Workflow optimiert

README.md

@@ -10,5 +10,7 @@
     * input/plauen.imp
     * input/riesa-exemplare.txt
     * input/riesa-titel.txt
-2. Datenverarbeitung: `./main.sh`
-3. Ergebnisse prüfen: `wc -l output/*/*.tsv`
+2. Installation und initiale Datenverarbeitung: `./main.sh`
+3. Weitere Datenverarbeitungen:
+    * `lib/task` für gesamten Workflow
+    * `lib/task --list` für eine Liste der verfügbaren Tasks

Taskfile.yml

@@ -5,8 +5,7 @@ version: '3'
 output: 'group'
 
 vars:
-  DATE:
-    sh: date +%Y%m%d_%H%M%S
+  DATE: '{{ now | date "20060102_150405"}}'
 
 env:
   REFINE_MEMORY: 8g
@@ -14,8 +13,8 @@ env:
 
 tasks:
   default:
-    desc: Workflow
-    deps: [bibliotheca, mkdir]
+    desc: Generierung PICA+
+    deps: [bibliotheca]
     cmds:
       - tasks/03-ba-sachsen.sh "output/02-bibliotheca-main"
     sources:
@@ -26,41 +25,15 @@ tasks:
       REFINE_WORKDIR: output/03-ba-sachsen
       REFINE_LOGFILE: log/03-ba-sachsen/{{.DATE}}.log
 
-  glauchau:
-    desc: Glauchau
-    deps: [mkdir]
-    cmds:
-      - tasks/01-bibliotheca-pre.sh "input/glauchau.imp"
-    sources:
-      - input/glauchau.imp
-    generates:
-      - output/01-bibliotheca-pre/glauchau.tsv
-    env:
-      REFINE_MEMORY: 6G
-      REFINE_ENDPOINT: http://localhost:3334
-      REFINE_WORKDIR: output/01-bibliotheca-pre
-      REFINE_LOGFILE: log/01-bibliotheca-pre/{{.DATE}}_glauchau.log
-
-  plauen:
-    desc: Plauen
-    deps: [mkdir]
-    cmds:
-      - mkdir -p output/01-bibliotheca-pre log/01-bibliotheca-pre
-      - tasks/01-bibliotheca-pre.sh "input/plauen.imp"
-    sources:
-      - input/plauen.imp
-    generates:
-      - output/01-bibliotheca-pre/plauen.tsv
-    env:
-      REFINE_MEMORY: 4G
-      REFINE_ENDPOINT: http://localhost:3335
-      REFINE_WORKDIR: output/01-bibliotheca-pre
-      REFINE_LOGFILE: log/01-bibliotheca-pre/{{.DATE}}_plauen.log
-
   bibliotheca:
-    desc: Hauptverarbeitung
-    deps: [glauchau, plauen, mkdir]
+    desc: Bibliotheca Hauptverarbeitung
+#   deps: [bautzen, breitenbrunn, dresden, glauchau, plauen]
     cmds:
+      - task: bautzen
+      - task: breitenbrunn
+      - task: dresden
+      - task: glauchau
+      - task: plauen
       - tasks/02-bibliotheca-main.sh "output/01-bibliotheca-pre"
     sources:
       - output/01-bibliotheca-pre/*.tsv
@@ -70,16 +43,92 @@ tasks:
       REFINE_WORKDIR: output/02-bibliotheca-main
       REFINE_LOGFILE: log/02-bibliotheca-main/{{.DATE}}.log
 
