Develop DSMolgenisArmadillo

Testing

The test are run each time you file a pull request on github. You can run the test locally as well using the following commands:

# load prerequisites
library(tibble)

# run all tests
devtools::test()
#> ✓ |  OK F W S | Context
#> |   0       | ArmadilloConnection
⠋ |   1       | ArmadilloConnection
⠦ |  77       | ArmadilloConnection
✓ | 128       | ArmadilloConnection [0.5 s]
#> |   0       | ArmadilloDriver
✓ |  34       | ArmadilloDriver
#> |   0       | ArmadilloOAuth
✓ |  11       | ArmadilloOAuth
#> |   0       | ArmadilloResult
✓ |  14       | ArmadilloResult
#> |   0       | utils
✓ |  25     1 | utils
#> ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> test-utils.R:78: skip: .deparse deparses vectors
#> Reason: I still don't get the .deparse arguments
#> ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> 
#> ══ Results ════════════════════════════════════════════════════════════════════════════════════════════════
#> Duration: 0.7 s
#> 
#> OK:       212
#> Failed:   0
#> Warnings: 0
#> Skipped:  1
# run a single test file
# make sure you have the test file open
# e.g. test-ArmadilloResult.R

devtools::test_file()

Vignettes

We use vignettes to expose the usage of the package. It includes examples of regular use cases and shows you how to setup the package.

The vignettes are automatically build and you can run them locally with the following command:

knitr::knit("vignettes/DSMolgenisArmadillo.Rmd.orig", output = "vignettes/DSMolgenisArmadillo.Rmd")

If you only want the R-output use:

knitr::purl("vignettes/DSMolgenisArmadillo.Rmd.orig", output = "vignettes/DSMolgenisArmadillo.R")

Tips and tricks

Some tips and tricks when you developing on DSMolgenisArmadillo

Authentication

You can login with basic auth when you are developing. The default credentials are username: admin and password: admin.

library(DSMolgenisArmadillo)

armadillo_url <- "https://armadillo.dev.molgenis.org"

builder <- DSI::newDSLoginBuilder()
builder$append(server = "armadillo",
               url = armadillo_url,
               user = "admin",
               password = "admin",
               table = "gecko/2_1-core-1_0/nonrep",
               driver = "ArmadilloDriver")

logindata <- builder$build()

conns <- datashield.login(login = logindata, assign = TRUE)

Version of the package

You can determine which version of the DSMolgenisArmadillo you are running by executing the following code:

dsGetInfo(armadillo())
#> $driver.version
#> [1] '1.1.3.9001'

Table handling

You can use several methods checking if tables in DataSHIELD. For checking existence of the tables you can use the following methods.

dsHasTable(conns$armadillo, "gecko/2_1-core-1_0/nonrep")
#> [1] TRUE
dsHasTable(conns$armadillo, "gecko/1_1-outcome-1_0/nonrep")
#> [1] TRUE

To check the accessibility you can use the table_status methods.

datashield.table_status(conns, "gecko/2_1-core-1_0/nonrep")
#>      server                     table accessible
#> 1 armadillo gecko/2_1-core-1_0/nonrep       TRUE

To check which tables are assigned you can use the dsListTables function.

dsListTables(conns$armadillo)
#> [1] "chicago/crime/crimes"            "gecko/1_1-outcome-1_0/nonrep"    "gecko/1_1-outcome-1_0/yearlyrep"
#> [4] "gecko/2_1-core-1_0/monthlyrep"   "gecko/2_1-core-1_0/nonrep"       "gecko/2_1-core-1_0/trimesterrep"
#> [7] "gecko/2_1-core-1_0/yearlyrep"    "load-test/data/patient"

Methods and packages

In DataSHIELD you can use a variety of methods and packages. To check which are avaiable you can execute the following code:

Available packages (serverside)

The available packages displayed by the method, are the serverside R-packages. Which means the packages available on the Armadillo.

