Merge pull request #34 from JGCRI/demo-prep

Prepare for demo and fix bugs found while doing so.
JGCRI · Sep 20, 2017 · 9787a0c · 9787a0c
2 parents bce3413 + 2f4f492
commit 9787a0c
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Showing 17 changed files with 88 additions and 45 deletions.
diff --git a/R/electricity.R b/R/electricity.R
@@ -4,12 +4,16 @@
 #'
 #' Produce electricity by region.
 #'
-#' Columns:
+#' The raw table used by this module has columns:
 #' \itemize{
+#'   \item{scenario}
 #'   \item{region}
+#'   \item{sector}
+#'   \item{subsector}
+#'   \item{technology}
 #'   \item{year}
 #'   \item{value}
-#'   \item{units}
+#'   \item{Units}
 #' }
 #'
 #' @keywords internal
@@ -26,8 +30,8 @@ module.electricity <- function(mode, allqueries, aggkeys, aggfn, strtyr, endyr,
         message('Function for processing variable: Electricity')
 
         electricity <- allqueries$'Electricity'
-        electricity <- aggregate(electricity, aggfn, aggkeys)
         electricity <- filter(electricity, strtyr, endyr, filters)
+        electricity <- aggregate(electricity, aggfn, aggkeys)
         electricity <- unitconv_energy(electricity, ounit)
         electricity
     }

diff --git a/R/mcl.R b/R/mcl.R
@@ -164,15 +164,15 @@ generate <- function(scenctl,
 
 
     if(fileformat == 'XLSX') {
-        output_xlsx(rslts, tabs, dirname)
+        output_xlsx(rslts, tabs, dbloc)
     }
     else if(fileformat == 'CSV') {
-        output_csv(rslts, tabs, dirname)
+        output_csv(rslts, tabs, dbloc)
     }
     else {
         warning('Unknown file format ', fileformat, ' requested. ',
                 'Writing as CSV.')
-        output_csv(rslts, tabs, dirname)
+        output_csv(rslts, tabs, dbloc)
     }
 
     message('FIN.')

diff --git a/R/output.R b/R/output.R
@@ -77,7 +77,7 @@ output_xlsx <- function(rslts, tabs, dirname)
 #' @keywords internal
 alternate_filename <- function(name)
 {
-    name <- normalizePath(name)
+    name <- name
     dir <- dirname(name)
     filename <- basename(name)
     np <- nameparse(filename)
@@ -96,7 +96,7 @@ alternate_filename <- function(name)
         name <- file.path(dir, filename)
     }
 
-    normalizePath(name)
+    normalizePath(name, mustWork=FALSE)
 }
 
 

diff --git a/R/runmodule.R b/R/runmodule.R
@@ -91,6 +91,13 @@ module.test_fun <- function(mode, allqueries, aggkeys, aggfn, strtyr, endyr,
 #' in their input more readable.  For example, the variable with canonical name
 #' \code{gdp_mer_} can be represented as \code{GDP(MER)} in input files.
 #'
+#' Processing the data for a variable is done in a function called
+#' module.varname, for example, the variable \code{gdp_mer_} is processed in
+#' \code{\link{module.gdp_mer_}}.  The documentation for these functions
+#' contains a list of the columns in the raw table produced by the function,
+#' prior to aggregation or filtering.  This information is potentially useful
+#' for planning filtering or aggregation operations.  The module documentation
+#' will also have any notes pertinent to the computation of the data.
 #' @importFrom magrittr %>%
 #' @export
 listVariables <- function()

diff --git a/R/socioeconomics.R b/R/socioeconomics.R
@@ -4,12 +4,13 @@
 #'
 #' Produce population by region.
 #'
-#' Columns:
+#' The raw table used by this module has columns:
 #' \itemize{
+#'   \item{scenario}
 #'   \item{region}
 #'   \item{year}
 #'   \item{value}
-#'   \item{units}
+#'   \item{Units}
 #' }
 #'
 #' @keywords internal
@@ -26,8 +27,8 @@ module.population <- function(mode, allqueries, aggkeys, aggfn, strtyr, endyr,
         message('Function for processing variable: Population')
 
