.ci/generateIndex.py

@@ -42,6 +42,35 @@ def build_section_start(title, shortcut):
 def build_section_end():
     return "\t\t</ul>\n\t</div>"
 
+def save_order(localroot, root, filename):
+    order = ""
+    os.chdir(root)
+
+    with open(filename, 'r') as f:
+        for line in f:
+            # check for the start of the section
+            if line[0:6] == "order:":
+                order = line[7:]
+                break
+
+    # change back to the local root
+    os.chdir(localroot)
+
+    return order.rstrip()
+
+def get_ignore():
+    return ["404.html",
+            "Gemfile",
+            "Gemfile.lock",
+            "README.md",
+            "_config.yml",
+            "_site",
+            "assets",
+            "help.md",
+            "index.md",
+            "pagination.md"
+            ]
+
 def save_legacy_from(localroot, root, filename):
     legacy_from = []
     os.chdir(root)
@@ -56,12 +85,13 @@ def save_legacy_from(localroot, root, filename):
                 legacy_from_flag = True
 
             # append lines from the legacy section
-            if legacy_from_flag and line[0:12]:
+            if legacy_from_flag:
                 legacy_from.append(line)
 
             # check for the end of the header
             if legacy_from_flag and line[0:3] == "---":
                legacy_from_flag = False
+               break
 
     # change back to the local root
     os.chdir(localroot)
@@ -75,6 +105,7 @@ def remove_header(localroot, root, filename):
 
     # count the number of lines
     count = 0
+    n = 0
     headerCheck = False
     with open(filename, 'r') as f:
         for line in f:
@@ -105,6 +136,8 @@ def remove_header(localroot, root, filename):
 # loop through the entire internal tree
 localroot = os.getcwd()
 
+# retrieve ignore list
+ignore = get_ignore()
 
 # generate the index properly speaking
 cardDirs = ["internal", "external", "policies"]
@@ -117,7 +150,7 @@ for direct in cardDirs:
         dirs = natsorted(dirs)
 
         for d in dirs:
-            if d[0] != ".":
+            if d[0] != "." and d not in ignore:
                 sections.append(d)
 
 sections = list(set(sections))
@@ -128,24 +161,27 @@ index = ''
 index += '\n<div class="index-box-container">\n'
 whiteList = ''
 
-localIndexArr = [[]] * len(sections)
+localIndexArr = {k: [] for k in range(len(sections))}
+orderArr = {k: [] for k in range(len(sections))}
+
 for folder in cardDirs:
+    # FolderFlag gets set to true at the first iteration
+    folderFlag = True
 
     # check if folder exists
-    if path.isdir(folder):
+    if path.isdir(folder) and folder not in ignore:
         dirs = os.listdir(folder)
         dirs = natsorted(dirs)
 
         for d in dirs:
-            if d[0] != ".":
+            if d[0] != "." and d not in ignore:
                 # set the header of the section
                 #index += "\n### " + d.replace("-", " ").capitalize() + "\n"
 
-
                 # get the index of the section
                 indexS = sections.index(d)
+                maxOrder = 0
 
-                #print(indexS)
                 if len(localIndexArr[indexS]) == 0:
                     localIndexArr[indexS] = ["\n"]
 
@@ -159,7 +195,8 @@ for folder in cardDirs:
                             if file[0] != "_":
                                 print(" > Generating header for: " + fileName)
 
-                                # save legacy section
+                                # save order and legacy section
+                                order = save_order(localroot, root, file)
                                 legacy_from = save_legacy_from(localroot, root, file)
 
                                 # remove the previous header
@@ -179,6 +216,26 @@ for folder in cardDirs:
 
                                 # define the header for each card
                                 header = "---\n"
+
+                                if len(order) > 0:
+                                    header += "order: " + str(order) + "\n"
+                                    # append the order of the card
+                                    # find the maximum of existing orders
+
+                                    if folderFlag:
+                                        if len(orderArr[indexS]) > 0:
+                                            maxOrder = max(orderArr[indexS])
+                                        else:
+                                            maxOrder = 0
+                                        # after determining the max order, set the folder flag to False to avoid another entry into the same block of code
+                                        folderFlag = False
+
+                                    tmp = orderArr[indexS].copy()
+                                    tmp.append(maxOrder + int(order))
+                                    orderArr[indexS] = tmp
+                                else:
+                                    orderArr[indexS] = []
+
                                 header += "layout: page\n"
                                 header += "permalink: " + permalink + "\n"
                                 header += "shortcut: " + root_handbook(shortcut) + "\n"
@@ -235,8 +292,21 @@ for folder in cardDirs:
                                 print(" + New header added.")
                                 print("-----------------------")
 
