Merge branch 'dev'

dbecd3f8 · Fabian Nuraddin Alexander Gabel · 9a1330f2 · 4f59ec3b · dbecd3f8 · dbecd3f8
Commit dbecd3f8 authored 3 years ago by Fabian Nuraddin Alexander Gabel
--- a/.gitignore
+++ b/.gitignore
-build/*
-*/build
+*build/
+*deploy/
 local/*
 public/*
 */public/*
@@ -8,3 +8,7 @@ public/*
 !static/home/*.html
 !static/topic/*.html
 *.log
+!testing/test_pandoc/*.html
+!testing/test_create_html/*.html
+*.swp
+!*ref_*
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,13 +3,14 @@
 #

 stages:
-  - preprocessor-test
+  - testing
  - build
+  - review
  - deploy

-# always test the preprocessor and pandoc build with unit tests
-testing:
-  stage: preprocessor-test
+# always test the preprocessor with unit tests
+test-preprocessor:
+  stage: testing
  allow_failure: false
  image: 
    name: alpine:latest
@@ -21,8 +22,117 @@ testing:
  artifacts:
    paths:
      - testing/*.log
+  only:
+    refs:
+      - branches
+      - merge_requests
+    changes:
+      - .gitlab-ci.yml
+      - bin
+      - testing

