1. Introduction to SeqWare
  2. Installation
  3. Getting Started
  4. SeqWare Pipeline
  5. SeqWare MetaDB
  6. SeqWare Portal
  7. SeqWare Web Service
  8. SeqWare Query Engine
  9. Glossary
  10. Frequently Asked Questions
  11. APIs
  12. Source Code
  13. Plugins
  14. Modules
  15. Advanced Topics

Metadata - Data Resources

Overview

This sub-domain is exclusively for low-level access of database tables. Each URI actually retrieves one or more rows from a database table. The output format is exclusively XML produced by JAXB.

Retrieving a list of all items in a table is plural e.g. /metadata/db/studies

  • GET: Grouped resources are of the type TableNameList, where TableName is the singular name of the table.
  • POST: Add a new row to the table
  • PUT and DELETE are not permitted

Queries on the table as a whole can be added to the URI as query parameters, e.g. /metadata/db/studies?title=PCSI to find all of the studies with the title of PCSI

Retrieving a particular table row is singular e.g. /metadata/db/study/63

  • GET: returns the table row with the given SWID
  • PUT: updates the row in the table with the row in the request
  • POST and DELETE are not permitted

Additional fields can be shown by adding ?show to the query parameters, e.g. /metadata/db/lanes/1234?show=workflowRun shows the workflow run associated with this lane.

Resources

The Web service that this API refers to is http://localhost:8888/seqware-webservice. For more information about each resource and the correct complete URI, please follow the link to the resource-specific page.

URI Description
GET
/files
Retrieves a list of files.
POST
/samples
Add a new sample to the database.
PUT
/processes/(processSWID)
Updates a processing object with the given SWID.
GET
/workflows/(workflowSWID)
Retrieves a workflow using its SWID.
GET
/workflowruns
Retrieves a list of workflow runs.
GET
/sequencerruns
Retrieves a list of sequencer runs.
GET
/experiments
Retrieves one or more experiments, depending on parameters.
POST
/processes
Add a new processing object to the database.
GET
/studies
Retrieves a list of studies
POST
/workflowparamvalues
Adds a workflow parameter value to the database
GET
/samples
Retrieves a list of samples
POST
/studies
Adds a new study to the database
GET
/workflowparamvalues
Retrieves a list of workflow parameter values.
GET
/lane/(laneSWID)
Retrieves a lane with a particular SWID.
GET
/ius
Retrieves a list of IUSes.
GET
/ius/(iusSWID)
Retrieves an experiment based on the SWID.
PUT
/workflowruns/(workflowRunSWID)
Updates a workflow run with the given SWID.
GET
/workflows/{workflowId}/runs
Retrieves all of the workflow runs for a particular workflow using the workflow’s SWID.
POST
/experiments
Adds a new experiment to the experiment table.
PUT
/ius/(iusSWID)
Update an ius with the given SWID.
GET
/experiments/(experimentSWID)
Retrieves a list of experiments.
GET
/samples/root
Retrieves a list of root samples (samples without parents in the sample hierarchy)
POST
/workflows
Adds a new workflow to the database.
PUT
/files/(fileSWID)
Updates a file with the given SWID.
GET
/workflowruns/{workflowRunId}/files
Retrieves the files produced by the workflow run with the given SWID.
GET
/processes
Retrieves a list of processings.
GET
/processes/{processSWID}/parents
Retrieves the parent processing events of the processing event with the given SWID.
GET
/files/(fileSWID)
Retrieves a file using its SWID.
GET
/processes/(processSWID)
Retrieves a processing object by its SWID.
GET
/workflowparams
Retrieves a list of workflow parameters.
POST
/experiments
Adds metadata about a file to the database.
PUT
/lane/(laneSWID)
Updates a lane with the given SWID.
POST
/workflowparams
Add a new workflow parameter to the database.
GET
/lanes
Retrieves a list of lanes.
GET
/samples/(sampleSWID)
Retrieves a sample using its SWID.
GET
/workflows
Retrieves a list of workflows.
GET
/sequencerrun/(sequencerRunSWID)
Retrieves a sequencer run by SWID.
POST
/workflowruns
Inserts a new workflow run into the database.
GET
/studies/(studySWID)
Retrieves a study using its SWID.
GET
/workflowruns/(workflowRunSWID)
Retrieves a workflow run by SWID
GET
/workflowruns/{workflowRunId}/processings
Retrieves the processing events produced by the workflow run with the given SWID.