         population <- allqueries$'Population'
-        population <- aggregate(population, aggfn, aggkeys)
         population <- filter(population, strtyr, endyr, filters)
+        population <- aggregate(population, aggfn, aggkeys)
         population <- unitconv_counts(population, ounit)
         population
     }
@@ -37,16 +38,16 @@ module.population <- function(mode, allqueries, aggkeys, aggfn, strtyr, endyr,
 #'
 #' Produce GDP MER by region.
 #'
-#' Columns:
+#' The raw table used by this module has columns:
 #' \itemize{
+#'   \item{scenario}
 #'   \item{region}
 #'   \item{year}
 #'   \item{value}
-#'   \item{units}
+#'   \item{Units}
 #' }
 #'
 #' @keywords internal
-
 module.gdp_mer_ <- function(mode, allqueries, aggkeys, aggfn, strtyr, endyr,
                               filters, ounit)
 {
@@ -59,8 +60,8 @@ module.gdp_mer_ <- function(mode, allqueries, aggkeys, aggfn, strtyr, endyr,
         message('Function for processing variable: GDP MER')
 
         gdp_mer <- allqueries$'GDP(MER)'
+        gdp_mer <- filter(gdp_mer, strtyr, endyr, filters)
         gdp_mer <- aggregate(gdp_mer, aggfn, aggkeys)
-        #gdp_mer <- filter(gdp_mer, strtyr, endyr, filters)
         gdp_mer <- unitconv_usdollar(gdp_mer, ounit)
         gdp_mer
     }
@@ -70,16 +71,16 @@ module.gdp_mer_ <- function(mode, allqueries, aggkeys, aggfn, strtyr, endyr,
 #'
 #' Produce GDP PPP by region.
 #'
-#' Columns:
+#' The raw table used by this module has columns:
 #' \itemize{
+#'   \item{scenario}
 #'   \item{region}
 #'   \item{year}
 #'   \item{value}
-#'   \item{units}
+#'   \item{Units}
 #' }
 #'
 #' @keywords internal
-
 module.pcgdp_ppp_ <- function(mode, allqueries, aggkeys, aggfn, strtyr, endyr,
                            filters, ounit)
 {
@@ -92,8 +93,8 @@ module.pcgdp_ppp_ <- function(mode, allqueries, aggkeys, aggfn, strtyr, endyr,
         message('Function for processing variable: Per capita GDP PPP')
 
         gdp_ppp <- allqueries$'pcGDP(PPP)'
+        gdp_ppp <- filter(gdp_ppp, strtyr, endyr, filters)
         gdp_ppp <- aggregate(gdp_ppp, aggfn, aggkeys)
-        #gdp_ppp <- filter(gdp_ppp, strtyr, endyr, filters)
         gdp_ppp <- unitconv_usdollar(gdp_ppp, ounit)
         gdp_ppp
     }

diff --git a/codecov.yml b/codecov.yml
@@ -1,3 +1,15 @@
 comment:
 	behavior: new
 ignore: R/mcl.R
+
+coverage:
+  precision: 1
+
+  status:
+    project:
+      default:
+        enabled: no
+
+    patch:
+      default:
+        enabled: no
diff --git a/inst/extdata/default-queries.xml b/inst/extdata/default-queries.xml
@@ -31,11 +31,12 @@
 	</aQuery>
 