-# build static webpage
+# always test the pandoc integration and pandoc build with unit tests
+pandoc-test:
+  stage: testing
+  allow_failure: false
+  image: 
+    name: alpine:latest
+  script:
+    - apk add --no-cache --upgrade bash
+    - RESEARCH_ROOT=`pwd`; export RESEARCH_ROOT;
+    # run shell script with testss
+    - $RESEARCH_ROOT/bin/test_pandoc.sh
+  artifacts:
+    paths:
+      - testing/test_pandoc/*.log
+
+# test that markdown is translated correctly 
+test-md-to-html:
+  stage: testing
+  allow_failure: false
+  image: 
+    name: eltenedor/ubuntu-pandoc:latest
+  script:
+    - mkdir -p log
+    - rm -rf log/test_create_html.log
+    - RESEARCH_ROOT=`pwd`; export RESEARCH_ROOT;
+    - $RESEARCH_ROOT/bin/test_create_html.sh | tee log/test_create_html.log
+  artifacts:
+    paths:
+      - log/test_create_html.log
+  only:
+    refs:
+      - branches
+      - merge_requests
+    changes:
+      - .gitlab-ci.yml
+      - bin
+      - testing
+
+# test that html is included correctly 
+test-replace_marker:
+  stage: testing
+  allow_failure: false
+  image: 
+    name: eltenedor/ubuntu-pandoc:latest
+  script:
+    - mkdir -p log
+    - rm -rf log/test_replace_marker.log
+    - RESEARCH_ROOT=`pwd`; export RESEARCH_ROOT;
+    - $RESEARCH_ROOT/bin/test_replace_marker.sh | tee log/test_replace_marker.log
+  artifacts:
+    paths:
+      - log/test_replace_marker.log
+  only:
+    refs:
+      - branches
+      - merge_requests
+    changes:
+      - .gitlab-ci.yml
+      - bin
+      - testing
+
+# test building standalone static webpage
+test-build-standalone:
+  stage: testing
+  allow_failure: false
+  image: 
+    name: eltenedor/ubuntu-pandoc:latest
+  script:
+    - mkdir -p log
+    - rm -rf log/test_build_standalone.log
+    - RESEARCH_ROOT=`pwd`; export RESEARCH_ROOT;
+    - $RESEARCH_ROOT/bin/test_build_standalone.sh | tee log/test_build_standalone.log
+  artifacts:
+    paths:
+      - log/test_build_standalone.log
+  only:
+    refs:
+      - branches
+      - merge_requests
+    changes:
+      - .gitlab-ci.yml
+      - bin
+      - testing
+
+# build standalone static webpage
+build-standalone-static:
+  stage: build
+  allow_failure: false
+  image: 
+    name: eltenedor/ubuntu-pandoc:latest
+  script:
+    - RESEARCH_ROOT=`pwd`; export RESEARCH_ROOT;
+    # build static webpage
+    - $RESEARCH_ROOT/bin/build_standalone.sh
+  artifacts:
+    paths:
+      - public 
+  rules:
+    - if: $CI_MERGE_REQUEST_ID
+    - if: $CI_COMMIT_BRANCH
+
+# build standalone static webpage
 build-static:
  stage: build
  allow_failure: false
@@ -35,18 +145,204 @@ build-static:
  artifacts:
    paths:
      - static
+  rules:
+    - if: $CI_MERGE_REQUEST_ID
+    - if: $CI_COMMIT_BRANCH
+
+# build tuhh-snippets
+build-tuhh:
+  stage: build
+  allow_failure: false
+  image: 
+    name: eltenedor/ubuntu-pandoc:latest
+  script:
+    - RESEARCH_ROOT=`pwd`; export RESEARCH_ROOT;
+    - $RESEARCH_ROOT/bin/preproc_topics.sh $RESEARCH_ROOT/build-tuhh $RESEARCH_ROOT/topics
+    - $RESEARCH_ROOT/bin/create_html.sh $RESEARCH_ROOT/build-tuhh $RESEARCH_ROOT/build-tuhh
+  artifacts:
+    paths:
+      - build-tuhh
+  rules:
+    - if: $CI_MERGE_REQUEST_ID
+    - if: $CI_COMMIT_BRANCH
+
+# deploy static webpage on issue-branch to web-server hosted asteroids
+deploy-on-asteroid:
+  stage: review
+  image: 
+    name: alpine:latest
+  before_script:
+    ## install dependencies
+    #- apk update && apk add openssh-client bash 
+    ## see https://docs.gitlab.com/ee/ci/ssh_keys/ for comments
+    #- 'command -v ssh-agent >/dev/null || ( apt-get update -y && apt-get install openssh-client -y )' #this command is for debian based systems
+    - apk update && apk add openssh-client bash  #this command is for alpine
+    - eval $(ssh-agent -s)
+    - echo "$ASTEROID_SSH_KEY" | tr -d '\r' | ssh-add -
+    # See https://stackoverflow.com/a/57332478  about known hosts
+    - mkdir -p ~/.ssh && touch ~/.ssh/known_hosts
+    - echo "$ASTEROID_KNOWN_HOSTS" >> ~/.ssh/known_hosts
+    - chmod 700 ~/.ssh
+  script:
+    - mkdir .public-asteroid
+    - cp -r public/*.html .public-asteroid
+    - cp -r img .public-asteroid
+    - cp -r css .public-asteroid
+    - mv .public-asteroid public-asteroid
+    # deploy webpage on asteroid
+    #- ssh $ASTEROID_USER@$ASTEROID_HOST "rm -rf $ASTEROID_DEPLOY/$CI_COMMIT_REF_NAME"
+    - ssh $ASTEROID_USER@$ASTEROID_HOST "mkdir -p $ASTEROID_DEPLOY/$CI_COMMIT_REF_NAME"
+    - scp -v -r public-asteroid "$ASTEROID_USER@$ASTEROID_HOST:$ASTEROID_DEPLOY/$CI_COMMIT_REF_NAME/$CI_COMMIT_SHORT_SHA"
+  artifacts:
+    paths:
+      - public-asteroid
+  rules:
+    - if: $CI_PROJECT_URL != 'https://collaborating.tuhh.de/cfg0846/research-topics-mat-tuhh'
+      when: never
+    - when: always
+
+# deploy static webpage on dev-branch to tuhh
+deploy-on-tuhh:
+  stage: deploy
+  image: 
+    name: alpine:latest
+  before_script:
+    ## install dependencies
+    - apk update && apk add openssh-client bash 
+    ## see https://docs.gitlab.com/ee/ci/ssh_keys/ for comments
+    #- 'command -v ssh-agent >/dev/null || ( apt-get update -y && apt-get install openssh-client -y )'
+    - eval $(ssh-agent -s)
+    - echo "$TUHH_SSH_KEY" | tr -d '\r' | ssh-add -
+    - mkdir -p ~/.ssh && touch ~/.ssh/known_hosts
+    - echo "$TUHH_KNOWN_HOSTS" >> ~/.ssh/known_hosts
+    - chmod 700 ~/.ssh
+  script:
+    - mkdir -p .public-tuhh
+    - cp -r build-tuhh/*.html .public-tuhh
+    - mv .public-tuhh public-tuhh
+    # deploy webpage on tuhh
+    - echo 'scp -v public-tuhh' "$TUHH_USER@$TUHH_HOST:$TUHH_DEPLOY"
+    - scp -v -r public-tuhh "$TUHH_USER@$TUHH_HOST:$TUHH_DEPLOY"
+  artifacts:
+    paths:
+      - public-tuhh
+  rules:
+    - if: $CI_PROJECT_URL != 'https://collaborating.tuhh.de/cfg0846/research-topics-mat-tuhh'
+      when: never
+    - if: $CI_COMMIT_BRANCH == 'dev'
+      when: always

