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

Author: Fran McDade

spa/src/app/files/hca-project/hca-project-mapper.mock.ts

@@ -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",
@@ -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",
@@ -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"
+};