Merge branch 'data-trigger' of https://github.com/PNNL-CompBio/srpAna…

…lytics into data-trigger

.github/workflows/docker-build.yml

@@ -4,8 +4,12 @@ defaults:
     working-directory: ./
 on:
   push:
-    branches:
-      - "*"
+    paths: 
+      - zfBmd/
+      - zfExp/
+      - sampleChemMapping/
+      - dbSchema/
+      - exposome/
 
 jobs:
   build-and-push:
@@ -73,4 +77,4 @@ jobs:
 	  file: zfExp/Dockerfile
           push: true
           tags: sgosline/srp-zfexp
-          platforms: linux/amd64,linux/arm64       
+          platforms: linux/amd64,linux/arm64       

data/srp_build_files.csv

@@ -30,8 +30,8 @@ dose8,dose,extract,https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/m
 fit6,fit,extract,https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/extracts/fit_vals_2021_04_09.csv,1
 fit7,fit,extract,https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/extracts/fit_vals_2021_08_18.csv,1
 fit8,fit,extract,https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/extracts/fit_vals_all_qc.csv,1
-gene1,expression,zebrafish,,https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/zfExp/ZF_gex.xlsx,3
-geneInfo,mapping,zebrafish,,https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/zfExp/allianceGenomeInfo.csv,3
+gene1,expression,zebrafish,https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/zfExp/ZF_gex.xlsx,3
+geneInfo,mapping,zebrafish,https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/zfExp/allianceGenomeInfo.csv,3
 chemId,mapping,chemical,https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/chemicalIdMapping.csv,1
 sampId,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

sampleChemMapping/Dockerfile

@@ -1,7 +1,6 @@
 FROM r-base:4.2.1
 # To setup other dependencies
 
-
 RUN apt-get update --allow-insecure-repositories
 RUN apt-get install -y --allow-unauthenticated --fix-missing gcc-12 build-essential libpq-dev python3-venv
 

sampleChemMapping/mapSamplesToChems.R

@@ -1,12 +1,10 @@
-##V2 database will be comprised of more files to distinctly track
+##V3 database will be comprised of more files to distinctly track
 ## gene, chemical, and sample metadata
-
 require(dplyr)
 require(rio)
 require(argparse)
 require(xml2)
 library(tidyr)
-
 ##The data release will be comprised of 9 files (note change from v1!)
 #' 1- list of environmental samples and the chemical composition (curated sample data)
 #' 2- ZF summary statistics for chemicals (and no chemical metadata)