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https://github.com/fhdsl/itn_course_search

A searchable table for ITN courses
https://github.com/fhdsl/itn_course_search

Last synced: 8 months ago
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A searchable table for ITN courses

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README 

          



# ITN\_course\_search



A auto-generating searchable table for ITN courses. The collection of

information about the courses is programmatically queried from GitHub

and processed..



## About



ITN\_course\_search uses the Github API to gather jhudsl and fhdsl

organization repositories, specifically ITN courses, that we have worked

on. It renders the table in a markdown-readable format. This repo has

workflows that trigger collection building and table rendering once a

week.



The table only includes repositories that meet the following

**required** criteria:



1.  Repository within the `jhudsl` or `fhdsl` organizations

2.  Public repository

3.  Have a homepage listed

4.  Have a description listed

5.  Have “itn” and “course” as part of the repository tags (e.g.,

    “itn-course”, or “itn” and “course”) (`str_detect(topics, "itn")` &

    `str_detect(topics, "course")`)

6.  Aren’t template per the tags (`!str_detect(topics, "template ")` –

    using a space because we want repos with tags of “templates” if the

    repo is providing templates, e.g., [the Overleaf/LaTeX

    Course](https://github.com/fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles))

7.  Has a repository tag for launch date specified by `launched-monYEAR`

    (e.g., `launched-aug2025` or `launched-dec2023`)



Shows the seven required criteria for including a course in the search table using the Overleaf course GitHub page as an example



## Interested in adding a course to the table?



At the moment, to add a course to the table, either wait for the repo to

fetch the collection data, or open a PR with a trivial change. A later

PR will add a way to manually trigger the workflow but this is not

available yet.



- ☐ Make sure the above required criteria (1-7) are met (jhudsl/fhdsl

  organization, public, homepage, description, itn-course tag, isn’t a

  template, launch date tag).



Make sure the rest of the information for the table (e.g., title, access

links/available course formats, etc.) is specified (where and how) the

query procedure expects (explained below).



### Course title specification



Course title specification is **within the course material files**,

usually the `index.Rmd` (or `_quarto.yml` for quarto book) file.



- ☐ Verify that the title is in the `index.Rmd` (or `_quarto.yml` for

  quarto book) file.

  - For Rmarkdown courses, need to follow the convention of being listed

    between `---` with `title:` at the front of the line

  - [Quarto books just replaces `title:` to extract the

    title.](https://github.com/fhdsl/ITN_course_search/blob/e389cbd43d2923649e5422c17189d53a812bfb13/scripts/query_collection.R#L149)



Rmarkdown courses specify the title in the index.Rmd file in the area between 3 dashes. The code looks for title with a colon at the beginning of the line to distinguish it from the subtitlet



Note that the query procedure looks for an `index.Rmd` file first, and

if it doesn’t find one in the repository, it then assumes it could be a

quarto course and looks for the `_quarto.yml` file next automatically.



A quarto course will have the title specified in the _quarto.yml file and replaces the title colon and space with nothing to extract the title.



### Available course formats specification



Available course formats specification is **within the course material

files**, usually the `index.Rmd` (or `index.qmd` for quarto book) file.



- ☐ Verify that available course formats are listed in `index.Rmd` (or

  `index.qmd` for quarto book) file, specifically for Coursera and

  Leanpub if applicable. (The GitHub source material and GitHub pages

  homepage information for the course table will be taken from the API

  call rather than this information, but it’s good practice to have both

  included within this chunk too)



Available Course Formats are listed in the index.Rmd file for the Overleaf course as an example for Rmarkdown courses



Note that the query procedure looks for an `index.Rmd` file first, and

if it doesn’t find one in the repository, it then assumes it could be a

quarto course and looks for the `index.qmd` file next automatically.



Available Course Formats are listed in the index.qmd file for the example quarto book from the Containers for Scientists example course



What the code is looking for exactly



Because the `get_linkOI()` function is set up to find line(s) with the

course format “pattern” (e.g., “Coursera” or “Leanpub”), then extract

all URLs from those lines, and then subset to the relevant URL if needed

(again using the “pattern”), these available course formats do not need

to be in an ordered, bulleted, or enumerated list. They could all be

mentioned in a notice box or paragraph. As long as the line with the

link says “Coursera” or “Leanpub”, this process will find and extract

the relevant links.



Available course formats do not need to be listed or enumerated in a bulleted or ordered list in order for the process to extract the information as seen with the NIH for Data Sharing course



### Necessary background information and learning objectives specification



Necessary background information and learning objectives are typically

specified as images (Google Slides grabbed with

`ottrpal::include_slide()` function) **within the course material

files**, usually the `01-intro.Rmd` (or `01-intro.qmd` for quarto book)

file. The code blocks where these are specified need to have specific

identifiers.



