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108 changes: 50 additions & 58 deletions episodes/04-nanoaod-exercises.md
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## Introduction
## Exercises with NanoAOD

This is a lesson created via The Carpentries Workbench. It is written in
[Pandoc-flavored Markdown](https://pandoc.org/MANUAL.txt) for static files and
[R Markdown][r-markdown] for dynamic files that can render code into output.
Please refer to the [Introduction to The Carpentries
Workbench](https://carpentries.github.io/sandpaper-docs/) for full documentation.
::::::::::::::::::::::::::::::::::::: challenge

What you need to know is that there are three sections required for a valid
Carpentries lesson:
## Exercise 1: Get data file locations

1. `questions` are displayed at the beginning of the episode to prime the
learner for the content.
2. `objectives` are the learning objectives for an episode displayed with
the questions.
3. `keypoints` are displayed at the end of the episode to reinforce the
objectives.
Let's select a ZprimeToTT sample for a given mass and using
the `cernopendata-client` to get the associated data files

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: instructor
Recall what you've learned from the [pre-exercise](https://cms-opendata-workshop.github.io/workshop2024-lesson-dataset-scouting/instructor/04-cli-through-cernopendata-client.html) on the `cernopendata-client`.

Inline instructor notes can help inform instructors of timing challenges
associated with the lessons. They appear in the "Instructor View"
:::::::::::::::::::::::: solution

::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
## Solution

::::::::::::::::::::::::::::::::::::: challenge
Search for the ZprimeToTT samples in the CERN Open Data Portal. The resulting query is [here](https://opendata.cern.ch/search?q=ZprimeToTT%2A&f=experiment%3ACMS&f=year%3A2016&f=file_type%3Ananoaodsim&f=category%3AExotica%2Bsubcategory%3AHeavy%20Gauge%20Bosons&f=type%3ADataset&l=list&order=asc&p=1&s=10&sort=bestmatch).

Check warning on line 36 in episodes/04-nanoaod-exercises.md

View workflow job for this annotation

GitHub Actions / Build markdown source files if valid 

 [uninformative link text]: [here](https://opendata.cern.ch/search?q=ZprimeToTT%2A&f=experiment%3ACMS&f=year%3A2016&f=file_type%3Ananoaodsim&f=category%3AExotica%2Bsubcategory%3AHeavy%20Gauge%20Bosons&f=type%3ADataset&l=list&order=asc&p=1&s=10&sort=bestmatch)

## Challenge 1: Can you do it?
Next, select a dataset. Here we fetch [this one](https://opendata.cern.ch/record/75124), record 75124, "Simulated dataset ZPrimeToTT_M1000_W100_TuneCP2_13TeV-madgraph-pythia8 in NANOAODSIM format for 2016 collision data" where the Z' mass is 1000 GeV.

What is the output of this command?
Fetch the Docker image for the `cernopendata-client`:

```r
paste("This", "new", "lesson", "looks", "good")
```bash
docker pull docker.io/cernopendata/cernopendata-client
```

:::::::::::::::::::::::: solution

## Output

```output
[1] "This new lesson looks good"
and refresh your memory on the commands:
```bash
docker run -i -t --rm docker.io/cernopendata/cernopendata-client --help
```
```output
Usage: cernopendata-client [OPTIONS] COMMAND [ARGS]...
:::::::::::::::::::::::::::::::::

Command-line client for interacting with CERN Open Data portal.
## Challenge 2: how do you nest solutions within challenge blocks?
Options:
--help Show this message and exit.
:::::::::::::::::::::::: solution
Commands:
download-files Download data files belonging to a record.
get-file-locations Get a list of data file locations of a record.
get-metadata Get metadata content of a record.
list-directory List contents of a EOSPUBLIC Open Data directory.
verify-files Verify downloaded data file integrity.
version Return cernopendata-client version.
```