 # deploy static webpage to web-server via GitLab pages
 pages:
  stage: deploy
  script:
-    - mkdir .public
-    - cp -r static/public/*.html .public
-    - cp -r img .public/.
-    - cp -r css .public/.
-    - mv .public public
+    - mkdir .public-pages
+    - cp -r public .public-pages
+    - mv .public-pages public-pages
  artifacts:
    paths:
-      - public
+      - public-pages
  rules:
    - if: $CI_COMMIT_BRANCH == 'master'
+
+deploy_review:
+  stage: deploy
+  script:
+    - echo "Deploy a review app on an asteroid"
+  environment:
+    name: asteroid/$CI_COMMIT_REF_NAME
+    url: https://review.fabian-gabel.de/$CI_COMMIT_REF_NAME/$CI_COMMIT_SHORT_SHA
+  #  on_stop: stop_review_app
+  #  auto_stop_in: 1 week
+  rules:
+    - if: $CI_PROJECT_URL != 'https://collaborating.tuhh.de/cfg0846/research-topics-mat-tuhh'
+      when: never
+    - if: $CI_MERGE_REQUEST_ID
+    - if: $CI_COMMIT_BRANCH == 'dev'
+
+review_tuhh:
+  stage: review
+  image: 
+    name: alpine:latest
+  before_script:
+    - apk update && apk add openssh-client bash  
+    - eval $(ssh-agent -s)
+    - echo "$REVIEW_SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add -
+    - mkdir -p ~/.ssh && touch ~/.ssh/known_hosts
+    - echo "$REVIEW_SSH_KNOWN_HOSTS" > ~/.ssh/known_hosts
+    - chmod 700 ~/.ssh/known_hosts
+  script:
+    - mkdir .public-review
+    - cp -r public/*.html .public-review
+    - cp -r img .public-review
+    - cp -r css .public-review
+    - mv .public-review public-review
+    - ssh -v -p "${REVIEW_SSH_PORT}" "${REVIEW_SSH_USER}"@"${REVIEW_HOST_NAME}" "mkdir -p /usr/local/apache2/htdocs/~${CI_COMMIT_REF_NAME}/$CI_COMMIT_SHORT_SHA"
+    - scp -v -P "${REVIEW_SSH_PORT}" -r public-review/* "${REVIEW_SSH_USER}"@"${REVIEW_HOST_NAME}":"/usr/local/apache2/htdocs/~${CI_COMMIT_REF_NAME}/$CI_COMMIT_SHORT_SHA"
+  environment:
+    name: tuhh/$CI_COMMIT_REF_NAME
+    url: https://${REVIEW_PROXY_HOST_NAME}${REVIEW_BASE_DIR}~${CI_COMMIT_REF_NAME}/$CI_COMMIT_SHORT_SHA/
+    on_stop: review_tuhh:stop
+  rules:
+    - if: $CI_PROJECT_URL != 'https://collaborating.tuhh.de/cfg0846/research-topics-mat-tuhh'
+      when: never
+    - if: '$CI_COMMIT_REF_NAME != "master"'
+  
+review_tuhh:stop:
+  stage: review
+  image: 
+    name: alpine:latest
+  before_script:
+    - apk update && apk add openssh-client bash  
+    - eval $(ssh-agent -s)
+    - echo "$REVIEW_SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add -
+    - mkdir -p ~/.ssh && touch ~/.ssh/known_hosts
+    - echo "$REVIEW_SSH_KNOWN_HOSTS" > ~/.ssh/known_hosts
+    - chmod 700 ~/.ssh/known_hosts
+  script:
+    - ssh -p "${REVIEW_SSH_PORT}" "${REVIEW_SSH_USER}"@"${REVIEW_HOST_NAME}" "rm -rf /usr/local/apache2/htdocs/~${CI_COMMIT_REF_NAME}"
+  rules:
+    - if: '$CI_COMMIT_REF_NAME != "master"'
+      when: manual
+  allow_failure: true
+  environment:
+    name: tuhh/$CI_COMMIT_REF_NAME
+    action: stop
+
+master-deploy:
+  stage: deploy
+  image: 
+    name: alpine:latest
+  before_script:
+    - apk update && apk add openssh-client bash  
+    - eval $(ssh-agent -s)
+    - echo "$SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add -
+    - mkdir -p ~/.ssh && touch ~/.ssh/known_hosts
+    - echo "$SSH_KNOWN_HOSTS" > ~/.ssh/known_hosts
+    - chmod 700 ~/.ssh/known_hosts
+  script:
+    - echo "$SSH_KNOWN_HOSTS" > ~/.ssh/known_hosts
+    - chmod 644 ~/.ssh/known_hosts
