Merge pull request #12 from moka-guys/develop

Develop (#12)

Co-Authored-By: rebeccahaines1 <84131466+rebeccahaines1@users.noreply.github.com>
Co-Authored-By: Graeme <graeme_c_smith@hotmail.com>
Co-Authored-By: Natasha Pinto <33454960+natashapinto@users.noreply.github.com>
Co-Authored-By: Bioin4matics <i.malashchuk@gmail.com>

Readme.md

@@ -1,6 +1,6 @@
 # DNAnexus Duty CSV
 
-This is the DNAnexus implementation of [duty_csv v2.3.0](https://github.com/moka-guys/duty_csv/releases/tag/v2.3.0). It is intended to run at the end of all DNAnexus workflows. For further details on what the underlying script does and produces, please refer to that repository.
+This is the DNAnexus implementation of [duty_csv v2.4.0](https://github.com/moka-guys/duty_csv/releases/tag/v2.4.0). It is intended to run at the end of all DNAnexus workflows. For further details on what the underlying script does and produces, please refer to that repository.
 
 ## Inputs
 
@@ -17,6 +17,7 @@ The app takes the following inputs:
 The app sends an email to config-specified address, and produces the following outputs:
 * CSV (optional) - file containing DNAnexus URLs
 * HTML - used for email message
+* TXT - text file containing chrome downloads commands
 * Logfile - for audit trail
 
 This app sends an email to mokaguys containg a csv file attachment with URL links for files required to be transfered to Dry Lab by the Duty Bioinformatician

dxapp.json

@@ -1,8 +1,8 @@
 {
-  "name": "duty_csv_v1.3.0",
+  "name": "duty_csv_v1.4.0",
   "summary": "Uses a python script to search for files required for Dry Lab transfer, creates a CSV file with URL links for the files and sends an email to MokaGuys",
   "properties": {
-    "github release": "v1.3.0"
+    "github release": "v1.4.0"
   },
   "dxapi": "1.0.0",
   "inputSpec": [
@@ -49,17 +49,24 @@
     },
     {
       "name": "csv",
-      "label": "csv",
+      "label": "DNAnexus URLs csv",
       "class": "file",
       "help": "CSV file containing DNAnexus URLs",
       "optional": true
     },
     {
       "name": "html",
-      "label": "html",
+      "label": "Email html",
       "class": "file",
       "help": "HTML file used for email message",
       "optional": false
+    },
+    {
+      "name": "txt",
+      "label": "Chrome downloads txt file",
+      "class": "file",
+      "help": "TXT file containing the chrome downloads commands",
+      "optional": true
     }
   ],
   "runSpec": {

src/code.sh

@@ -11,52 +11,52 @@ function main() {
     AUTH_TOKEN=$(dx cat project-FQqXfYQ0Z0gqx7XG9Z2b4K43:mokaguys_nexus_auth_key)
 
     # Get project ID form project name
-    if (dx find projects --auth $AUTH_TOKEN | grep $project_name);
+    if (dx find projects --auth "${AUTH_TOKEN}" | grep "${project_name}");
         then
             echo "Project $project_name exists"
-            PROJ_ID=$(dx find projects --auth $AUTH_TOKEN | grep $project_name | grep -Eo '^\S*')
+            PROJ_ID=$(dx find projects --auth "${AUTH_TOKEN}" | grep "${project_name}" | grep -Eo '^\S*')
         else
             echo "Project $project_name does not exist"
             exit 1
     fi
 
     OUTDIR=/home/dnanexus/out
-    CSV_OUTDIR=${OUTDIR}/csv/duty_csv
-    HTML_OUTDIR=${OUTDIR}/html/duty_csv
-    LOGFILE_OUTDIR=${OUTDIR}/logfile/duty_csv
+    CSV_OUTDIR="${OUTDIR}/csv/duty_csv"
+    HTML_OUTDIR="${OUTDIR}/html/duty_csv"
+    TXT_OUTDIR="${OUTDIR}/txt/duty_csv"
+    LOGFILE_OUTDIR="${OUTDIR}/logfile/duty_csv"
 
-    mkdir -p $CSV_OUTDIR $HTML_OUTDIR $LOGFILE_OUTDIR # Create in and out dirs
+    mkdir -p $CSV_OUTDIR $HTML_OUTDIR $LOGFILE_OUTDIR $TXT_OUTDIR # Create in and out dirs
 
-    DOCKER_FILEID='project-ByfFPz00jy1fk6PjpZ95F27J:file-Gb6PGp00jy1yzfZ3vYbq47zY'
+    DOCKER_FILEID='project-ByfFPz00jy1fk6PjpZ95F27J:file-GkkzFq00jy1j4G1pPJQFyjkx'
     dx download $DOCKER_FILEID
     DOCKER_FILENAME=$(dx describe $DOCKER_FILEID --name)
     # --force-local required as if tarfile name contains a colon it tries to resolve the tarfile to a machine name
-    DOCKER_IMAGENAME=$(tar xfO $DOCKER_FILENAME manifest.json --force-local | sed -E 's/.*"RepoTags":\["?([^"]*)"?.*/\1/')
+    DOCKER_IMAGENAME=$(tar xfO "${DOCKER_FILENAME}" manifest.json --force-local | sed -E 's/.*"RepoTags":\["?([^"]*)"?.*/\1/')
     docker load < "$DOCKER_FILENAME"  # Load docker image
     sudo docker images
 
-    # Turn comma separated strings into space separated strings
-    CP_CAP_PANNOS=${cp_capture_pannos//,/ }
-    STG_PANNOS=${stg_pannumbers//,/ }
-    TSO_PANNOS=${tso_pannumbers//,/ }
+    DOCKER_CMD="docker run -e DX_API_TOKEN=$AUTH_TOKEN -v /data/:/data/ -v $OUTDIR:/outputs/ $DOCKER_IMAGENAME -P $project_name -I $PROJ_ID -EU $AMAZON_U -PW $AMAZON_PW -TP $tso_pannumbers  -SP $stg_pannumbers  -CP $cp_capture_pannos"
 
-    DOCKER_CMD="docker run -e DX_API_TOKEN=$AUTH_TOKEN -v /data/:/data/ -v $OUTDIR:/outputs/ $DOCKER_IMAGENAME -P $project_name -I $PROJ_ID -EU $AMAZON_U -PW $AMAZON_PW -TP $TSO_PANNOS  -SP $STG_PANNOS  -CP $CP_CAP_PANNOS"
-
-    if [ "$testing" == true ];
+    if [ "${testing}" == true ];
         then
             DOCKER_CMD+=" -T"
     fi
 
-    eval $DOCKER_CMD
+    eval "${DOCKER_CMD}"
 
     # Move outputs into output folders to delocalise into dnanexus project
     mv ${OUTDIR}/*.log $LOGFILE_OUTDIR
     mv ${OUTDIR}/*.html $HTML_OUTDIR
 
-    if compgen -G "$OUTDIR/*.csv" > /dev/null;  # If CSV exists
-        then
-            mv ${OUTDIR}/*.csv $CSV_OUTDIR
-    fi
-
+    declare -A dir_dict
+    dir_dict=( [".csv"]="$CSV_OUTDIR" [".txt"]="$TXT_OUTDIR" )
+
+    for filetype in "${!dir_dict[@]}"; do
+        if compgen -G "${OUTDIR}/*${filetype}" > /dev/null; then  # If file exists (i.e. run has files requiring download)
+            mv ${OUTDIR}/*${filetype} ${dir_dict[$filetype]}
+        fi
+    done
+
     dx-upload-all-outputs --parallel
 }