tests for 'Add sample type, model organ to project detail page'. Resolves #805. #899

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242 changes: 218 additions & 24 deletions spa/src/app/files/hca-project/hca-project-mapper.mock.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,11 @@
*/

// Example of project detail with single values
export const PROJECT_DETAIL_SINGLE_VALUE = {
export const PROJECT_DETAIL_SINGLE_VALUES = {
"ageUnit": "month",
"arrayExpressAccessions": "Unspecified",
"bamCount": "--",
"biologicalSex": "female, male",
"arrayExpressAccessions": "E-AAAA-00",
"bamCount": 2,
"biologicalSex": "female",
"contributors": [
{
"contactName": "Spyros,,Darmanis",
Expand All @@ -21,49 +21,153 @@ export const PROJECT_DETAIL_SINGLE_VALUE = {
"projectRole": "principal investigator"
},
],
"disease": "Unspecified",
"disease": "H syndrome",
"donorCount": 10,
"entryId": "2cd14cf5-f8e0-4c97-91a2-9e8957f41ea8",
"fileType": ["fastq.gz"],
"genusSpecies": "Mus musculus",
"geoSeriesAccessions": "Unspecified",
"insdcProjectAccessions": "Unspecified",
"insdcStudyAccessions": "Unspecified",
"libraryConstructionApproach": "Smart-seq2",
"matrixCount": "--",
"modelOrgan": null,
"organ": "large intestine, spleen , diaphragm, muscle, mammary gland, liver, lung endomucin, heart, thymus, brain, tongue , fat, bone, skin, pancreas, kidney , bladder , trachea , lung , lung epcam",
"organPart": "Unspecified",
"organismAge": "3",
"otherCount": "--",
"pairedEnd": "true",
"projectDescription": "We have created a compendium of single cell transcriptome data from the model↵organism Mus musculus comprising more than 100,000 cells from 20 organs and↵tissues. These data represent a new resource for cell biology, revealing gene↵expression in poorly characterized cell populations and allowing for direct and↵controlled comparison of gene expression in cell types shared between tissues, such↵as T-lymphocytes and endothelial cells from distinct anatomical locations. Two distinct technical approaches were used for most tissues.",
"projectShortname": "Tabula Muris",
"genusSpecies": "Homo sapiens",
"geoSeriesAccessions": "GSE00000",
"insdcProjectAccessions": "SRP000000",
"insdcStudyAccessions": "PRJNA000000",
"libraryConstructionApproach": "10X v2 sequencing",
"matrixCount": 1,
"modelOrgan": "brain",
"organ": "brain",
"organPart": "amygdala",
"organismAge": "20",
"otherCount": 16,
"pairedEnd": "false",
"projectDescription": "Contains a small file set from the dataset: 4k PBMCs from a Healthy Donor, a Single Cell Gene Expression Dataset by Cell Ranger 2.1.0. Peripheral blood mononuclear cells (PBMCs) were taken from a healthy donor (same donor as pbmc8k). PBMCs are primary cells with relatively small amounts of RNA (~1pg RNA/cell). Data/Analysis can be found here https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/pbmc4k and all data is licensed under the creative commons attribution license (https://creativecommons.org/licenses/by/4.0/). This test also contains extensive metadata for browser testing. Metadata is fabricated.",
"projectShortname": "integration/optimus/2019-09-24T11:02:18Z",
"projectTitle": "Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution",
"publications": [
{
"publicationTitle": "Transcriptomic characterization of 20 organs and tissues from mouse at single cell resolution creates a Tabula Muris",
"publicationUrl": "https://www.biorxiv.org/content/early/2018/03/29/237446"
}],
"rawCount": 199640,
"sampleEntityType": "specimens",
"selectedCellType": "Unspecified",
"sampleEntityType": "cellLines",
"selectedCellType": "arcuate artery endothelial cell",
"totalCells": 53755,
"totalCount": 199640,
"workflow": "optimus_v1.3.1"
};