+    - eval $(ssh-agent -s)
+    - echo "$SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add - > /dev/null
+    - ssh -p "${SSH_PORT}" "${SSH_USER}"@"${HOST_NAME}" "mkdir -p /usr/local/apache2/htdocs"
+    - scp -P "${SSH_PORT}" -r public/* "${SSH_USER}"@"${HOST_NAME}":"/usr/local/apache2/htdocs"
+  cache:
+    key: "$CI_COMMIT_REF_SLUG"
+  environment:
+    name: $CI_COMMIT_REF_NAME
+    url: https://$PROXY_HOST_NAME$BASE_DIR
+  rules:
+    - if: '$CI_COMMIT_REF_NAME == "master"'
+
+
+# uncomment for manual stopping
+#stop_review_app:
+#  stage: deploy
+#  script: stop-review-app
+#  environment:
+#    name: review/$CI_COMMIT_REF_NAME
+#    action: stop
+#  rules:
+#    - if: $CI_MERGE_REQUEST_ID
+#      when: manual
--- a/README.md
+++ b/README.md
+# Research Interests
+
+This page hopefully features the past, current and future research interests of our institute.
+
+You browse this webpage either by clicking on a **research topic**, a **working group** or a particular **researcher**.
+
+If you are looking for a guided tour, watch [https://media.tuhh.de/e10/gabel/research-topics/video1_rundgang.mp4](https://media.tuhh.de/e10/gabel/research-topics/video1_rundgang.mp4) (DE)
+
+If you want to contribute a research topic, see the [CONTRIBUTING.md](https://collaborating.tuhh.de/cfg0846/research-topics-mat-tuhh/-/blob/master/CONTRIBUTING.md).
+
+
+## List of Sites
+
+### `Master`
+
+The [master](https://collaborating.tuhh.de/cfg0846/research-topics-mat-tuhh/-/tree/master) is currently delivered to 
+* [https://fabiangabel.gitlab.io/research-topics-mat-tuhh](https://fabiangabel.gitlab.io/research-topics-mat-tuhh)
+* [https://www3.tuhh.de/cfg0846/research-topics-mat-tuhh/](https://www3.tuhh.de/cfg0846/research-topics-mat-tuhh/) (only to be reached from TUHH-network)
+
+### `Dev`
+
+The development version of this webpage for review is currently delivered to [https://review.fabian-gabel.de/dev](https://review.fabian-gabel.de/dev).
+
+### Review Apps
+
+[GitLab Review Apps](https://docs.gitlab.com/ee/ci/review_apps/) can be accessed on 
+* [https://review.fabian-gabel.de/](https://review.fabian-gabel.de/)
+* [https://www3-dev.tuhh.de/cfg0846/research-topics-mat-tuhh/](https://www3-dev.tuhh.de/cfg0846/research-topics-mat-tuhh/) (only to be reached from TUHH-network)  
+
+### GitLab Repository
+
+The corresponding [GitLab](https://collaborating.tuhh.de) repository is 
+* hosted at [https://collaborating.tuhh.de/cfg0846/research-topics-mat-tuhh](https://collaborating.tuhh.de/cfg0846/research-topics-mat-tuhh) 
+* [push-mirrored](https://docs.gitlab.com/ee/user/project/repository/repository_mirroring.html#pushing-to-a-remote-repository) to [https://gitlab.com/fabiangabel/research-topics-mat-tuhh](https://gitlab.com/fabiangabel/research-topics-mat-tuhh)
+
--- a/bin/adapt_html.sh
+++ b/bin/adapt_html.sh
@@ -36,3 +36,4 @@ do
    sed -i "s;/include/javascript/jquery.quicksilver.js;https://www.mat.tuhh.de/include/javascript/toggleme.js;" $f
    sed -i "s;/include/javascript/jquery.simpleFAQ.js;https://www.mat.tuhh.de/include/javascript/jquery.simpleFAQ.js;" $f
 done
+
--- a/bin/buildPandoc.sh
+++ b/bin/buildPandoc.sh
@@ -13,3 +13,4 @@ do
    -c "css/superfish-vertical.css" \
    -c "css/base_mode.css"
 done
+
--- a/bin/buildWebpage.sh
+++ b/bin/buildWebpage.sh
@@ -20,3 +20,4 @@ cp -r $RESEARCH_ROOT/css $DEPLOY_DIR/.public
 mv $DEPLOY_DIR/.public $DEPLOY_DIR/public

