intermine
constructing a new query
I am using intermineR to query the TargetMine. Following the instructions in the intermineR.pdf and manual page I should be able to get a query template using getTemplateQuery or construct a new query using newQuery, in either cases the documentations say there should be at least three items in each query. These are view, constrains and constrainLogic.
Using the function names on the output object from getTemplateQuery gives:
"model" "title" "description" "select" "name" "comment" "tags" "orderBy" "where"
Using the function args on the function newQuery gives:
function (name = "", view = character(), sortOrder = "", longDescription = "", constraintLogic = NULL)
I tried modifying the slot where of the query object, as explained for the item constrain however as a list not as a matrix and it works for a single value only.
There might be some changes in the query scheme that I am not aware of or doesn't show in the documentation yet.
I am using R (3.3.2 (2016-10-31) on x86_64-apple-darwin13.4.0 (64-bit) running on macOS Sierra 10.12.2. Both intermineR and bioconductor are the last releases; InterMineR_0.99.4 Biobase_2.34.0.
I think you are right! Let me check tomorrow (and update the docs!).
Closing as fixed. Please reopen this ticket if you still have an issue.
I'm encountering this issue as well.
See this file - I had to set constraints separately in order to get them to stick.
https://github.com/intermine/interminer-workshop/commit/7a3abb154152c014ac8bdb4022141aa0e8ebd598#diff-926d80f72da226377e21accd790046c7R27
