add loops and necessary modifications for multiple topic files

bin/preprocIndexMd.sh

 #!/bin/bash
 
-# generate namelist of collaborators from topic file
-original="$RESEARCH_ROOT/index.md"
-filename="index.md"
-build_dir="$RESEARCH_ROOT/build"
+RESEARCH_BUILD="$RESEARCH_ROOT/build"
+mkdir -p $RESEARCH_BUILD
 baseurl='https://www.mat.tuhh.de'
-
-cd $RESEARCH_ROOT
-
+full_filename="$RESEARCH_ROOT/index.md"
+filename=$(basename -- "$full_filename")
 #make output copy
-mkdir -p build
 echo "Preprocessing $filename..."
-cp $original $build_dir/$filename
+cp $full_filename $RESEARCH_BUILD/$filename
 
 #replace working group
 echo "Replacing working group keys..."
-for wg in {aa,cm,dm,nm,st}
+namelist=`grep -h -i -m 1 -r "###\s*Working Groups:" $RESEARCH_BUILD/$filename | sed -e 's/^###\s*Working Groups:\s*//I' -e 's/\s*,\s*/\n/g'  | sort -u`
+echo "Found the following keys: " $namelist
+for wg in $namelist
 do
     fullname=`wget -qO- $baseurl/forschung/$wg | grep h1 | sed -e "s;<h1>\s*\(.*\)</h1>.*$;\1;g" | sed -e 's;^[ \t]*;;'`
     echo "Found working group $fullname"
-    echo "# $fullname" > ./build/$wg.md
+    echo "# $fullname" > $RESEARCH_BUILD/$wg.md
     # append research to staffiles
-    echo -e "\n$title\n" >> ./build/$wg.md
-    sed -i "s;### Working Groups:\(.*\)$wg\(.*\);### Working Groups:\1\[$fullname\]($wg.html)\2;g" $build_dir/$filename  
-    #sed -i "s;### Working Groups:\(.*\)$wg\(.*\);### Working Groups:\1\[$fullname\]($baseurl/forschung/$wg)\2;g" $build_dir/$filename  #uncomment this line for linking the mat.tuhh.de webpage
-done
+    echo -e "\n$title\n" >> $RESEARCH_BUILD/$wg.md
+    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
 
+    #initialize wg file
+    echo "# $fullname" > $RESEARCH_BUILD/$wg.md
+done
 
 echo "Replacing collaborator keys..."
-namelist=`grep -h -i -m 1 -r "###\s*Collaborators (MAT):" $build_dir/$filename | sed -e 's/^###\s*Collaborators (MAT):\s*//I' -e 's/\s*,\s*/\n/g'  | sort -u`
+namelist=`grep -h -i -m 1 -r "###\s*Collaborators (MAT):" $RESEARCH_BUILD/$filename | sed -e 's/^###\s*Collaborators (MAT):\s*//I' -e 's/\s*,\s*/\n/g'  | sort -u`
+echo "Found the following keys: " $namelist
 for name in $namelist
 do
     # pipeline to get full name of staff-member from mat-homepage
@@ -39,10 +40,16 @@ do
     wget -qO- $baseurl/home/$name/?homepage_id=$name > page.html
     iconv -f WINDOWS-1252 -t UTF-8 ./page.html > ./utf.html
     fullname=`grep h1 ./utf.html |  sed -e "s/<h1>\s*\(.*\)<\/h1>.*$/\1/g" | sed -e 's/^[ \t]*//'`
+
     echo "Found collaborator $fullname" 
 
-    # replace name in index.md file
+    # replace name in .md file
+    sed -i "s;$name;\[$fullname\]($name.html);g" $RESEARCH_BUILD/$filename 
+    #sed -i "s;$name;\[$fullname\]($baseurl/home/$name);g" $RESEARCH_BUILD/$filename #uncomment this line for linking the mat.tuhh.de webpage
 
-    sed -i "s;$name;\[$fullname\]($name.html);g" $build_dir/$filename 
-    #sed -i "s;$name;\[$fullname\]($baseurl/home/$name);g" $build_dir/$filename #uncomment this line for linking the mat.tuhh.de webpage
+    #initialize staff file
+    echo "# $fullname" > $RESEARCH_BUILD/$name.md
 done
+
+# adpat img path (prefix a dot)
+sed -i "s;\](/img/;\](./img/;g" $RESEARCH_BUILD/$filename 
\ No newline at end of file

bin/preprocMd.sh

 #!/bin/bash
 
-    # generate namelist of collaborators from topic file
-    original="$RESEARCH_ROOT/topics/topic-template.md"
-    filename='topic-template.md'
-    build_dir="$RESEARCH_ROOT/build"
-    baseurl='https://www.mat.tuhh.de'
+RESEARCH_BUILD="$RESEARCH_ROOT/build"
+mkdir -p $RESEARCH_BUILD
+baseurl='https://www.mat.tuhh.de'
 