 echo "Done. Visit file://$DEPLOY_DIR/public/index.html ."
+
--- a/bin/build_standalone.sh
+++ b/bin/build_standalone.sh
+#!/bin/bash
+# building the a standalone static webpage
+RESEARCH_BIN=$RESEARCH_ROOT/bin
+RESEARCH_STATIC=$RESEARCH_ROOT/static
+
+# Check commandline arguments
+if [ $# -lt 1 ]
+then
+    RESEARCH_DEPLOY=`pwd`
+    RESEARCH_TOPICS=`pwd`"/topics"
+    RESEARCH_BUILD=`pwd`"/build"
+    echo -e "No deploy directory was specified."
+    # clean up directories
+    rm -rf $RESEARCH_BUILD
+    rm -rf $RESEARCH_DEPLOY/{.public,public}
+elif [ $# -lt 2 ] 
+then
+    RESEARCH_BUILD="$1"
+    RESEARCH_TOPICS=$RESEARCH_BUILD
+    RESEARCH_BUILD="$1/build"
+    echo -e "No extra topics directory was specified."
+    # clean up directories
+    rm -rf $RESEARCH_BUILD
+    rm -rf $RESEARCH_DEPLOY/{.public,public}
+elif [ $# -lt 3 ] 
+then
+    RESEARCH_DEPLOY="$1"
+    RESEARCH_TOPICS="$2"
+    RESEARCH_BUILD="$1/build"
+    echo -e "No extra build directory was specified."
+    # clean up directories
+    rm -rf $RESEARCH_BUILD
+    rm -rf $RESEARCH_DEPLOY/{.public,public}
+else
+    RESEARCH_DEPLOY="$1"
+    RESEARCH_TOPICS="$2"
+    RESEARCH_BUILD="$3"
+fi
+
+# prepare directories / clean-up
+mkdir -p $RESEARCH_DEPLOY
+mkdir -p $RESEARCH_BUILD
+cp -vf $RESEARCH_TOPICS/*.md $RESEARCH_BUILD
+
+echo -e "Deploying to $RESEARCH_DEPLOY ...;"
+echo -e "Building into directory $RESEARCH_BUILD ..."
+echo -e "Using .md-files from $RESEARCH_TOPICS ..."
+
+# preprocess .md-files 
+echo "Preproc Topics"
+$RESEARCH_BIN/preproc_topics.sh $RESEARCH_BUILD $RESEARCH_TOPICS
+
+# build html files
+echo "Creating HTML Files with pandoc"
+$RESEARCH_BIN/create_html.sh $RESEARCH_BUILD 
+
+# replace markers
+echo "Replacing markers"
+$RESEARCH_BIN/replace_marker.sh $RESEARCH_BUILD 
+
+#make public directory and copy files
+mkdir -p $RESEARCH_DEPLOY/.public
+for f in $RESEARCH_BUILD/*_final.html
+do
+    filename=$(basename -- "$f")
+    cp $f $RESEARCH_DEPLOY/.public/${filename%_final.html}.html
+done
+
+echo "Copying files to final destination ..."
+cp -r $RESEARCH_ROOT/{img,css}  $RESEARCH_DEPLOY/.public
+mv -v $RESEARCH_DEPLOY/.public  $RESEARCH_DEPLOY/public
+
+echo "Done. Visit file://$RESEARCH_DEPLOY/public/index.html ."
+
--- a/bin/build_static.sh
+++ b/bin/build_static.sh
@@ -8,9 +8,16 @@ BIN_DIR=$RESEARCH_ROOT/bin
 rm -rf  $BUILD_DIR
 rm -rf $DEPLOY_DIR/{.public,public}