You can add a line with at least three colons and a `solution` tag.
Then fetch the files for record 75124:
```python
cernopendata-client get-file-locations --recid 75124
```

```output
http://opendata.cern.ch/eos/opendata/cms/mc/RunIISummer20UL16NanoAODv9/ZPrimeToTT_M1000_W100_TuneCP2_13TeV-madgraph-pythia8/NANOAODSIM/106X_mcRun2_asymptotic_v17-v2/2520000/65A0736B-22F3-C94C-99AE-36717B28629C.root
http://opendata.cern.ch/eos/opendata/cms/mc/RunIISummer20UL16NanoAODv9/ZPrimeToTT_M1000_W100_TuneCP2_13TeV-madgraph-pythia8/NANOAODSIM/106X_mcRun2_asymptotic_v17-v2/2520000/6E508763-A12F-8846-A295-F39EE7DDAA52.root
http://opendata.cern.ch/eos/opendata/cms/mc/RunIISummer20UL16NanoAODv9/ZPrimeToTT_M1000_W100_TuneCP2_13TeV-madgraph-pythia8/NANOAODSIM/106X_mcRun2_asymptotic_v17-v2/2530000/7B2D5CD5-9CAE-C046-A9AB-50CE9D48B187.root
http://opendata.cern.ch/eos/opendata/cms/mc/RunIISummer20UL16NanoAODv9/ZPrimeToTT_M1000_W100_TuneCP2_13TeV-madgraph-pythia8/NANOAODSIM/106X_mcRun2_asymptotic_v17-v2/260000/1A50245D-8213-6340-8EA0-CB064EEC6AF3.root
http://opendata.cern.ch/eos/opendata/cms/mc/RunIISummer20UL16NanoAODv9/ZPrimeToTT_M1000_W100_TuneCP2_13TeV-madgraph-pythia8/NANOAODSIM/106X_mcRun2_asymptotic_v17-v2/270000/09FA6C37-21D6-7846-B3E1-F8086CBA0E9E.root
http://opendata.cern.ch/eos/opendata/cms/mc/RunIISummer20UL16NanoAODv9/ZPrimeToTT_M1000_W100_TuneCP2_13TeV-madgraph-pythia8/NANOAODSIM/106X_mcRun2_asymptotic_v17-v2/270000/3AAB5B1E-7169-9C4D-841C-CB2D6E40CBAE.root
http://opendata.cern.ch/eos/opendata/cms/mc/RunIISummer20UL16NanoAODv9/ZPrimeToTT_M1000_W100_TuneCP2_13TeV-madgraph-pythia8/NANOAODSIM/106X_mcRun2_asymptotic_v17-v2/270000/820C3EBC-0E1D-CE41-9418-FA1615123FC2.root
http://opendata.cern.ch/eos/opendata/cms/mc/RunIISummer20UL16NanoAODv9/ZPrimeToTT_M1000_W100_TuneCP2_13TeV-madgraph-pythia8/NANOAODSIM/106X_mcRun2_asymptotic_v17-v2/270000/CF54D079-349C-FB4F-B6E5-3D579D89EDE4.root
http://opendata.cern.ch/eos/opendata/cms/mc/RunIISummer20UL16NanoAODv9/ZPrimeToTT_M1000_W100_TuneCP2_13TeV-madgraph-pythia8/NANOAODSIM/106X_mcRun2_asymptotic_v17-v2/80000/E964C281-43FB-D349-A436-9A3FDA0BAA28.root
```
:::::::::::::::::::::::::::::::::
::::::::::::::::::::::::::::::::::::::::::::::::

## Figures

You can use standard markdown for static figures with the following syntax:

`![optional caption that appears below the figure](figure url){alt='alt text for
accessibility purposes'}`

![You belong in The Carpentries!](https://raw.githubusercontent.com/carpentries/logo/master/Badge_Carpentries.svg){alt='Blue Carpentries hex person logo with no text.'}

::::::::::::::::::::::::::::::::::::: callout

Callout sections can highlight information.

They are sometimes used to emphasise particularly important points
but are also used in some lessons to present "asides":
content that is not central to the narrative of the lesson,
e.g. by providing the answer to a commonly-asked question.

::::::::::::::::::::::::::::::::::::::::::::::::

::::::::::::::::::::: challenge

## Exercise 2: Inspect the data file

## Math
:::::::::::::: solution

One of our episodes contains $\LaTeX$ equations when describing how to create
dynamic reports with {knitr}, so we now use mathjax to describe this:

`$\alpha = \dfrac{1}{(1 - \beta)^2}$` becomes: $\alpha = \dfrac{1}{(1 - \beta)^2}$
::::::::::::::

Cool, right?
::::::::::::::::::::

::::::::::::::::::::::::::::::::::::: keypoints

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## Dataformats in CMS

Most previous releases of CMS open data have been in the Analysis Object Data (AOD) format.
This is a complex format and specific CMS software (CMSSW) is required in order to read and analyze it.

From 2015 data releases have been a slimmed-down format called MiniAOD, which has the same essential structure and software requirements for analysis as AOD. Essentially there are few
physics object collections and often the physics objects themselves are different.

For data released in 2016 and beyond a new format called NanoAOD is used. NanoAOD is not just simply slimmed-down MiniAOD. In contrast to AOD and MiniAOD which is stored in CMSSW C++ objects, NanoAOD is stored using ROOT TTree objects. You therefore do not need to use the CMS Virtual Machine or docker container to analyze NanoAOD data. NanoAOD can be analyzed using the ROOT program and/or python libraries capable of interpreting the ROOT's TTree structure.

TO-DO we can "borrow" information from below:

miniAOD links for use: [Getting started with miniAOD](https://opendata.cern.ch/docs/cms-getting-started-miniaod), [miniAOD in Workbook](https://twiki.cern.ch/twiki/bin/view/CMSPublic/WorkBookMiniAOD2016#High_level_physics_objects)

nanoAOD links for use: [Getting started with nanoAOD](https://opendata.cern.ch/docs/cms-getting-started-nanoaod)



::::::::::::::::::::::::::::::::::::: keypoints

- Use `.md` files for episodes when you want static content
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