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None of the tabs appearing on the experiment page when plotTypesAndOptions empty in the content payload #362

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ke4 opened this issue Oct 19, 2023 · 3 comments · May be fixed by #375
Open

None of the tabs appearing on the experiment page when plotTypesAndOptions empty in the content payload #362

ke4 opened this issue Oct 19, 2023 · 3 comments · May be fixed by #375
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@upendrakumbham
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bug Something isn't working

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@ke4
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ke4 commented Oct 19, 2023 •
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When we have proper data in the payload for the tabs on the experiment page the tabs should be appear on the page.
Currently none of the tab is appearing for E-ANND-3 experiment given the following payload:

{
  content: {
    "experimentAccession": "E-ANND-3",
    "accessKey": "",
    "species": "homo sapiens",
    "disclaimer": "",
    "tabs": [
      {
        "type": "results",
        "name": "Results",
        "props": {
          "ks": [
            914,
            925,
            932,
            937,
            946,
            967,
            981,
            998,
            1008
          ],
          "ksWithMarkerGenes": [
            
          ],
          "selectedK": 914,
          "plotTypesAndOptions": {
            
          },
          "defaultPlotMethodAndParameterisation": {
            
          },
          "metadata": [
            {
              "value": "sampling_site",
              "label": "Sampling site"
            },
            {
              "value": "inferred_cell_type_-_ontology_labels",
              "label": "Inferred cell type - ontology labels"
            },
            {
              "value": "sex",
              "label": "Sex"
            },
            {
              "value": "organism_part",
              "label": "Organism part"
            },
            {
              "value": "inferred_cell_type_-_authors_labels",
              "label": "Inferred cell type - authors labels"
            },
            {
              "value": "individual",
              "label": "Individual"
            },
            {
              "value": "age",
              "label": "Age"
            },
            {
              "value": "disease",
              "label": "Disease"
            }
          ],
          "units": [
            "CPM"
          ],
          "suggesterEndpoint": "json/suggestions",
          "anatomogram": {
            "pancreas": [
              "CL_0000084",
              "CL_0000097",
              "CL_0000115",
              "CL_0000169",
              "CL_0000171",
              "CL_0000236",
              "CL_0000763",
              "CL_0002064",
              "CL_0002079",
              "CL_0002275",
              "CL_0002410",
              "HANCESTRO_0005",
              "HANCESTRO_0014",
              "NCBITaxon_9606",
              "PATO_0000383",
              "PATO_0000384",
              "PATO_0000461",
              "UBERON_0000016",
              "UBERON_0000017",
              "UBERON_0001264",
              "EFO_0001272",
              "EFO_0009505"
            ],
            "kidney": [
              "CL_0000235",
              "CL_0000236",
              "CL_0000492",
              "CL_0000623",
              "CL_0000625",
              "HANCESTRO_0568",
              "NCBITaxon_9606",
              "PATO_0000383",
              "UBERON_0002113",
              "EFO_0001272"
            ],
            "liver": [
              "CL_0000084",
              "CL_0000115",
              "CL_0000182",
              "CL_0000232",
              "CL_0000451",
              "CL_0000576",
              "CL_0000623",
              "CL_0000763",
              "CL_0000775",
              "CL_0000786",
              "CL_1000488",
              "HANCESTRO_0005",
              "NCBITaxon_9606",
              "PATO_0000384",
              "UBERON_0002107",
              "EFO_0001272"
            ],
            "lung": [
              "CL_0000057",
              "CL_0000077",
              "CL_0000158",
              "CL_0000235",
              "CL_0000236",
              "CL_0000451",
              "CL_0000540",
              "CL_0000623",
              "CL_0000624",
              "CL_0000625",
              "CL_0000646",
              "CL_0000669",
              "CL_0000767",
              "CL_0000775",
              "CL_0000784",
              "CL_0000786",
              "CL_0000860",
              "CL_0000875",
              "CL_0002062",
              "CL_0002063",
              "CL_0002138",
              "CL_0002144",
              "CL_0002370",
              "CL_0002543",
              "CL_0002553",
              "CL_0002598",
              "CL_0002633",
              "CL_0009086",
              "CL_0009089",
              "CL_1000271",
              "CL_1000413",
              "CL_1001567",
              "CL_2000016",
              "CL_4028001",
              "HANCESTRO_0005",
              "HANCESTRO_0568",
              "NCBITaxon_9606",
              "PATO_0000383",
              "UBERON_0002048",
              "EFO_0001272",
              "EFO_0001661"
            ],
            "gut": [
              "CL_0000057",
              "CL_0000160",
              "CL_0000236",
              "CL_0000625",
              "CL_0000775",
              "CL_0002250",
              "CL_0009006",
              "CL_0009011",
              "CL_0009012",
              "CL_0009017",
              "CL_0009039",
              "CL_0009041",
              "CL_0009042",
              "CL_0009043",
              "CL_1000334",
              "CL_1000343",
              "CL_1000347",
              "CL_1000495",
              "CL_1001516",
              "HANCESTRO_0568",
              "NCBITaxon_9606",
              "PATO_0000383",
              "UBERON_0000059",
              "UBERON_0002108",
              "EFO_0001272",
              "EFO_0001655",
              "EFO_0001661"
            ]
          }
        }
      },
      {
