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Galaxy POST command

Galaxy integration with STENCIL​

JSON payload​

projectId

  • projectId is the highest level of categorizing the data in STENCIL.
  • STENCIL consists of many projects.
  • Each project consists of many samples and each sample consist of many libraries.

libraryType

  • Type of the library that is POSTed to STENCIL.
  • Examples are "RNA-seq", "ATAC-seq", and "ChIP-seq".

sampleId

  • Name of the sample which the library belongs.
  • One sample can have multiple libraries.
  • An example of multiple libraries for a sample may be different replicates for a sample.

libraryId

  • An ID given to a library that is POSTed from Galaxy to STENCIL.

libraryDescription

  • Optional free-form string description about the library

createdBy

  • Username of the Galaxy account under which the library is POSTed.

createTimestamp

  • The time the library is originally POSTed to STENCIL

updatedBy

  • Username of the Galaxy account under which the POST is updated.

updateTimestamp

  • Timestamp from when the library was last updated.

token

  • API key that is used to verify permission to POST to Stencil
  • This is defined in the backend's .env file under SVC_STENCIL_PWD

groupTag

  • An array of additional meta information associated with each library.
  • An example is Galaxy HistoryID where the associated data read by STENCIL resides.

libraryData

  • An array element containing the meta-information for each plot/chart/table/image POSTed to STENCIL.
  • The format of this element is detailed below.

libraryData Array​

id

  • A unique id assigned to each dataset in Galaxy
  • If a Galaxy historyID is POSTed to STENCIL using this parameter, the path to reproducibility is maintained

dataType

  • Type of data to be visualized in STENCIL.
  • Examples are PNG, SVG, JPG, basictable, lineplot, barchart, scatterplot, heatmap

layoutId

  • This is the unique ID of the layoutID that this data should be applied to.
  • See Configure Layout for additional details.

layoutTitle

  • This is title for the layout section.

tabId

  • Each Layout may consists of multiple Tabs.
  • This variable sets the displayed name of Tabs.

URL

  • URL of the location where STENCIL can access the data resides in Galaxy.
  • This can be any arbitrary URL

stepId

  • Each Tab consists of multiple “Steps”.
  • Steps indicates where exactly in the Tab the data needs to be visualized.

Example Payload​

Example payload:

{
  "projectId": "Yeast Epigenome Project",
  "libraryType": "Meta-analysis",
  "sampleId": "UMAP meta-analysis",
  "libraryId": "UMAP",
  "libraryDescription": "UMAP meta-analysis of all ChIP-exo data-sets generated in the Yeast Epigenome Project",
  "createdBy": "cegr@cornell.edu",
  "token": "SGAN9WTPAUCAYDO8A8HD",
  "submitter": "cegr@cornell.edu",
  "libraryData": [
    {
        "id": "UMAP_plot",
        "dataType": "scatterplot",
        "layoutId": "SingleChart",
        "layoutTitle": "UMAP of Yeast Epigenome",
        "tabId": "Scatter Plot",
        "URL": "http://localhost:8081/localdata/YEP/UMAP/UMAP_scatterplot.json",
        "stepId": "0"
    },
    {
      "id": "UMAP_rawdata",
        "dataType": "basictable",
      "layoutId": "SingleChart",
        "layoutTitle": "UMAP of Yeast Epigenome",
      "tabId": "UMAP Data",
      "URL": "http://localhost:8081/localdata/YEP/UMAP/UMAP_table.json",
      "stepId": "0"
    }
  ]
}