 	<aQuery>
-		<supplyDemandQuery title="Electricity">
-			<axis1 name="technology">technology</axis1>
-			<axis2 name="Year">physical-output[@vintage]</axis2>
-			<xPath buildList="true" dataName="output" group="false" sumAll="false">*[@type = 'sector' (: collapse :) and (@name='electricity' or @name='elect_td_bld' or @name='industrial energy use')]//*[@type = 'technology' and not (@name='elect_td_bld' or @name='electricity')]/*[@type='output' (:collapse:) and (@name='electricity' or @name='elect_td_bld')]/physical-output/node()</xPath>
-			<comments/>
-        	</supplyDemandQuery>
+	  <supplyDemandQuery title="Electricity">
+            <axis1 name="region">region</axis1>
+            <axis2 name="Year">physical-output[@vintage]</axis2>
+            <xPath buildList="true" dataName="output" group="false" sumAll="false">*[@type = 'sector' and ((@name='electricity' or @name='elect_td_bld' or @name='industrial energy use'))]//*[@type = 'subsector']//*[@type = 'technology' and not (@name='elect_td_bld')]/*[@type='output' (:collapse:)  and (@name='electricity' or @name='elect_td_bld')]/physical-output/node()</xPath>
+            <comments/>
+	  </supplyDemandQuery> 
 	</aQuery>
+
 </queries>
diff --git a/inst/extdata/scenario-electricity.ctl → inst/extdata/example-scenario.ctl b/inst/extdata/scenario-electricity.ctl → inst/extdata/example-scenario.ctl
diff --git a/inst/extdata/example-variable.ctl b/inst/extdata/example-variable.ctl
@@ -0,0 +1,5 @@
+GCAM variable,output variable,aggregation keys,aggregation function,start year,end year,filters,output units
+Population,Population,,,1990,2020,,thous
+pcGDP(PPP),Per-capita GDP (PPP),,,,,,Thous80US$/per
+Electricity,Electricity by Technology,"region,technology",,1990,2050,,MWh
+Electricity,Electricity by Subsector,"region, subsector",,1990,2050,(matches; sector; electricity),
diff --git a/inst/extdata/scenario.ctl b/inst/extdata/scenario.ctl
diff --git a/inst/extdata/variable.ctl b/inst/extdata/variable.ctl
diff --git a/man/listVariables.Rd b/man/listVariables.Rd
diff --git a/man/module.electricity.Rd b/man/module.electricity.Rd
diff --git a/man/module.gdp_mer_.Rd b/man/module.gdp_mer_.Rd
diff --git a/man/module.pcgdp_ppp_.Rd b/man/module.pcgdp_ppp_.Rd
diff --git a/man/module.population.Rd b/man/module.population.Rd
diff --git a/tests/testthat/test_output.R b/tests/testthat/test_output.R
@@ -45,15 +45,16 @@ test_that('alternate_filename does the right thing with xyz.csv.', {
     on.exit(unlink(file.path(dir, '*.csv')))
 
     expect_identical(alternate_filename(filename),
-                     normalizePath(filename))
+                     normalizePath(filename, mustWork=FALSE))
 
     lastfilename <- filename
     for(i in 1:3) {
         fcon <- file(lastfilename, 'w')
         close(fcon)
         lastfilename <- alternate_filename(filename)
         expect_identical(lastfilename,
-                         normalizePath(file.path(dir,sprintf('xyz%03d.csv',i))))
+                         normalizePath(file.path(dir,sprintf('xyz%03d.csv',i)),
+                                       mustWork=FALSE))
     }
 })
 
@@ -65,15 +66,16 @@ test_that('alternate_filename does the right thing with xyz.abc.csv.', {
     on.exit(unlink(file.path(dir, '*.csv')))
 
     expect_identical(alternate_filename(filename),
-                     normalizePath(filename))
+                     normalizePath(filename, mustWork=FALSE))
 
     lastfilename <- filename
     for(i in 1:3) {
         fcon <- file(lastfilename, 'w')
         close(fcon)
         lastfilename <- alternate_filename(filename)
         expect_identical(lastfilename,
-                         normalizePath(file.path(dir,sprintf('xyz.abc%03d.csv',i))))
+                         normalizePath(file.path(dir,sprintf('xyz.abc%03d.csv',i)),
+                                       mustWork=FALSE))
     }
 })
 
@@ -85,15 +87,16 @@ test_that('alternate_filename does the right thing with no file extension.', {
     on.exit(unlink(file.path(dir, '*.csv')))
 
     expect_identical(alternate_filename(filename),
-                     normalizePath(filename))
+                     normalizePath(filename, mustWork=FALSE))
 
     lastfilename <- filename
     for(i in 1:3) {
         fcon <- file(lastfilename, 'w')
         close(fcon)
         lastfilename <- alternate_filename(filename)
         expect_identical(lastfilename,
-                         normalizePath(file.path(dir,sprintf('xyz%03d',i))))
+                         normalizePath(file.path(dir,sprintf('xyz%03d',i)),
+                                       mustWork=FALSE))
     }
 })