conns <- datashield.login(logins = logindata, assign = F)
dsListPackages(conns$armadillo)
#>              name   version
#> 1           arrow     1.0.0
#> 2      assertthat     0.2.1
#> 3              BH  1.72.0-3
#> 4             bit     4.0.4
#> 5           bit64     4.0.2
#> 6             cli     2.0.2
#> 7          crayon     1.3.4
#> 8          digest    0.6.25
#> 9          docopt     0.6.1
#> 10          dplyr     0.8.5
#> 11         dsBase     6.0.1
#> 12       ellipsis     0.3.0
#> 13          fansi     0.4.1
#> 14           glue     1.4.0
#> 15      lifecycle     0.2.0
#> 16        littler     0.3.9
#> 17           lme4    1.1-23
#> 18       magrittr       1.5
#> 19          minqa     1.2.4
#> 20 MolgenisRserve     0.1.2
#> 21         nloptr   1.2.2.2
#> 22         pillar     1.4.3
#> 23      pkgconfig     2.0.3
#> 24          plogr     0.2.0
#> 25             ps     1.3.2
#> 26          purrr     0.3.4
#> 27             R6     2.4.1
#> 28           RANN     2.6.1
#> 29           Rcpp   1.0.4.6
#> 30      RcppEigen 0.3.3.7.0
#> 31          rlang     0.4.5
#> 32        statmod    1.4.34
#> 33        stringi     1.4.6
#> 34        stringr     1.4.0
#> 35         tibble     3.0.1
#> 36     tidyselect     1.0.0
#> 37           utf8     1.1.4
#> 38          vctrs     0.2.4
#> 39           base     3.6.3
#> 40           boot    1.3-24
#> 41          class    7.3-15
#> 42        cluster     2.1.0
#> 43      codetools    0.2-16
#> 44       compiler     3.6.3
#> 45       datasets     3.6.3
#> 46        foreign    0.8-75
#> 47       graphics     3.6.3
#> 48      grDevices     3.6.3
#> 49           grid     3.6.3
#> 50     KernSmooth   2.23-16
#> 51        lattice   0.20-38
#> 52           MASS  7.3-51.5
#> 53         Matrix    1.2-18
#> 54        methods     3.6.3
#> 55           mgcv    1.8-31
#> 56           nlme   3.1-144
#> 57           nnet    7.3-12
#> 58       parallel     3.6.3
#> 59          rpart    4.1-15
#> 60        spatial    7.3-11
#> 61        splines     3.6.3
#> 62          stats     3.6.3
#> 63         stats4     3.6.3
#> 64       survival     3.1-8
#> 65          tcltk     3.6.3
#> 66          tools     3.6.3
#> 67          utils     3.6.3
Available methods (clientside)

These are the available methods on the Armadillo server.

