Merge pull request #259 from Sage-Bionetworks/fix-dashboard

Fix dashboard

bin/database_to_staging.py

@@ -219,7 +219,10 @@ def main(genie_version,
             'Rscript',
             os.path.join(os.path.dirname(os.path.abspath(__file__)),
                          '../genie/dashboard_markdown_generator.R'),
-            genie_version]
+            genie_version,
+            '--template_path',
+            os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                         '../genie/dashboardTemplate.Rmd')]
 
         if genie_user is not None and genie_pass is not None:
             dashboard_markdown_html_commands.extend(

genie/dashboardTemplate.Rmd

@@ -345,6 +345,7 @@ if (is.null(this_bed)) {
 }
 this_assays = as.character(unique(this_samples$SEQ_ASSAY_ID))
 this_mut <- getFileDf("data_mutations_extended.txt", releaseFiles)
+assay_infodf = getFileDf("assay_information.txt", releaseFiles)
 black_list_variants <- synTableQuery("select * from syn18459663",
                                      includeRowIdAndRowVersion = F)
 black_list_variantsdf = black_list_variants$asDataFrame()
@@ -557,11 +558,9 @@ if (!is.null(assay_infodf) & !is.null(this_bed)) {
   number_of_genes[names(num_submitted_genes), "num_genes_submitted"] = num_submitted_genes
   number_of_genes[assay_infodf$SEQ_ASSAY_ID, "num_expected_genes"] = assay_infodf$number_of_genes
 
-  different_from_expected = number_of_genes[c(which(number_of_genes$num_genes_submitted != number_of_genes$num_expected_genes),
+  different_from_expected = number_of_genes[c(which(number_of_genes$num_genes_remapped != number_of_genes$num_expected_genes),
                                               which(is.na(number_of_genes$num_expected_genes))),]
   kable(different_from_expected,
         caption = "Number of submitted vs expected genes in a bed file")
 }
-
-
-```
+```

genie/dashboard_markdown_generator.R

@@ -3,6 +3,9 @@ suppressPackageStartupMessages(library(argparse))
 parser <- ArgumentParser()
 parser$add_argument("release",
                     help = "Release version (ie. 5.3-consortium)")
+parser$add_argument("--template_path",
+                    help = "Path to dashboardTemplate.Rmd",
+                    default="dashboardTemplate.Rmd")
 parser$add_argument("--staging",
                     action = "store_true",
                     help = "Use staging files")
@@ -18,6 +21,7 @@ args <- parser$parse_args()
 genie_user <- args$syn_user
 genie_pass <- args$syn_pass
 release <- args$release
+template_path <- args$template_path
 suppressPackageStartupMessages(library(synapser))
 suppressPackageStartupMessages(library(rmarkdown))
 
@@ -85,7 +89,7 @@ if (!any(releases$releases %in% release)) {
 #release_folder_fileview_synid = "syn17019650"
 release_folder = synTableQuery(sprintf("select id from %s where name = '%s'", release_folder_fileview_synid, release))
 release_folder_synid = release_folder$asDataFrame()$id
-template = readLines("dashboardTemplate.Rmd")
+template = readLines(template_path)
 
 rmarkdown_path = create_markdown(release, release_folder_synid, template)
 rmarkdown::render(rmarkdown_path,params = list("genieUser"=genie_user, "geniePass"=genie_pass))