moved artifact files

.github/workflows/database-update.yml

@@ -58,11 +58,11 @@ jobs:
          run: |
            docker run -v $PWD:/tmp sgosline/srp-exposome
        - name: List files cwd
-         run: ls -la /tmp/
+         run: ls -la 
        - name: Copy files to artifact
          run: |
            mkdir expo-files
-           mv /tmp/*.csv expo-files
+           mv *.csv expo-files
        - name: upload artifact
          uses: actions/upload-artifact@v2
          with:
@@ -83,11 +83,11 @@ jobs:
          run: |
            docker run -v $PWD:/tmp sgosline/srp-zfexp
        - name: List files cwd
-         run: ls -lah /tmp/
+         run: ls -lah
        - name: Copy files to artifact
          run: |
-           mkdir exp-files
-           mv /tmp/*csv expr-files
+           mkdir expr--files
+           mv *csv expr-files
        - name: upload artifact
          uses: actions/upload-artifact@v2
          with:
@@ -109,6 +109,6 @@ jobs:
          with:
            name: expo-files
        - name: List files cwd
-         run: ls -lah /tmp/
+         run: ls -lah 
 #zipfiles push to figshare
 

build_script.py

@@ -166,10 +166,10 @@ def main():
         runExposome(cid)
         runSchemaCheck()
     if args.geneEx:
-        if not os.path.exists("/tmp/chemicals.csv"):
+        if not os.path.exists("chemicals.csv"):
             runSampMap(False,[],smap,cid,emap,cclass,ctfile,fses,desfile)
 
-        runExpression(gex1,'/tmp/chemicals.csv',ginfo)
+        runExpression(gex1,'chemicals.csv',ginfo)
         runSchemaCheck()
 
 

exposome/exposome_summary_stats.R

@@ -13,7 +13,7 @@ if(length(args)<1){
 }
 
 
-out.dir='/tmp/'
+out.dir='.'#/tmp/'
 
                                         #library(cowplot)
 url <- "https://montilab.bu.edu/Xposome-API/projects?all=Yes"

sampleChemMapping/mapSamplesToChems.R

@@ -72,8 +72,8 @@ required_bmd_columns<-list(bmd=c('Chemical_ID','End_Point','Model','BMD10','BMD5
 
 #data.dir='./data/'
 ##output directory is fixed
-out.dir<-'/tmp/'
-#out.dir<-'./'
+#out.dir<-'/tmp/'
+out.dir<-'./'
 
 
 

zfExp/parseGexData.R

@@ -15,7 +15,7 @@ schema<-data.frame(Project=c(),
 
 
 data.dir<-'https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/zfExp'
-out.dir='/tmp/'
+out.dir='./'#/tmp/'
 
 generateGeneExamples<-function(genelist,chems){
   library(ggplot2)