-#build html 
+# preprocess .md-files 
 echo "Preproc Topics"
-$BIN_DIR/preproc_topics.sh $RESEARCH_ROOT/static
+$BIN_DIR/preproc_topics.sh $RESEARCH_ROOT/static $RESEARCH_ROOT/topics
+
+# get full TUHH staff pages ready for insertion
+mkdir -p $RESEARCH_ROOT/static/build/plain
+cp $RESEARCH_ROOT/static/home/*.html $RESEARCH_ROOT/static/build/plain
+cp $RESEARCH_ROOT/static/forschung/*.html $RESEARCH_ROOT/static/build/plain
+
+# build html files
 echo "Run Pandoc"
 $BIN_DIR/integrate_pandoc.sh
 echo "Pandoc finished."
@@ -27,3 +34,4 @@ cp -r $RESEARCH_ROOT/css $DEPLOY_DIR/.public
 mv $DEPLOY_DIR/.public $DEPLOY_DIR/public

 echo "Done. Visit file://$DEPLOY_DIR/public/index.html ."
+
--- a/bin/create-staff-yml.sh
+++ b/bin/create-staff-yml.sh
 #!/bin/bash
-    namelist=`grep -h -i -m 1 -r "###\s*Collaborators (MAT):" topics/topic-template.md | sed -e 's/^###\s*Collaborators (MAT):\s*//I' -e 's/\s*,\s*/\n/g'  | sort -u`
-    for name in $namelist
-    do
-        # pipeline to get full name of staff-member from mat-homepage
-        # -> wget the staff homepage of $name
-        # -> grep the line with the <h1>-tag, something like <h1>Fabian Gabel, M. Sc.</h1><div class='staffIntro'><p><img src='/home/fgabel/images/portrait.png' title='Foto von Fabian Gabel, M. Sc.' class='staffPicture'></p><div class='staffContact'>
-        # -> strip the string such that only the portion between <h1></h1> remains
-        # -> remove leading spaces
-        
-        echo "Found collaborator $name"
+namelist=`grep -h -i -m 1 -r "###\s*Collaborators (MAT):" topics/topic-template.md | sed -e 's/^###\s*Collaborators (MAT):\s*//I' -e 's/\s*,\s*/\n/g'  | sort -u`
+for name in $namelist
+do
+    # pipeline to get full name of staff-member from mat-homepage
+    # -> wget the staff homepage of $name
+    # -> grep the line with the <h1>-tag, something like <h1>Fabian Gabel, M. Sc.</h1><div class='staffIntro'><p><img src='/home/fgabel/images/portrait.png' title='Foto von Fabian Gabel, M. Sc.' class='staffPicture'></p><div class='staffContact'>
+    # -> strip the string such that only the portion between <h1></h1> remains
+    # -> remove leading spaces
+    
+    echo "Found collaborator $name"

-        # replace name in .md file
-        echo "- pandoc --standalone ./build/$name.md -o ./build/$name.html --mathjax" >> out.yml
+    # replace name in .md file
+    echo "- pandoc --standalone ./build/$name.md -o ./build/$name.html --mathjax" >> out.yml
+
+done

-    done
\ No newline at end of file
--- a/bin/create_html.sh
+++ b/bin/create_html.sh
+#!/bin/bash
+# processing command line arguments
+# Define variables
+MATHJAX_URL='https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js'
+
+# Check commandline arguments
+if [ $# -lt 1 ]
+then
+    RESEARCH_BUILD=`pwd`"/build"
+    RESEARCH_TOPICS=`pwd`
+    echo -e "No building directory was specified."
+elif [ $# -lt 2 ] 
+then
+    RESEARCH_BUILD="$1"
+    RESEARCH_TOPICS=$RESEARCH_BUILD
+    echo -e "No extra topics directory was specified."
+else
+    RESEARCH_BUILD="$1"
+    RESEARCH_TOPICS="$2"
+fi
+mkdir -p $RESEARCH_BUILD
+echo -e "Building into directory $RESEARCH_BUILD ..."
+echo -e "Using .md-files from $RESEARCH_TOPICS ..."
+
+# specify URL to avoid use of local library
+# see https://docs.mathjax.org/en/latest/web/start.html#ways-of-accessing-mathjax
+# and https://www.jsdelivr.com/package/npm/mathjax
+
+# create plain _research.html to be integrated into other files
+for f in $RESEARCH_TOPICS/*.md
+do
+    filename=$(basename -- "$f")
+    echo "Creating " $RESEARCH_BUILD/"${filename%.md}"_research.html " ..."
+    pandoc  $f -o  $RESEARCH_BUILD/"${filename%.md}"_research.html \
+    --mathjax=$MATHJAX_URL \
+    -c css/base.css \
+    -c css/extra.css \
+    -c "css/print.css" \
+    -c "css/superfish.css" \
+    -c "css/superfish-vertical.css" \
+    -c "css/base_mode.css"
+done
+
--- a/bin/extract_title.sh
+++ b/bin/extract_title.sh
@@ -3,4 +3,5 @@

 filename=$(basename -- "$1")

-echo "## `head -n 1 $1 | sed -e "s;#\s*;\[;g" -e "s;\(.*\);\1\](${filename%.md}.html);g"`"
\ No newline at end of file
+echo "## `head -n 1 $1 | sed -e "s;#\s*;\[;g" -e "s;\(.*\);\1\](${filename%.md}.html);g"`"
+
--- a/bin/get_static.sh
+++ b/bin/get_static.sh
@@ -49,4 +49,5 @@ do
    echo $wg
    wget -qO- $baseurl/forschung/$wg > $RESEARCH_BUILD/forschung/$wg.tmp
    iconv -f ISO-8859-1 -t UTF-8 $RESEARCH_BUILD/forschung/$wg.tmp > $RESEARCH_BUILD/forschung/$wg.html
-done
\ No newline at end of file
+done
+
--- a/bin/integrate_pandoc.sh
+++ b/bin/integrate_pandoc.sh
 #!/bin/bash