+  bautzen:
+    desc: Bibliotheca Vorverarbeitung
+    cmds:
+      - tasks/01-bibliotheca-pre.sh "{{.INPUT}}"
+    sources:
+      - '{{.INPUT}}'
+    generates:
+      - output/01-bibliotheca-pre/bautzen.tsv
+    vars:
+      INPUT: '{{.INPUT | default "input/bautzen.imp"}}'
+    env:
+      REFINE_MEMORY: '{{.REFINE_MEMORY | default "8G"}}'
+      REFINE_ENDPOINT: http://localhost:3335
+      REFINE_WORKDIR: output/01-bibliotheca-pre
+      REFINE_LOGFILE: log/01-bibliotheca-pre/{{.DATE}}}_bautzen.log
+
+  breitenbrunn:
+    desc: Bibliotheca Vorverarbeitung
+    cmds:
+      - tasks/01-bibliotheca-pre.sh "{{.INPUT}}"
+    sources:
+      - '{{.INPUT}}'
+    generates:
+      - output/01-bibliotheca-pre/breitenbrunn.tsv
+    vars:
+      INPUT: '{{.INPUT | default "input/breitenbrunn.imp"}}'
+    env:
+      REFINE_MEMORY: '{{.REFINE_MEMORY | default "8G"}}'
+      REFINE_ENDPOINT: http://localhost:3335
+      REFINE_WORKDIR: output/01-bibliotheca-pre
+      REFINE_LOGFILE: log/01-bibliotheca-pre/{{.DATE}}_breitenbrunn.log
+
+  dresden:
+    desc: Bibliotheca Vorverarbeitung
+    cmds:
+      - tasks/01-bibliotheca-pre.sh "{{.INPUT}}"
+    sources:
+      - '{{.INPUT}}'
+    generates:
+      - output/01-bibliotheca-pre/dresdeb.tsv
+    vars:
+      INPUT: '{{.INPUT | default "input/dresden.imp"}}'
+    env:
+      REFINE_MEMORY: '{{.REFINE_MEMORY | default "8G"}}'
+      REFINE_ENDPOINT: http://localhost:3336
+      REFINE_WORKDIR: output/01-bibliotheca-pre
+      REFINE_LOGFILE: log/01-bibliotheca-pre/{{.DATE}}_dresden.log
+
+  glauchau:
+    desc: Bibliotheca Vorverarbeitung
+    cmds:
+      - tasks/01-bibliotheca-pre.sh "{{.INPUT}}"
+    sources:
+      - '{{.INPUT}}'
+    generates:
+      - output/01-bibliotheca-pre/glauchau.tsv
+    vars:
+      INPUT: '{{.INPUT | default "input/glauchau.imp"}}'
+    env:
+      REFINE_MEMORY: '{{.REFINE_MEMORY | default "4G"}}'
+      REFINE_ENDPOINT: http://localhost:3337
+      REFINE_WORKDIR: output/01-bibliotheca-pre
+      REFINE_LOGFILE: log/01-bibliotheca-pre/{{.DATE}}_glauchau.log
+
+  plauen:
+    desc: Bibliotheca Vorverarbeitung
+    cmds:
+      - tasks/01-bibliotheca-pre.sh "input/plauen.imp"
+    sources:
+      - input/plauen.imp
+    generates:
+      - output/01-bibliotheca-pre/plauen.tsv
+    env:
+      REFINE_MEMORY: '{{.REFINE_MEMORY | default "2G"}}'
+      REFINE_ENDPOINT: http://localhost:3338
+      REFINE_WORKDIR: output/01-bibliotheca-pre
+      REFINE_LOGFILE: log/01-bibliotheca-pre/{{.DATE}}_plauen.log
+
+  clean:
+    desc: Alle Daten löschen (reset auf Ausgangszustand)
+    cmds:
+      - rm -r lib log output
+
   mkdir:
     desc: Ordner erstellen
     cmds:
       - mkdir -p output/01-bibliotheca-pre log/01-bibliotheca-pre
       - mkdir -p output/02-bibliotheca-main log/02-bibliotheca-main
       - mkdir -p output/03-ba-sachsen log/03-ba-sachsen
-    status:
-      - test -d output/01-bibliotheca-pre
-      - test -d log/01-bibliotheca-pre
-      - test -d output/02-bibliotheca-main
-      - test -d log/02-bibliotheca-main
-      - test -d output/03-ba-sachsen
-      - test -d log/03-ba-sachsen

main.sh

@@ -1,7 +1,11 @@
 #!/bin/bash
 # Scripte zur Transformation von Bibliotheca und Alephino nach PICA+
 
-# download task if necessary
+# check and install requirements for bash-refine
+source "${BASH_SOURCE%/*}/bash-refine.sh" || exit 1
+requirements
+
+# download task runner
 task="$(readlink -m "${BASH_SOURCE%/*}/lib/task")"
 if [[ -z "$(readlink -e "${task}")" ]]; then
   echo "Download task..."
@@ -12,5 +16,11 @@ if [[ -z "$(readlink -e "${task}")" ]]; then
   rm -f task.tar.gz
 fi
 
+# make script executable from another directory
+cd "${BASH_SOURCE%/*}/" || exit 1
+
+# create folders
+"${task}" mkdir
+
 # execute default task (cf. Taskfile.yml)
 "${task}"

tasks/01-bibliotheca-pre.sh

@@ -17,9 +17,6 @@ else
   echo 1>&2 "Please provide path to input file"; exit 1
 fi
 
-# make script executable from another directory
-cd "${BASH_SOURCE%/*}/" || exit 1
-
 # check requirements, set trap, create workdir and tee to logfile
 init
 
@@ -27,6 +24,9 @@ init
 
 checkpoint "Startup"; echo
 
+# print environment variables
+printenv | grep REFINE; echo
+
 # start OpenRefine server
 refine_start; echo
 

tasks/02-bibliotheca-main.sh

@@ -16,9 +16,6 @@ else
   echo 1>&2 "Please provide path to directory with input file(s)"; exit 1
 fi
 
-# make script executable from another directory
-cd "${BASH_SOURCE%/*}/" || exit 1
-
 # check requirements, set trap, create workdir and tee to logfile
 init
 

tasks/03-ba-sachsen.sh

@@ -18,9 +18,6 @@ if [[ $2 ]]; then
   inputdir2="$(readlink -e "$2")"
 fi
 
-# make script executable from another directory
-cd "${BASH_SOURCE%/*}/" || exit 1
-
 # check requirements, set trap, create workdir and tee to logfile
 init