        "type": "supplementary-information",
        "name": "Supplementary Information",
        "props": {
          "sections": [
            {
              "type": "static-table",
              "name": "Analysis Methods",
              "props": {
                "data": [
                  [
                    "analysis",
                    "asset",
                    "citation",
                    "kind",
                    "version"
                  ],
                  [
                    "reference",
                    "Gencode",
                    "https://www.gencodegenes.org/human/release_30.html",
                    "file",
                    "Release 30 (GRCh38.p12)"
                  ],
                  [
                    "mapping",
                    "STAR",
                    "https://github.com/alexdobin/STAR",
                    "software",
                    "2.6.1a_08-27"
                  ],
                  [
                    "Gene/transcript quantification",
                    "HTSeq",
                    "https://github.com/htseq/htseq",
                    "software",
                    "0.9.1"
                  ],
                  [
                    "Data integration with metadata variables",
                    "Scanpy",
                    "https://github.com/scverse/scanpy",
                    "software",
                    "1.7.2"
                  ],
                  [
                    "Batch effect correction, data analysis",
                    "scVI",
                    "https://github.com/scverse/scvi-tools",
                    "software",
                    "0.91.1"
                  ],
                  [
                    "Cell annotation",
                    "CellxGene",
                    "https://github.com/chanzuckerberg/cellxgene",
                    "software",
                    "unknown"
                  ],
                  [
                    "Quality control on cell annotations",
                    "popularVote",
                    "https://tabula-sapiens-portal.ds.czbiohub.org/annotateuserdata",
                    "software",
                    "unknown"
                  ]
                ]
              }
            },
            {
              "type": "resources",
              "name": "Resources",
              "props": {
                "url": "json/experiments/E-ANND-3/resources/SUPPLEMENTARY_INFORMATION"
              }
            }
          ]
        }
      },
      {
        "type": "downloads",
        "name": "Downloads",
        "props": {
          "data": [
            {
              "title": "Metadata files",
              "files": [
                {
                  "url": "experiment/E-ANND-3/download/zip?fileType\u003dexperiment-metadata\u0026accessKey\u003d",
                  "type": "icon-tsv",
                  "description": "Experiment metadata (SDRF and IDF files archive)",
                  "isDownload": true
                },
                {
                  "url": "experiment/E-ANND-3/download?fileType\u003dexperiment-design\u0026accessKey\u003d",
                  "type": "icon-experiment-design",
                  "description": "Experiment design file (TSV format)",
                  "isDownload": true
                }
              ]
            },
            {
              "title": "Result files",
              "files": [
                {
                  "url": "experiment/E-ANND-3/download?fileType\u003dcluster\u0026accessKey\u003d",
                  "type": "icon-tsv",
                  "description": "Clustering file (TSV format)",
                  "isDownload": true
                },
                {
                  "url": "experiment/E-ANND-3/download/zip?fileType\u003dquantification-filtered\u0026accessKey\u003d",
                  "type": "icon-tsv",
                  "description": "Filtered TPMs files (MatrixMarket archive)",
                  "isDownload": true
                },
                {
                  "url": "experiment/E-ANND-3/download/zip?fileType\u003dmarker-genes\u0026accessKey\u003d",
                  "type": "icon-tsv",
                  "description": "Marker gene files (TSV files archive)",
                  "isDownload": true
                },
                {
                  "url": "experiment/E-ANND-3/download/zip?fileType\u003dnormalised\u0026accessKey\u003d",
                  "type": "icon-tsv",
                  "description": "Normalised counts files (MatrixMarket archive)",
                  "isDownload": true
                },
                {
                  "url": "experiment/E-ANND-3/download/zip?fileType\u003dquantification-raw\u0026accessKey\u003d",
                  "type": "icon-tsv",
                  "description": "Raw counts files (MatrixMarket archive)",
                  "isDownload": true
                }
              ]
            }
          ]
        }
      }
    ]
  }
}
@ke4 ke4 added the bug Something isn't working label Oct 19, 2023
@ke4
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ke4 commented Oct 19, 2023 •
edited
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Even if there is no plotTypesAndOptions the tabs should be appear on the page.
In that case there should be a message on the result tab something like this:

No plot types and/or options could be found for this experiment. Please, report this issue to this e-mail address: <atls feedback email address>

and all the other tabs should be there.

@lingyun1010 lingyun1010 self-assigned this Nov 14, 2023
@upendrakumbham
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Hi, moving back to the Sprint board as we are supposed to link PR in this issue.

@upendrakumbham upendrakumbham linked a pull request Jan 10, 2024 that will close this issue
Decoupling tabs in the experiment page and display them after validating #375
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@ke4
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ke4 commented Jul 31, 2024

@upendrakumbham
I am adding the new condition for displaying the Marker Genes tab:
If the accession starts with E-ANND AND no marker gene info, then we don't display that tab.

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@ke4 @upendrakumbham @lingyun1010