datashield.methods(conns = conns, type = "aggregate")
#>                        name                            value version package      type    class    server
#> 1              is.character               base::is.character    NULL    base aggregate function armadillo
#> 2        dataFrameSubsetDS1       dsBase::dataFrameSubsetDS1   6.0.1  dsBase aggregate function armadillo
#> 3                meanSdGpDS               dsBase::meanSdGpDS   6.0.1  dsBase aggregate function armadillo
#> 4             scatterPlotDS            dsBase::scatterPlotDS   6.0.1  dsBase aggregate function armadillo
#> 5                 setSeedDS                dsBase::setSeedDS   6.0.1  dsBase aggregate function armadillo
#> 6              matrixDetDS1             dsBase::matrixDetDS1   6.0.1  dsBase aggregate function armadillo
#> 7                   numNaDS                  dsBase::numNaDS   6.0.1  dsBase aggregate function armadillo
#> 8                  asListDS                 dsBase::asListDS   6.0.1  dsBase aggregate function armadillo
#> 9                is.numeric                 base::is.numeric    NULL    base aggregate function armadillo
#> 10                   t.test                    stats::t.test    NULL   stats aggregate function armadillo
#> 11                  is.list                    base::is.list    NULL    base aggregate function armadillo
#> 12                 lengthDS                 dsBase::lengthDS   6.0.1  dsBase aggregate function armadillo
#> 13            heatmapPlotDS            dsBase::heatmapPlotDS   6.0.1  dsBase aggregate function armadillo
#> 14                    dimDS                    dsBase::dimDS   6.0.1  dsBase aggregate function armadillo
#> 15                  is.null                    base::is.null    NULL    base aggregate function armadillo
#> 16                   meanDS                   dsBase::meanDS   6.0.1  dsBase aggregate function armadillo
#> 17                  tableDS                  dsBase::tableDS   6.0.1  dsBase aggregate function armadillo
#> 18                is.factor                  base::is.factor    NULL    base aggregate function armadillo
#> 19                    corDS                    dsBase::corDS   6.0.1  dsBase aggregate function armadillo
#> 20          testObjExistsDS          dsBase::testObjExistsDS   6.0.1  dsBase aggregate function armadillo
#> 21                isValidDS                dsBase::isValidDS   6.0.1  dsBase aggregate function armadillo
#> 22                table1DDS                dsBase::table1DDS   6.0.1  dsBase aggregate function armadillo
#> 23              asFactorDS1              dsBase::asFactorDS1   6.0.1  dsBase aggregate function armadillo
#> 24                   glmDS2                   dsBase::glmDS2   6.0.1  dsBase aggregate function armadillo
#> 25                   glmDS1                   dsBase::glmDS1   6.0.1  dsBase aggregate function armadillo
#> 26                    covDS                    dsBase::covDS   6.0.1  dsBase aggregate function armadillo
#> 27              lmerSLMADS2              dsBase::lmerSLMADS2   6.0.1  dsBase aggregate function armadillo
#> 28                     rmDS                     dsBase::rmDS   6.0.1  dsBase aggregate function armadillo
#> 29                   exists                     base::exists    NULL    base aggregate function armadillo
#> 30                  rangeDS                  dsBase::rangeDS   6.0.1  dsBase aggregate function armadillo
#> 31                table2DDS                dsBase::table2DDS   6.0.1  dsBase aggregate function armadillo
#> 32                     NROW                       base::NROW    NULL    base aggregate function armadillo
#> 33              scoreVectDS              dsBase::scoreVectDS   6.0.1  dsBase aggregate function armadillo
#> 34                 tapplyDS                 dsBase::tapplyDS   6.0.1  dsBase aggregate function armadillo
#> 35                 levelsDS                 dsBase::levelsDS   6.0.1  dsBase aggregate function armadillo
#> 36            densityGridDS            dsBase::densityGridDS   6.0.1  dsBase aggregate function armadillo
#> 37                 lexisDS1                 dsBase::lexisDS1   6.0.1  dsBase aggregate function armadillo
#> 38             histogramDS1             dsBase::histogramDS1   6.0.1  dsBase aggregate function armadillo
#> 39             histogramDS2             dsBase::histogramDS2   6.0.1  dsBase aggregate function armadillo
#> 40                 tableDS2                 dsBase::tableDS2   6.0.1  dsBase aggregate function armadillo
#> 41          checkNegValueDS          dsBase::checkNegValueDS   6.0.1  dsBase aggregate function armadillo
#> 42           quantileMeanDS           dsBase::quantileMeanDS   6.0.1  dsBase aggregate function armadillo
#> 43                tTestFDS2                dsBase::tTestFDS2   6.0.1  dsBase aggregate function armadillo
#> 44                    varDS                    dsBase::varDS   6.0.1  dsBase aggregate function armadillo
#> 45               colnamesDS               dsBase::colnamesDS   6.0.1  dsBase aggregate function armadillo
#> 46                     lsDS                     dsBase::lsDS   6.0.1  dsBase aggregate function armadillo
#> 47                  classDS                  dsBase::classDS   6.0.1  dsBase aggregate function armadillo
#> 48                   isNaDS                   dsBase::isNaDS   6.0.1  dsBase aggregate function armadillo
#> 49 listDisclosureSettingsDS dsBase::listDisclosureSettingsDS   6.0.1  dsBase aggregate function armadillo
#> 50             glmerSLMADS2             dsBase::glmerSLMADS2   6.0.1  dsBase aggregate function armadillo
#> 51               glmSLMADS1               dsBase::glmSLMADS1   6.0.1  dsBase aggregate function armadillo
#> 52               glmSLMADS2               dsBase::glmSLMADS2   6.0.1  dsBase aggregate function armadillo
#> 53          recodeValuesDS1          dsBase::recodeValuesDS1   6.0.1  dsBase aggregate function armadillo
#> 54                  namesDS                  dsBase::namesDS   6.0.1  dsBase aggregate function armadillo
#> 55                corTestDS                dsBase::corTestDS   6.0.1  dsBase aggregate function armadillo