// Example of project detail with multiple values
export const PROJECT_DETAIL_MULTIPLE_VALUES = {
"ageUnit": "month, year",
"arrayExpressAccessions": "E-MTAB-7427, E-MTAB-7417",
"bamCount": 2,
"biologicalSex": "female, male",
"contributors": [
{
"contactName": "Spyros,,Darmanis",
"correspondingContributor": true,
"email": "spyros.darmanis@czbiohub.org",
"institution": "Biohub",
"laboratory": "Quake",
"projectRole": "principal investigator"
},
{
"contactName": "Jane,,Smith",
"correspondingContributor": false,
"email": "j.smith@smithemail.org",
"institution": "University of Washington",
"laboratory": "Department of Biology",
"projectRole": "computational scientist"
},
],
"disease": "colitis (disease), ulcerative colitis (disease)",
"donorCount": 10,
"entryId": "2cd14cf5-f8e0-4c97-91a2-9e8957f41ea8",
"fileType": ["fastq.gz", "bam"],
"genusSpecies": "Homo sapiens, Mus musculus",
"geoSeriesAccessions": "GSE95446, GSE95435",
"insdcProjectAccessions": "SRP145547, SRP100786",
"insdcStudyAccessions": "PRJNA471188, PRJNA377118",
"libraryConstructionApproach": "Smart-Seq, 10X 3' v2 sequencing",
"matrixCount": 1,
"modelOrgan": "brain, tissue",
"organ": "brain, liver",
"organPart": "amygdala, lamina propria of mucosa of colon",
"organismAge": "20, 30",
"otherCount": 16,
"pairedEnd": "false, true",
"projectDescription": "Contains a small file set from the dataset: 4k PBMCs from a Healthy Donor, a Single Cell Gene Expression Dataset by Cell Ranger 2.1.0. Peripheral blood mononuclear cells (PBMCs) were taken from a healthy donor (same donor as pbmc8k). PBMCs are primary cells with relatively small amounts of RNA (~1pg RNA/cell). Data/Analysis can be found here https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/pbmc4k and all data is licensed under the creative commons attribution license (https://creativecommons.org/licenses/by/4.0/). This test also contains extensive metadata for browser testing. Metadata is fabricated.",
"projectShortname": "integration/optimus/2019-09-24T11:02:18Z",
"projectTitle": "Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution",
"publications": [
{
"publicationTitle": "Transcriptomic characterization of 20 organs and tissues from mouse at single cell resolution creates a Tabula Muris",
"publicationUrl": "https://www.biorxiv.org/content/early/2018/03/29/237446"
},
{
"publicationTitle": "A single‐cell transcriptome atlas of the adult human retina",
"publicationUrl": "https://www.ncbi.nlm.nih.gov/pubmed/31436334"
}],
"rawCount": 199640,
"sampleEntityType": "cellLines, specimens",
"selectedCellType": "arcuate artery endothelial cell, stromal cell",
"totalCells": 53755,
"totalCount": 199640,
"workflow": "optimus_v1.3.1, optimus_v1.3.2"
};

// Example of project detail with empty values
export const PROJECT_DETAIL_EMPTY_VALUES = {
"ageUnit": "",
"arrayExpressAccessions": "",
"bamCount": "",
"biologicalSex": "",
"contributors": [],
"disease": "",
"donorCount": "",
"entryId": "2cd14cf5-f8e0-4c97-91a2-9e8957f41ea8",
"fileType": [],
"genusSpecies": "",
"geoSeriesAccessions": "",
"insdcProjectAccessions": "",
"insdcStudyAccessions": "",
"libraryConstructionApproach": "",
"matrixCount": "",
"modelOrgan": "",
"organ": "",
"organPart": "",
"organismAge": "",
"otherCount": "",
"pairedEnd": "",
"projectDescription": "",
"projectShortname": "",
"projectTitle": "",
"publications": [],
"rawCount": "",
"sampleEntityType": "",
"selectedCellType": "",
"totalCells": "",
"totalCount": "",
"workflow": ""
};