-    cd $RESEARCH_ROOT 
 
+for f in $RESEARCH_ROOT/topics/*.md
+do
+    echo $f
+    filename=$(basename -- "$f")
     #make output copy
-    mkdir -p $RESEARCH_ROOT/build
     echo "Preprocessing $filename..."
-    cp $original $build_dir/$filename
+    cp $f $RESEARCH_BUILD/$filename
 
     #extract title of topic
-    title="## `head -n 1 $build_dir/$filename | sed -e "s;#\s*;\[;g" -e "s;\(.*\);\1\](${filename%.md}.html);g"`"
+    title="## `head -n 1 $RESEARCH_BUILD/$filename | sed -e "s;#\s*;\[;g" -e "s;\(.*\);\1\](${filename%.md}.html);g"`"
 
     # prepare index
     # append research topic to index
     echo "Creating index.md ..."
-    echo -e "\n$title\n" >>  ./build/index.md
+    echo -e "\n$title\n" >>  $RESEARCH_BUILD/index.md
 
     #replace working group
     echo "Replacing working group keys..."
-    for wg in {aa,cm,dm,nm,st}
+    namelist=`grep -h -i -m 1 -r "###\s*Working Groups:" $RESEARCH_BUILD/$filename | sed -e 's/^###\s*Working Groups:\s*//I' -e 's/\s*,\s*/\n/g'  | sort -u`
+    echo "Found the following keys: " $namelist
+    for wg in $namelist
     do
+        #extract full name from tuhh-webpage
         fullname=`wget -qO- $baseurl/forschung/$wg | grep h1 | sed -e "s;<h1>\s*\(.*\)</h1>.*$;\1;g" | sed -e 's;^[ \t]*;;'`
+
         echo "Found working group $fullname"
-        echo "# $fullname" > ./build/$wg.md
+
         # append research to staffiles
-        echo -e "\n$title\n" >> ./build/$wg.md
-        sed -i "s;### Working Groups:\(.*\)$wg\(.*\);### Working Groups:\1\[$fullname\]($wg.html)\2;g" $build_dir/$filename  
-        #sed -i "s;### Working Groups:\(.*\)$wg\(.*\);### Working Groups:\1\[$fullname\]($baseurl/forschung/$wg)\2;g" $build_dir/$filename  #uncomment this line for linking the mat.tuhh.de webpage
+        echo -e "\n$title\n" >> $RESEARCH_BUILD/$wg.md
+
+        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
 
     echo "Replacing collaborator keys..."
-    namelist=`grep -h -i -m 1 -r "###\s*Collaborators (MAT):" $build_dir/$filename | sed -e 's/^###\s*Collaborators (MAT):\s*//I' -e 's/\s*,\s*/\n/g'  | sort -u`
+    namelist=`grep -h -i -m 1 -r "###\s*Collaborators (MAT):" $RESEARCH_BUILD/$filename | sed -e 's/^###\s*Collaborators (MAT):\s*//I' -e 's/\s*,\s*/\n/g'  | sort -u`
     echo "Found the following keys: " $namelist
     for name in $namelist
     do
@@ -51,15 +56,13 @@
         echo "Found collaborator $fullname" 
 
         # replace name in .md file
-        sed -i "s;$name;\[$fullname\]($name.html);g" $build_dir/$filename 
-        #sed -i "s;$name;\[$fullname\]($baseurl/home/$name);g" $build_dir/$filename #uncomment this line for linking the mat.tuhh.de webpage
-
-        echo "# $fullname" > ./build/$name.md
+        sed -i "s;$name;\[$fullname\]($name.html);g" $RESEARCH_BUILD/$filename 
+        #sed -i "s;$name;\[$fullname\]($baseurl/home/$name);g" $RESEARCH_BUILD/$filename #uncomment this line for linking the mat.tuhh.de webpage
 
         # append research to staffiles
-        echo -e "\n$title\n" >> ./build/$name.md
-
+        echo -e "\n$title\n" >> $RESEARCH_BUILD/$name.md
     done
 
 # adpat img path (prefix a dot)
-sed -i "s;\](/img/;\](./img/;g" $build_dir/$filename 
+sed -i "s;\](/img/;\](./img/;g" $RESEARCH_BUILD/$filename 
+done
\ No newline at end of file