202 integrate ccdR into tcpl load data

[cthunes]

This PR closes #202. ccdR is integrated into tcplConf, tcplLoadData, and tcplLoadAeid. tcplQueryAPI was added to interface with ccdR. Other tcplLoadXxxx functions can be integrated soon after with new tickets.

Here are a bunch of tests, copy+paste to try it out!

devtools::install_github("USEPA/ccdR")
library("ccdR") #while ccdR is not on CRAN, must load manually

devtools::load_all() # or install_git from this branch, then library(tcpl)
tcplConf(pass='<apikey>', drvr = 'API') # add your API key


# tcplQueryAPI -- main use is by another function, like the tcplLoadAeid and tcplLoadData
# still possible to use directly however
tcplQueryAPI(resource = "assay", fld = "asid", val = 7)
tcplQueryAPI(resource = "assay", fld = "aeid", val = 891, return_flds = "acid")
tcplQueryAPI(fld = c("aeid", "acid"), val = 891) #error is right! if using tcplQueryAPI with default "data" for 'resource' parameter, can only use one fld (aeid, spid, m4id, dtxsid)


# tcplLoadAeid
tcplLoadAeid(fld = "acid", val = 400)
tcplLoadAeid(fld = "intended_target_type", val = "protein")
tcplLoadAeid(fld = "detection_technology_type", val = "Colorimetric")
tcplLoadAeid(fld = "aeid", val = 891)
tcplLoadAeid(fld = c("intended_target_type", "detection_technology_type"), val = list("protein", "Colorimetric"))
tcplLoadAeid(fld = c("intended_target_type", "detection_technology_type"), val = list("protein", "Radiometry", "Colorimetric")) #error is right! fld and val must be equal. put the last two elements in a vector to make the lengths match
tcplLoadAeid(fld = c("intended_target_type", "detection_technology_type"), val = list("protein", c("Radiometry", "Colorimetric")))
tcplLoadAeid(fld = "intended_target_type", val = c("protein", "rna"))
tcplLoadAeid(add.fld = "intended_target_type") #add any column(s) to table
tcplLoadAeid(fld = c("hello", "goodbye"), val = list(0,1)) #error is right! "hello" and "goodbye" are not valid fields to query with


# tcplLoadData
# five levels are available to load and there are four flds to query on, here some combinations
tcplLoadData(lvl = 3, fld = "aeid", val = 891, add.fld = FALSE) # each conc-resp gets its own row
tcplLoadData(lvl = 4, fld = "spid", val = "TP0001055F12", add.fld = FALSE)
tcplLoadData(lvl = 5, fld = "m4id", val = 739695, add.fld = FALSE)
tcplLoadData(lvl = 6, fld = "dtxsid", val = "DTXSID7020182", add.fld = FALSE) # each flag gets its own row
tcplLoadData(lvl = "agg", fld = "aeid", val = 891, add.fld = TRUE) # use add.fld = TRUE (default), if you want every field returned regardless of level and what is normally returned
# error cases
tcplLoadData(lvl = 5, fld = c("aeid", "spid"), val = list(891, "TP0001055F12"), add.fld = FALSE) # can only query by 1 fld for tcplLoadData
tcplLoadData(lvl = 5, fld = "acid", val = 400, add.fld = FALSE) # must query by one of the four supported by ccdR
tcplLoadData(lvl = 2, fld = "aeid", val = 891, add.fld = FALSE) # only levels 3-6 are supported using the API
tcplLoadData(lvl = "agg", fld = "aeid", val = 891, type = "sc", add.fld = FALSE) # only "mc" is supported using the API
tcplLoadData(lvl = 4, fld = "spid", val = "helloworld", add.fld = FALSE) # null data.table return, no "helloworld" spid found
tcplLoadData(lvl = 4, fld = "spid", val = c("TP0001055F12", "helloworld", "goodbye"), add.fld = FALSE) # some data returned if found, rest shows warning that it is missing

[brown-jason]

calling register_ccdr requires @import statement in roxygen skeleton/documentation

[cthunes]

purposefully haven't added ccdR imports as they would would make it so you couldn't load the package i thought. Waiting until ccdR is on CRAN

[brown-jason]

All of the examples you provided could/should be made as unit tests. Let's discuss how we implemented mocking into ccdr and how it can be applied in this situation.

[cthunes]

Imports added. Unit tests are a great idea.

Known problem with CRAN version of ccdR as an import to tcpl: when calling register_ccdr() within tcplConf, an error prints when saving api key for session. However, the key is already saved at the point of error and this does not affect functionality. ccdR team will plan to patch this soon, so I have chosen to not suppress this on the tcpl side, by forcibly fully loading ccdR with if (is.null(getOption('ccdr'))) library('ccdR', quietly = TRUE). This means that for now, we will just ignore the error when running tcplConf.

[brown-jason]

Tested with dev version of ccdr and is working.
l5 <- tcplLoadData(lvl = 5, fld = "DTXSID", val = "DTXSID7020182")
Takes a while to load, we should investigate keys with asif to ensure we have keys for each fld specified.