hschellman · hschellman · Nov 3, 2025 · Nov 3, 2025
diff --git a/_episodes/03-data-management.md b/_episodes/03-data-management.md
@@ -441,7 +441,8 @@ export SAM_EXPERIMENT=dune
 -->
 ## Getting file locations using Rucio
 
-### What is Rucio? <a name="Rucio"></a>
+### What is Rucio? 
+<!-- <a name="Rucio"></a> -->
 Rucio is the next-generation Data Replica service and is part of DUNE's new Distributed Data Management (DDM) system that is currently in deployment. 
 Rucio has two functions:
 1. A rule-based system to get files to Rucio Storage Elements around the world and keep them there.
@@ -451,7 +452,7 @@ As of the date of the 2025 tutorial:
 - The Rucio client is available in CVMFS and Spack
 - Most DUNE users are now enabled to use it. New users may not automatically be added. 
 
-### You will need to authenticate to use read files
+### You will need to authenticate to read files
 
 > #### For SL7 use justin to get a token
 {:.callout}

diff --git a/_includes/02-storage-spaces.toc.md b/_includes/02-storage-spaces.toc.md
@@ -18,7 +18,7 @@
       - [Tape-backed dCache](#tape-backed-dcache)
       - [Rucio Storage Elements](#rucio-storage-elements)
    - [CVMFS](#cvmfs)
-   - [What is my quota?](#what-is-my-quota?)
+   - [What is my quota?](#what-is-my-quota)
       - [Your home area at FNAL](#your-home-area-at-fnal)
       - [Your home area at CERN](#your-home-area-at-cern)
       - [The /app/ and /data/ areas at FNAL](#the-/app/-and-/data/-areas-at-fnal)

diff --git a/_includes/03-data-management.toc.md b/_includes/03-data-management.toc.md
@@ -3,33 +3,33 @@
       - [Live Notes](#live-notes)
 - [Introduction](#introduction)
    - [What we need to do to produce accurate physics results](#what-we-need-to-do-to-produce-accurate-physics-results)
-   - [How we do it ?](#how-we-do-it-?)
+   - [How we do it ?](#how-we-do-it-)
    - [How do I use this.](#how-do-i-use-this.)
 - [How to find and access official data](#how-to-find-and-access-official-data)
-- [Official datasets](#official-datasets)
+- [Official datasets <a name="Official_Datasets"></a>](#Official_Datasets)
    - [Fast web catalog queries](#fast-web-catalog-queries)
    - [Command line tools and advanced queries](#command-line-tools-and-advanced-queries)
    - [metacat web interface](#metacat-web-interface)
    - [Example of finding reconstructed Monte Carlo](#example-of-finding-reconstructed-monte-carlo)
    - [you can use the web data catalog to do advanced searches](#you-can-use-the-web-data-catalog-to-do-advanced-searches)
-- [What is metacat?](#what-is-metacat?)
+- [What is metacat?](#what-is-metacat)
    - [Find a file in metacat](#find-a-file-in-metacat)
    - [Example of doing a metacat search](#example-of-doing-a-metacat-search)
    - [then do queries to find particular groups of files](#then-do-queries-to-find-particular-groups-of-files)
-   - [What do those fields mean?](#what-do-those-fields-mean?)
+   - [What do those fields mean?](#what-do-those-fields-mean)
    - [find out how much raw data there is in a run using the summary option](#find-out-how-much-raw-data-there-is-in-a-run-using-the-summary-option)
    - [Fast web catalog queries](#fast-web-catalog-queries)
    - [Command line tools and advanced queries](#command-line-tools-and-advanced-queries)
    - [metacat web interface](#metacat-web-interface)
    - [Example of finding reconstructed Monte Carlo](#example-of-finding-reconstructed-monte-carlo)
    - [you can use the web data catalog to do advanced searches](#you-can-use-the-web-data-catalog-to-do-advanced-searches)
    - [find out how much data there is in a dataset](#find-out-how-much-data-there-is-in-a-dataset)
-   - [What describes a dataset?](#what-describes-a-dataset?)
-   - [What files are in that dataset and how do I use them?](#what-files-are-in-that-dataset-and-how-do-i-use-them?)
+   - [What describes a dataset?](#what-describes-a-dataset)
+   - [What files are in that dataset and how do I use them?](#what-files-are-in-that-dataset-and-how-do-i-use-them)
 - [Finding those files on disk](#finding-those-files-on-disk)
 - [Getting file locations using Rucio](#getting-file-locations-using-rucio)
-   - [What is Rucio?](#what-is-rucio?)
-   - [You will need to authenticate to use read files](#you-will-need-to-authenticate-to-use-read-files)
+   - [What is Rucio?](#what-is-rucio)
+   - [You will need to authenticate to read files](#you-will-need-to-authenticate-to-read-files)
 - [Accessing `rucio` and `justin` require a bit more](#accessing-`rucio`-and-`justin`-require-a-bit-more)
    - [getting a token for xroot access in AL9](#getting-a-token-for-xroot-access-in-al9)
    - [finding a file](#finding-a-file)

diff --git a/_includes/03.2-UPS.toc.md b/_includes/03.2-UPS.toc.md
@@ -1,3 +1,3 @@
 ## Table of Contents
-- [What is UPS and why do we need it?](#what-is-ups-and-why-do-we-need-it?)
+- [What is UPS and why do we need it?](#what-is-ups-and-why-do-we-need-it)
    - [UPS basic commands](#ups-basic-commands)
diff --git a/_includes/04-Spack.toc.md b/_includes/04-Spack.toc.md
@@ -1,5 +1,5 @@
 ## Table of Contents
-- [What is Spack and why do we need it?](#what-is-spack-and-why-do-we-need-it?)
+- [What is Spack and why do we need it?](#what-is-spack-and-why-do-we-need-it)
 - [Minimal spack for root analysis and file access](#minimal-spack-for-root-analysis-and-file-access)
 - [A more flexible environment with more packages but you have to make choices of versions](#a-more-flexible-environment-with-more-packages-but-you-have-to-make-choices-of-versions)
    - [Spack basic commands](#spack-basic-commands)
diff --git a/code/tocgen.py b/code/tocgen.py
@@ -10,7 +10,8 @@ def dealwithline(input,toclines):
             dealwithline(newlines,toclines)
             continue
         # remove any labels
-        line = line.split('<a')[0]
+        # if "<a" in line:
+        # line = line.split(' <a')[0]
         level = 1
         name = ""
         indent = ''
@@ -26,10 +27,15 @@ def dealwithline(input,toclines):
             name = line[2:].strip()
         else:
             continue
-        print (level,indent,name)
+        # if labeled get the label name
+        if "<a" in line:
+            linkname = line.split(' <a')[1].strip().split("name=\"")[1].split('"')[0]
+        else: 
+            linkname=name.lower().strip().replace('?','').replace(' ',"-")
+        print (level,indent,name,linkname)
 
 
-        newline = '%s- [%s](#%s)' % (indent,name,name.lower().replace(' ',"-"))
+        newline = '%s- [%s](#%s)' % (indent,name,linkname)
         toclines.append(newline)
         print (newline)
     return toclines