#> 56                messageDS                dsBase::messageDS   6.0.1  dsBase aggregate function armadillo
datashield.methods(conns = conns, type = "assign")
#>                  name                      value version package   type    class    server
#> 1    changeRefGroupDS   dsBase::changeRefGroupDS   6.0.1  dsBase assign function armadillo
#> 2  dataFrameSubsetDS2 dsBase::dataFrameSubsetDS2   6.0.1  dsBase assign function armadillo
#> 3        matrixDiagDS       dsBase::matrixDiagDS   6.0.1  dsBase assign function armadillo
#> 4         asNumericDS        dsBase::asNumericDS   6.0.1  dsBase assign function armadillo
#> 5          asMatrixDS         dsBase::asMatrixDS   6.0.1  dsBase assign function armadillo
#> 6        matrixDetDS2       dsBase::matrixDetDS2   6.0.1  dsBase assign function armadillo
#> 7   matrixTransposeDS  dsBase::matrixTransposeDS   6.0.1  dsBase assign function armadillo
#> 8             mergeDS            dsBase::mergeDS   6.0.1  dsBase assign function armadillo
#> 9             cbindDS            dsBase::cbindDS   6.0.1  dsBase assign function armadillo
#> 10           asListDS           dsBase::asListDS   6.0.1  dsBase assign function armadillo
#> 11                log                  base::log    NULL    base assign function armadillo
#> 12           matrixDS           dsBase::matrixDS   6.0.1  dsBase assign function armadillo
#> 13         asFactorDS         dsBase::asFactorDS   6.0.1  dsBase assign function armadillo
#> 14     tableDS.assign     dsBase::tableDS.assign   6.0.1  dsBase assign function armadillo
#> 15              repDS              dsBase::repDS   6.0.1  dsBase assign function armadillo
#> 16            rPoisDS            dsBase::rPoisDS   6.0.1  dsBase assign function armadillo
#> 17           unListDS           dsBase::unListDS   6.0.1  dsBase assign function armadillo
#> 18     matrixInvertDS     dsBase::matrixInvertDS   6.0.1  dsBase assign function armadillo
#> 19    tapplyDS.assign    dsBase::tapplyDS.assign   6.0.1  dsBase assign function armadillo
#> 20              seqDS              dsBase::seqDS   6.0.1  dsBase assign function armadillo
#> 21    dataFrameFillDS    dsBase::dataFrameFillDS   6.0.1  dsBase assign function armadillo
#> 22           subsetDS           dsBase::subsetDS   6.0.1  dsBase assign function armadillo
#> 23            rNormDS            dsBase::rNormDS   6.0.1  dsBase assign function armadillo
#> 24     recodeLevelsDS     dsBase::recodeLevelsDS   6.0.1  dsBase assign function armadillo
#> 25    dataFrameSortDS    dsBase::dataFrameSortDS   6.0.1  dsBase assign function armadillo
#> 26           rBinomDS           dsBase::rBinomDS   6.0.1  dsBase assign function armadillo
#> 27                cDS                dsBase::cDS   6.0.1  dsBase assign function armadillo
#> 28        dataFrameDS        dsBase::dataFrameDS   6.0.1  dsBase assign function armadillo
#> 29        asFactorDS2        dsBase::asFactorDS2   6.0.1  dsBase assign function armadillo
#> 30    completeCasesDS    dsBase::completeCasesDS   6.0.1  dsBase assign function armadillo
#> 31       matrixMultDS       dsBase::matrixMultDS   6.0.1  dsBase assign function armadillo
#> 32             seedDS             dsBase::seedDS   6.0.1  dsBase assign function armadillo
#> 33    subsetByClassDS    dsBase::subsetByClassDS   6.0.1  dsBase assign function armadillo
#> 34              cbind                base::cbind    NULL    base assign function armadillo
#> 35             unlist               base::unlist    NULL    base assign function armadillo
#> 36            rbindDS            dsBase::rbindDS   6.0.1  dsBase assign function armadillo
#> 37          reShapeDS          dsBase::reShapeDS   6.0.1  dsBase assign function armadillo
#> 38            rUnifDS            dsBase::rUnifDS   6.0.1  dsBase assign function armadillo
#> 39         as.numeric           base::as.numeric    NULL    base assign function armadillo
#> 40               list                 base::list    NULL    base assign function armadillo
#> 41        asIntegerDS        dsBase::asIntegerDS   6.0.1  dsBase assign function armadillo
#> 42           lexisDS2           dsBase::lexisDS2   6.0.1  dsBase assign function armadillo
#> 43            as.null              base::as.null    NULL    base assign function armadillo
#> 44                sum                  base::sum    NULL    base assign function armadillo
#> 45           lexisDS3           dsBase::lexisDS3   6.0.1  dsBase assign function armadillo
#> 46        asLogicalDS        dsBase::asLogicalDS   6.0.1  dsBase assign function armadillo
#> 47   matrixDimnamesDS   dsBase::matrixDimnamesDS   6.0.1  dsBase assign function armadillo
#> 48     complete.cases      stats::complete.cases    NULL   stats assign function armadillo
#> 49             listDS             dsBase::listDS   6.0.1  dsBase assign function armadillo
#> 50             attach               base::attach    NULL    base assign function armadillo
#> 51      asCharacterDS      dsBase::asCharacterDS   6.0.1  dsBase assign function armadillo
#> 52                exp                  base::exp    NULL    base assign function armadillo
#> 53    recodeValuesDS2    dsBase::recodeValuesDS2   6.0.1  dsBase assign function armadillo
#> 54                  c                    base::c    NULL    base assign function armadillo
#> 55        replaceNaDS        dsBase::replaceNaDS   6.0.1  dsBase assign function armadillo
#> 56       rowColCalcDS       dsBase::rowColCalcDS   6.0.1  dsBase assign function armadillo
#> 57           sampleDS           dsBase::sampleDS   6.0.1  dsBase assign function armadillo
#> 58       as.character         base::as.character    NULL    base assign function armadillo
#> 59                rep                  base::rep    NULL    base assign function armadillo
#> 60            BooleDS            dsBase::BooleDS   6.0.1  dsBase assign function armadillo
#> 61     asDataMatrixDS     dsBase::asDataMatrixDS   6.0.1  dsBase assign function armadillo


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DSMolgenisArmadillo documentation built on Oct. 25, 2021, 9:06 a.m.