-RESEARCH_STATIC=$RESEARCH_ROOT/static
-RESEARCH_BUILD=$RESEARCH_STATIC/build
+if [ $# -lt 1 ]
+then
+    RESEARCH_BUILD=$RESEARCH_ROOT/static/build
+    echo -e "No building directory was specified."
+else
+    RESEARCH_BUILD="$1"/build
+fi
+mkdir -p $RESEARCH_BUILD
+echo -e "Building into directory $RESEARCH_BUILD ..."
+

 cd $RESEARCH_BUILD

@@ -23,15 +31,6 @@ do
    -c "css/base_mode.css"
 done

-# get full TUHH staff pages ready for insertion
-rm -rf $RESEARCH_ROOT/static/build/plain
-mkdir -p $RESEARCH_ROOT/static/build/plain
-cp $RESEARCH_ROOT/static/home/*.html $RESEARCH_ROOT/static/build/plain
-cp $RESEARCH_ROOT/static/forschung/*.html $RESEARCH_ROOT/static/build/plain
-
-cd $RESEARCH_ROOT/static/build
-rm -rf *_final.html 
-
 # replace "MARKER" in .html files with research topics
 for f in $RESEARCH_ROOT/static/build/plain/*html
 do
@@ -45,3 +44,4 @@ do
    filename=$(basename -- "$f")
    sed -e "/MARKER/r $RESEARCH_ROOT/static/build/${filename%.md}_research.html" -e '/MARKER/d' $RESEARCH_ROOT/static/topic/topic-template.html > "${filename%.md}"_final.html
 done
+
--- a/bin/preprocIndexMd.sh
+++ b/bin/preprocIndexMd.sh
@@ -54,4 +54,5 @@ do
 done

 # adpat img path (prefix a dot)
-sed -i "s;\](/img/;\](./img/;g" $RESEARCH_BUILD/$filename 
\ No newline at end of file
+sed -i "s;\](/img/;\](./img/;g" $RESEARCH_BUILD/$filename 
+
--- a/bin/preprocMd.sh
+++ b/bin/preprocMd.sh
@@ -65,4 +65,5 @@ do

 # adpat img path (prefix a dot)
 sed -i "s;\](/img/;\](./img/;g" $RESEARCH_BUILD/$filename 
-done
\ No newline at end of file
+done
+
--- a/bin/preproc_staff.sh
+++ b/bin/preproc_staff.sh
@@ -68,4 +68,5 @@ do
 done

 # adpat img path (prefix a dot)
-sed -i "s;\](/img/;\](./img/;g" $RESEARCH_BUILD/$filename 
\ No newline at end of file
+sed -i "s;\](/img/;\](./img/;g" $RESEARCH_BUILD/$filename 
+
--- a/bin/preproc_topics.sh
+++ b/bin/preproc_topics.sh
 #!/bin/bash
 # processing command line arguments
+# Check commandline arguments
 if [ $# -lt 1 ]
 then
-    RESEARCH_BUILD="$RESEARCH_ROOT/build"
+    RESEARCH_BUILD=`pwd`"/build"
+    RESEARCH_TOPICS=`pwd`
    echo -e "No building directory was specified."
+elif [ $# -lt 2 ] 
+then
+    RESEARCH_BUILD="$1"
+    RESEARCH_TOPICS=$RESEARCH_BUILD
+    echo -e "No extra topics directory was specified."
 else
-    RESEARCH_BUILD="$1"/build
+    RESEARCH_BUILD="$1"
+    RESEARCH_TOPICS="$2"
 fi
-echo -e "Building into directory $RESEARCH_BUILD ..."
-rm -rf $RESEARCH_BUILD 
 mkdir -p $RESEARCH_BUILD
+echo -e "Building into directory $RESEARCH_BUILD ..."
+echo -e "Using .md-files from $RESEARCH_TOPICS ..."
+echo -e "Building into directory $RESEARCH_BUILD ..."
+#rm -rf $RESEARCH_BUILD 
+
 baseurl='https://www.mat.tuhh.de'