-                # join all subcategories to the index
-                localIndexArr[indexS] = natsorted(localIndexArr[indexS])
+
+# ordering of cards
+for d in sections:
+    indexS = sections.index(d)
+
+    # join all subcategories to the index
+    # if all subcategories have a predefined order
+    if len(orderArr[indexS]) == len(localIndexArr[indexS])-1 and len(orderArr[indexS]) > 0:
+        print("")
+        X = localIndexArr[indexS][1:]
+        Y = orderArr[indexS]
+        localIndexArr[indexS] = [x for _, x in sorted(zip(Y, X))]
+    # natural sorting otherwise
+    else:
+        localIndexArr[indexS] = natsorted(localIndexArr[indexS])
 
 print(localIndexArr)
 

.gitattributes

+*.PNG filter=lfs diff=lfs merge=lfs -text
 *.png filter=lfs diff=lfs merge=lfs -text
 *.jpg filter=lfs diff=lfs merge=lfs -text
 *.jpeg filter=lfs diff=lfs merge=lfs -text

.gitlab-ci.yml

@@ -89,6 +89,8 @@ build:pages:
     - apt-get install -y -qq git-lfs
     - gem install bundler:$BUNDLER_VERSION && bundle install
   script:
+    # copy the index
+    - cp .tmp/cards.md .
     # Generate the configuration for forks (will use Gitlab Pages on personal namespaces)
     - |
       if [ $CI_MERGE_REQUEST_ID ]; then

_includes/scripts-head.html

+<script src="{{ '/assets/vendor/js/jquery-3.6.0.min.js' | relative_url }}"></script>

_includes/scripts.html

-<script type="text/javascript" src="https://analytics.lcsb.uni.lu/lap/static/js/jquery.min.js"></script>
 <script type="text/javascript" src="{{ "assets/js/router.js" | relative_url }}"></script>
 <script type="text/javascript" src="{{ "assets/js/box_hider.js" | relative_url }}"></script>
 <script>

cards.md

@@ -39,14 +39,12 @@ order: -1
 			<li><a href="{{ 'external/access/passwords' | relative_url }}">Managing your passwords</a></li>
 			<li><a href="{{ 'external/access/vpn-cerbere-access' | relative_url }}">VPN/CERBERE connection</a></li>
 			<li><a href="{{ 'external/access/wifiNetworkAccessGuests' | relative_url }}">WiFi network access for guests</a></li>
-
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="backup-card">
 		<h3>Backup</h3>
 		<ul>
 			<li><a href="{{ 'external/backup/computer' | relative_url }}">Staff Computer</a></li>
-
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="contribute-card">
@@ -64,23 +62,21 @@ order: -1
 	<div class="index-box noborderbox" id="exchange-channels-card">
 		<h3>Exchange channels</h3>
 		<ul>
-			<li><a href="{{ 'external/exchange-channels/asperaweb' | relative_url }}">AsperaWEB Quick Guide</a></li>
 			<li><a href="{{ 'external/exchange-channels/calendar' | relative_url }}">Sharing calendar in Microsoft Exchange</a></li>
+			<li><a href="{{ 'external/exchange-channels/asperaweb' | relative_url }}">AsperaWEB Quick Guide</a></li>
 			<li><a href="{{ 'external/exchange-channels/owncloud' | relative_url }}">Owncloud</a></li>
-
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="general-card">
 		<h3>General</h3>
 		<ul>
-			<li><a href="{{ 'external/general/BelvalCampusMap' | relative_url }}">Belval Campus Map</a></li>
-			<li><a href="{{ 'external/general/attend-webex' | relative_url }}">Attend the LCSB Team Meeting online (webex)</a></li>
+			<li><a href="{{ 'external/general/usefulLinks' | relative_url }}">Useful links for living in Luxembourg</a></li>
 			<li><a href="{{ 'external/general/getToLCSB' | relative_url }}">How to get to the Luxembourg Centre for Systems Biomedicine</a></li>
+			<li><a href="{{ 'external/general/BelvalCampusMap' | relative_url }}">Belval Campus Map</a></li>
 			<li><a href="{{ 'external/general/glossary' | relative_url }}">Glossary</a></li>
 			<li><a href="{{ 'external/general/links' | relative_url }}">Important websites</a></li>
 			<li><a href="{{ 'external/general/remote-working' | relative_url }}">Work remotely</a></li>
-			<li><a href="{{ 'external/general/usefulLinks' | relative_url }}">Useful links for living in Luxemburg</a></li>
-
+			<li><a href="{{ 'external/general/attend-webex' | relative_url }}">Attend the LCSB Team Meeting online (webex)</a></li>
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="integrity-card">
@@ -118,23 +114,21 @@ order: -1
 	<div class="index-box noborderbox" id="on-offboarding-card">
 		<h3>On offboarding</h3>
 		<ul>
-			<li><a href="{{ 'external/on-offboarding/checklistArrival' | relative_url }}">Checklist upon arrival in Luxemburg</a></li>
-			<li><a href="{{ 'external/on-offboarding/checklistBeforeArriving' | relative_url }}">Newcomer Checklist before Arriving in Luxembourg</a></li>
 			<li><a href="{{ 'external/on-offboarding/checklistGetStarted' | relative_url }}">Newcomer's checklist</a></li>
+			<li><a href="{{ 'external/on-offboarding/checklistArrival' | relative_url }}">Checklist upon arrival in Luxembourg</a></li>
 			<li><a href="{{ 'external/on-offboarding/checklistGodparent' | relative_url }}">Checklist for godparents</a></li>
-			<li><a href="{{ 'external/on-offboarding/godparent' | relative_url }}">Godparents for Newcomers</a></li>
+			<li><a href="{{ 'external/on-offboarding/checklistBeforeArriving' | relative_url }}">Newcomer Checklist before Arriving in Luxembourg</a></li>
 			<li><a href="{{ 'external/on-offboarding/onboarding' | relative_url }}">Onboarding new members at the LCSB</a></li>
-
+			<li><a href="{{ 'external/on-offboarding/godparent' | relative_url }}">Godparents for Newcomers</a></li>
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="publication-card">
 		<h3>Publication</h3>
 		<ul>
-			<li><a href="{{ 'external/publication/10WaysImproveEnglish' | relative_url }}">10 ways to improve your English</a></li>
-			<li><a href="{{ 'external/publication/add-gitignore' | relative_url }}">Add a .gitignore to your repository</a></li>
 			<li><a href="{{ 'external/publication/publish-repo' | relative_url }}">Publish a repository</a></li>
+			<li><a href="{{ 'external/publication/add-gitignore' | relative_url }}">Add a .gitignore to your repository</a></li>
 			<li><a href="{{ 'external/publication/publishInBiotools' | relative_url }}">Publishing a tool in *bio.tools*</a></li>
-
+			<li><a href="{{ 'external/publication/10WaysImproveEnglish' | relative_url }}">10 ways to improve your English</a></li>
 		</ul>
 	</div>
 </div><br><center><a href="{{ '/' | relative_url }}">go back</a></center><br><center><a href="{{ '/cards' | relative_url }}">Overview of all HowTo cards</a></center>
\ No newline at end of file

