Hello,
I'm working on adding a feature to blend4j (java interface to the Galaxy API) to access Galaxy Tool Data Tables. My repository is here:
https://github.com/dfornika/blend4j/tree/tool-data-client
I'm working on a method that deletes entries from Galaxy Tool Data Tables, but I'm having some trouble with the API calls.
How can I construct a DELETE api call on an entry in a Tool Data Table? For example, how could I delete hg38 from the "igv_broad_genomes" tool data table (using Postman or curl or whatever HTTP client)? Specifically, how do I pass the extra argument(s) besides the table name (id) that goes in the URL?
In bioblend, we pass "a “|” separated list of column contents, there must be a value for all the columns of the data table" https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#bioblend....
I can see the "igv_broad_genomes" tool data table when I send a GET request:
GET /api/tool_data/igv_broad_genomes { "model_class": "TabularToolDataTable", "name": "igv_broad_genomes", "columns": [ "name", "url", "value" ], "fields": [ [ "A. baumannii str. ATCC", " http://s3.amazonaws.com/igv.broadinstitute.org/genomes/ABaumannii_ATCC_17978... ", "ABaumannii_ATCC_17978" ], [ "A. baumannii str. AYE", " http://s3.amazonaws.com/igv.broadinstitute.org/genomes/ABaumannii_AYE_uid616... ", "ABaumannii_AYE_uid61637" ], ...(removed for brevity)... [ "Human hg38", " http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg38.genome", "hg38" ], ...(removed for brevity)... ] }
The closest I've got is to send this:
DELETE /api/tool_data/igv_broad_genomes Content-Type: application/json { "values": "Human hg38\thttp:// s3.amazonaws.com/igv.broadinstitute.org/genomes/hg38.genome\thg38" }
I get the same JSON description of the original Tool Data Table, including hg38:
{ "model_class": "TabularToolDataTable", "name": "igv_broad_genomes", "columns": [ "name", "url", "value" ], "fields": [ [ "A. baumannii str. ATCC", " http://s3.amazonaws.com/igv.broadinstitute.org/genomes/ABaumannii_ATCC_17978... ", "ABaumannii_ATCC_17978" ], [ "A. baumannii str. AYE", " http://s3.amazonaws.com/igv.broadinstitute.org/genomes/ABaumannii_AYE_uid616... ", "ABaumannii_AYE_uid61637" ], ...(removed for brevity)... [ "Human hg38", " http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg38.genome", "hg38" ], ...(removed for brevity)... ] }