 #build index.html
 #replace working group
-cp $RESEARCH_ROOT/index.md $RESEARCH_BUILD/index.md
-$RESEARCH_ROOT/bin/preproc_wg.sh $RESEARCH_BUILD/index.md $RESEARCH_BUILD >> $RESEARCH_BUILD/build.log 2>&1
-
-#replace staff names
-$RESEARCH_ROOT/bin/preproc_staff.sh $RESEARCH_BUILD/index.md $RESEARCH_BUILD >> $RESEARCH_BUILD/build.log 2>&1
-
-#finalize file
-sed -i "s;\](/img/;\](./img/;g" -e '/PROCESSED AUTOMATICALLY/ d' $RESEARCH_BUILD/index.md
+#echo "Preprocessing Working Groups"
+cp $RESEARCH_ROOT/static/index.md $RESEARCH_BUILD/index.md
+#$RESEARCH_ROOT/bin/preproc_wg.sh $RESEARCH_BUILD/index.md $RESEARCH_BUILD >> $RESEARCH_BUILD/build.log 2>&1
+#
+##replace staff names
+#echo "Preprocessing Staff"
+#$RESEARCH_ROOT/bin/preproc_staff.sh $RESEARCH_BUILD/index.md $RESEARCH_BUILD >> $RESEARCH_BUILD/build.log 2>&1
+#
+##finalize file
+#sed -i -e "s;\](/img/;\](./img/;g" -e '/PROCESSED AUTOMATICALLY/ d' $RESEARCH_BUILD/index.md


 #build rest of the topics
-for f in $RESEARCH_ROOT/topics/*.md
+for f in $RESEARCH_TOPICS/*.md
 do
    filename=$(basename -- "$f")
    #make output copy
-    echo "Preprocessing $filename..."
    cp $f $RESEARCH_BUILD/$filename

    #extract title of topic
@@ -49,4 +61,4 @@ do
    sed -i "s;\](/img/;\](./img/;g" $RESEARCH_BUILD/$filename
 done

-echo "Finished preprocessing topics."
\ No newline at end of file
+echo "Finished preprocessing topics."
--- a/bin/preproc_wg.sh
+++ b/bin/preproc_wg.sh
@@ -55,4 +55,5 @@ do

    sed -i "s;### Working Groups:\(.*\)$wg\(.*\);### Working Groups:\1\[$fullname\]($wg.html)\2;g" $RESEARCH_BUILD/$filename  
    #sed -i "s;### Working Groups:\(.*\)$wg\(.*\);### Working Groups:\1\[$fullname\]($baseurl/forschung/$wg)\2;g" $RESEARCH_BUILD/$filename  #uncomment this line for linking the mat.tuhh.de webpage
-done
\ No newline at end of file
+done
+
--- a/bin/replace_marker.sh
+++ b/bin/replace_marker.sh
+#!/bin/bash
+# processing command line arguments
+
+# Check commandline arguments
+if [ $# -lt 1 ]
+then
+    RESEARCH_BUILD=`pwd`"/build"
+    RESEARCH_TOPICS=`pwd`
+    echo -e "No building directory was specified."
+elif [ $# -lt 2 ] 
+then
+    RESEARCH_BUILD="$1"
+    RESEARCH_TOPICS=$RESEARCH_BUILD
+    echo -e "No extra topics directory was specified."
+else
+    RESEARCH_BUILD="$1"
+    RESEARCH_TOPICS="$2"
+fi
+mkdir -p $RESEARCH_BUILD
+echo -e "Building into directory $RESEARCH_BUILD ..."
+echo -e "Including _research.html-files from $RESEARCH_TOPICS ..."
+# replace "MARKER" in .html files with research topics
+for f in $RESEARCH_ROOT/static/{home,forschung}/*.html
+do
+    filename=$(basename -- "$f")
+    if [ -f "$RESEARCH_TOPICS/${filename%.html}_research.html" ] 
+    then
+        echo "found $f"
+        sed -e "/MARKER/r  $RESEARCH_TOPICS/${filename%.html}_research.html" \
+            -e '/MARKER/d' $f > "$RESEARCH_BUILD/${filename%.html}"_final.html
+    fi
+
+done
+
+# Building standalone topics and index
+RESEARCH_TEMPLATE="$RESEARCH_ROOT/static/topic/topic-template.html"
+for f in $RESEARCH_ROOT/topics/*.md $RESEARCH_BUILD/index.md
+do
+    filename=$(basename -- "$f")
+    echo "Looking for $RESEARCH_TOPICS/${filename%.md}_research.html"
+    if [ -f "$RESEARCH_TOPICS/${filename%.md}_research.html" ] 
+    then
+        echo "found $f"
+        echo "creating "$RESEARCH_BUILD/${filename%.md}"_final.html"
+        sed -e "/MARKER/r $RESEARCH_TOPICS/${filename%.md}_research.html" \
+            -e '/MARKER/d' $RESEARCH_TEMPLATE > "$RESEARCH_BUILD/${filename%.md}"_final.html
+    fi
+done
--- a/bin/run-tests.sh
+++ b/bin/run-tests.sh
@@ -63,4 +63,5 @@ fi
 #END Test 4

 #this should be the last line (errors exit earlier)
-exit 0
\ No newline at end of file
+exit 0
+