// Example of project detail with unspecified values
export const PROJECT_DETAIL_UNSPECIFIED_VALUES = {
"ageUnit": "Unspecified",
"arrayExpressAccessions": "Unspecified",
"bamCount": "Unspecified",
"biologicalSex": "Unspecified",
"contributors": [],
"contributors": [
{
"contactName": "Unspecified",
"correspondingContributor": false,
"email": "Unspecified",
"institution": "Unspecified",
"laboratory": "Unspecified",
"projectRole": "Unspecified"
}
],
"disease": "Unspecified",
"donorCount": "Unspecified",
"entryId": "2cd14cf5-f8e0-4c97-91a2-9e8957f41ea8",
"fileType": [],
"fileType": ["Unspecified"],
"genusSpecies": "Unspecified",
"geoSeriesAccessions": "Unspecified",
"insdcProjectAccessions": "Unspecified",
Expand All @@ -79,11 +183,101 @@ export const PROJECT_DETAIL_UNSPECIFIED_VALUES = {
"projectDescription": "Unspecified",
"projectShortname": "Unspecified",
"projectTitle": "Unspecified",
"publications": [],
"publications": [
{
"publicationTitle": "Unspecified",
"publicationUrl": "Unspecified"
},
],
"rawCount": "Unspecified",
"sampleEntityType": "Unspecified",
"selectedCellType": "Unspecified",
"totalCells": "Unspecified",
"totalCount": "Unspecified",
"workflow": "Unspecified"
};

// Example of project detail with null values
export const PROJECT_DETAIL_NULL_VALUES = {
"ageUnit": null,
"arrayExpressAccessions": null,
"bamCount": null,
"biologicalSex": null,
"contributors": null,
"disease": null,
"donorCount": null,
"entryId": "2cd14cf5-f8e0-4c97-91a2-9e8957f41ea8",
"fileType": null,
"genusSpecies": null,
"geoSeriesAccessions": null,
"insdcProjectAccessions": null,
"insdcStudyAccessions": null,
"libraryConstructionApproach": null,
"matrixCount": null,
"modelOrgan": null,
"organ": null,
"organPart": null,
"organismAge": null,
"otherCount": null,
"pairedEnd": null,
"projectDescription": null,
"projectShortname": null,
"projectTitle": null,
"publications": null,
"rawCount": null,
"sampleEntityType": null,
"selectedCellType": null,
"totalCells": null,
"totalCount": null,
"workflow": null
};

// Example of project detail with specific values,
// sample entity type as "specimens",
// workflow as "Unspecified"
export const PROJECT_DETAIL_SPECIFIC_VALUES = {
"ageUnit": "month",
"arrayExpressAccessions": "E-AAAA-00",
"bamCount": 2,
"biologicalSex": "female",
"contributors": [
{
"contactName": "Spyros,,Darmanis",
"correspondingContributor": true,
"email": "spyros.darmanis@czbiohub.org",
"institution": "Biohub",
"laboratory": "Quake",
"projectRole": "principal investigator"
},
],
"disease": "H syndrome",
"donorCount": 10,
"entryId": "2cd14cf5-f8e0-4c97-91a2-9e8957f41ea8",
"fileType": ["fastq.gz"],
"genusSpecies": "Homo sapiens",
"geoSeriesAccessions": "GSE00000",
"insdcProjectAccessions": "SRP000000",
"insdcStudyAccessions": "PRJNA000000",
"libraryConstructionApproach": "10X v2 sequencing",
"matrixCount": 1,
"modelOrgan": "Unspecified",
"organ": "brain",
"organPart": "amygdala",
"organismAge": "20",
"otherCount": 16,
"pairedEnd": "false",
"projectDescription": "Contains a small file set from the dataset: 4k PBMCs from a Healthy Donor, a Single Cell Gene Expression Dataset by Cell Ranger 2.1.0. Peripheral blood mononuclear cells (PBMCs) were taken from a healthy donor (same donor as pbmc8k). PBMCs are primary cells with relatively small amounts of RNA (~1pg RNA/cell). Data/Analysis can be found here https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/pbmc4k and all data is licensed under the creative commons attribution license (https://creativecommons.org/licenses/by/4.0/). This test also contains extensive metadata for browser testing. Metadata is fabricated.",
"projectShortname": "integration/optimus/2019-09-24T11:02:18Z",
"projectTitle": "Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution",
"publications": [
{
"publicationTitle": "Transcriptomic characterization of 20 organs and tissues from mouse at single cell resolution creates a Tabula Muris",
"publicationUrl": "https://www.biorxiv.org/content/early/2018/03/29/237446"
}],
"rawCount": 199640,
"sampleEntityType": "specimens",
"selectedCellType": "arcuate artery endothelial cell",
"totalCells": 53755,
"totalCount": 199640,
"workflow": "optimus_v1.3.1"
};
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