external/access/harrenhal-access/harrenhal-access.md

 ---
+order: 100
 layout: page
 permalink: /external/access/harrenhal-access/
 shortcut: access:harrenhal-access

external/access/lums-passwords/lums-passwords.md

 ---
+order: 200
 layout: page
 permalink: /external/access/lums-passwords/
 shortcut: access:lums-passwords

external/access/passwords/passwords.md

 ---
+order: 300
 layout: page
 permalink: /external/access/passwords/
 shortcut: access:passwords

external/access/vpn-cerbere-access/vpn-cerbere-access.md

 ---
+order: 400
 layout: page
 permalink: /external/access/vpn-cerbere-access/
 shortcut: access:vpn-cerbere-access

external/access/wifiNetworkAccessGuests/wifiNetworkAccessGuests.md

 ---
+order: 500
 layout: page
 permalink: /external/access/wifiNetworkAccessGuests/
 shortcut: access:wifiNetworkAccessGuests

external/backup/computer/computer.md

 ---
+order: 100
 layout: page
 permalink: /external/backup/computer/
 shortcut: backup:computer

external/exchange-channels/asperaweb/asperaweb.md

 ---
+order: 300
 layout: page
 permalink: /external/exchange-channels/asperaweb/
 shortcut: exchange-channels:asperaweb

external/exchange-channels/calendar/exchange-calendar.md

 ---
+order: 200
 layout: page
 permalink: /external/exchange-channels/calendar/
 shortcut: exchange-channels:calendar

external/exchange-channels/owncloud/owncloud.md

 ---
+order: 400
 layout: page
 permalink: /external/exchange-channels/owncloud/
 shortcut: exchange-channels:owncloud

external/general/BelvalCampusMap/BelvalCampusMap.md

 ---
+order: 300
 layout: page
 permalink: /external/general/BelvalCampusMap/
 shortcut: general:BelvalCampusMap

external/general/attend-webex/attend-webex.md

 ---
+order: 900
 layout: page
 permalink: /external/general/attend-webex/
 shortcut: general:attend-webex
@@ -21,4 +22,4 @@ You can then login with your university credentials. Once you logged in, a popup
 
 ![](img/image2.png)
 
-**Note:** On Windows, you might not be asked for a password.
\ No newline at end of file
+**Note:** On Windows, you might not be asked for a password.

external/general/getToLCSB/getToLCSB.md

 ---
+order: 200
 layout: page
 permalink: /external/general/getToLCSB/
 shortcut: general:getToLCSB

external/general/glossary/glossary.md

 ---
+order: 500
 layout: page
 permalink: /external/general/glossary/
 shortcut: general:glossary