Merge pull request #83 from PNNL-CompBio/data-trigger

more build files added
PNNL-CompBio · Apr 17, 2024 · 9a72fd9 · 9a72fd9
2 parents ad189ce + 2ac15e2
commit 9a72fd9
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Showing 3 changed files with 13 additions and 10 deletions.
diff --git a/bmd2Samps_v3/buildv3database.R b/bmd2Samps_v3/buildv3database.R
@@ -892,13 +892,14 @@ main<-function(){
     parser$add_argument('-s','--sample',dest='is_sample',action='store_true',default=FALSE,help='Flag to indicate file are for samples')
     parser$add_argument('-c','--chemical',dest='is_chem',default=FALSE,action='store_true',
                         help='Flag to indicate file is for chemicals')
-    parser$add_argument('-d','--drcFile',dest='dose_res_stat',default'',help='dose response curve file')
+    parser$add_argument('-d','--drcFiles',dest='dose_res_stat',default='',help='dose response curve file')
     parser$add_argument('-p','--sampMap',dest='sample_mapping_file',default='',help='Sample mapping file location')
     parser$add_argument('-m','--chemMap',dest='chem_meta_file',default='',help='Chemical metadata file location')
     parser$add_argument('-e','--epMap',dest='endpoint_mapping_file',default='',help='Endpoint naming file location')
     parser$add_argument('-l','--chemClass',dest='chem_class_file',default='',help='chemical class file location')
     parser$add_argument('-x','--compToxFile',dest='comp_tox_mapping',default='',help='comptox data file location')
     parser$add_argument('-f','--sampleFiles',dest='sample_files',default='',help='comma dlimited list of fses files to merge' )
+    parser$add_argument('-h','--chemDesc',dest='chem_desc',default='',help='Descriptions of chemicals')
 
 
     args <- parser$parse_args()

diff --git a/data/srp_build_files.csv b/data/srp_build_files.csv
@@ -35,4 +35,5 @@ chemMap,mapping,chemical,https://raw.githubusercontent.com/PNNL-CompBio/srpAnaly
 sampMap,mapping,sample,https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/sampleIdMapping.csv,1
 class1,classification,chemical,https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/MASV%20Classifications%202021.xlsx,1
 compTox,mapping,chemical,https://github.com/PNNL-CompBio/srpAnalytics/blob/main/data/CCDBatch_2022-01-26_AND_2021_11_05.xlsx,1
-endpointMap,mapping,endpoint,https://github.com/PNNL-CompBio/srpAnalytics/blob/main/data/SuperEndpoint%20Mapping%202021NOV04.xlsx,1
+endpointMap,mapping,endpoint,https://github.com/PNNL-CompBio/srpAnalytics/blob/main/data/SuperEndpoint%20Mapping%202021NOV04.xlsx,1
+chemdesc,classification,chemical,https://github.com/PNNL-CompBio/srpAnalytics/blob/main/data/ChemicalDescriptions.xlsx,1
diff --git a/v3_buildScript.py b/v3_buildScript.py
@@ -75,17 +75,18 @@ def main():
                 sampfiles.append(fname)
 
     ##now map sample information
-    smap = df.loc[df.name=='sampMap'].location
-    cmap = df.loc[df.name=='chemMap'].location
-    cclass = df.loc[df.name=='class1'].location
-    emap = df.loc[df.name=='endpointMap'].location
-    fses = ','.join(df.loc[df.data_type=='sample'].location)
-    ctfile = df.loc[df.name=='colmpTox'].location
+    smap = list(df.loc[df.name=='sampMap'].location)[0]
+    cmap = list(df.loc[df.name=='chemMap'].location)[0]
+    cclass = list(df.loc[df.name=='class1'].location)[0]
+    emap = list(df.loc[df.name=='endpointMap'].location)[0]
+    fses = ','.join(list(df.loc[df.data_type=='sample'].location))
+    ctfile = list(df.loc[df.name=='compTox'].location)[0]
+    desfile = list(df.loc[df.name=='chemdesc'].location)[0]
 
     ##call script with sample files
-    cmd = "Rscript bmd2Samps_v3/buildV3database.R --sample --drcFile="+','.join(sampfiles)+\
+    cmd = "Rscript bmd2Samps_v3/buildV3database.R --sample --drcFiles="+','.join(sampfiles)+\
         ' --sampMap='+smap+' --chemMap='+cmap+' --epMap='+emap+' --chemClass='+cclass+\
-        ' --compToxFile='+ctfile+' --sampleFiles='+fses
+        ' --compToxFile='+ctfile+' --sampleFiles='+fses+' --chemDesc='+desfile
     print(cmd)
     os.system(cmd)
     ##call script with chemical files