- ☐ Verify that the `01-intro.Rmd` (or `01-intro.qmd` file for quarto

  courses, [ex: Containers for

  Scientists](https://github.com/fhdsl/Containers_for_Scientists/blob/main/01-intro.qmd))

  file has identifiers for code blocks grabbing relevant google slide

  images.

  - LOs: `learning_objectives`

  - Audience: `for_individuals_who`

  - Topics covered: `topics_covered`

  - Pre-reqs (if applicable): `prereqs`



What the code is looking for exactly



The code in the `get_slide_info()` function within the

`query_collection.R` file looks for these code block identifiers exactly



Note that the query procedure first checks the course name to make sure

it’s not part of a special set of courses that don’t follow the usual

convention/location for this information. If the course isn’t in that

list, the procedure checks for the `01-intro.Rmd` file first and if that

file isn’t found it assumes it could be a quarto course and looks for

`01-intro.qmd` automatically next.



Example of learning objectives, audience, and topics covered code blocks from the Overleaf Course



Example of a prereqs code block from the GitHub Automation for Scientists Course



If a different file contains the information, you’ll need to edit the

`get_slide_info()` function within the `query_collection.R` file.



Examples where these blocks aren’t in the expected files include



- AI for Efficient Programming: They’re in

  [index.Rmd](https://github.com/fhdsl/AI_for_Efficient_Programming/blob/main/index.Rmd)

  instead.

- NIH for Data Sharing:

  - LOs are in their own file (and the chunk is commented out, but still

    accessible to this table building)

    [Learning\_objectives.Rmd](https://github.com/fhdsl/NIH_Data_Sharing/blob/main/Learning_objectives.Rmd)

    instead.

  - Audience and Topics covered are in

    [index.Rmd](https://github.com/fhdsl/NIH_Data_Sharing/blob/main/index.Rmd)

- AI for Decision Makers: They’re in 4 different files on 4 difference

  branches – one for each sub-course.



If your course’s introductory material isn’t located within the expected

`01-intro.Rmd` or `01-intro.qmd` file locations, [add the course name

here within

query\_collection.R](https://github.com/fhdsl/ITN_course_search/blob/e389cbd43d2923649e5422c17189d53a812bfb13/scripts/query_collection.R#L245)

and then [add the checking with the alternative file(s) for your course

within this

`else`](https://github.com/fhdsl/ITN_course_search/blob/e389cbd43d2923649e5422c17189d53a812bfb13/scripts/query_collection.R#L278),

following the example of AI for Efficient Programming and NIH for Data

Sharing, unless your course has sub-courses within the main repo (that

aren’t in the table and will need new rows) or information on branches

in which case, you’ll want to [follow the example used for AI for

Decision

Makers](https://github.com/fhdsl/ITN_course_search/blob/e389cbd43d2923649e5422c17189d53a812bfb13/scripts/query_collection.R#L528)

and use a [similar special

function](https://github.com/fhdsl/ITN_course_search/blob/e389cbd43d2923649e5422c17189d53a812bfb13/scripts/query_collection.R#L383)



### Audience specification



Audience specification is **not within the course material files** but

instead **is within the repository settings**



- ☐ Add repo tags for audience (at least one of the following):

  - `audience-software-developers`

  - `audience-researchers`

  - `audience-leaders`



Audience tags are specified in the repository settings and can be any combination of the choices



What the code is looking for exactly



[The code in the `query_collection.R` file that traverses the pages of

the GitHub API request results looks for these tags

exactly.](https://github.com/fhdsl/ITN_course_search/blob/e389cbd43d2923649e5422c17189d53a812bfb13/scripts/query_collection.R#L490-L496)



### Category specification



Category specification is **not within the course material files** but

instead **is within the repository settings**.



- ☐ Add repo tags for category (only one of the following):

  - `category-best-practices`

  - `category-software-dev`

  - `category-fundamentals-tools-resources`

  - `category-hands-on-practice`



Category tags are specified in the repository settings and should be only one of the choices. 



What the code is looking for exactly



[The code in the `query_collection.R` file that traverses the pages of

the GitHub API request results either looks for these tags exactly

(which is the case for `category-software-dev` and

`category-best-practices`), or it looks for the prefix

(`category-fundamentals-` rather than the full

`category-fundamentals-tools-resources` and `category-hands-on-` rather

than the full

`category-hands-on-practice`).](https://github.com/fhdsl/ITN_course_search/blob/8facb2d4ec0a9beca5612a3277457881a2e9bcee/scripts/query_collection.R#L498-L506)



### Funding



All courses with an `itn-course` or just `itn` tag are assumed to be ITN

funded. Add a `hutch-course` topic tag to the repo if it was Hutch

funded and should include Hutch branding as well.



### Cleaning up topic tags for display in the table



The `query_collection.R` file does NOT clean the topic tags data. Very

minimal cleaning is done within the `prep_table()` function within the

`format-tables.R` script. This minimal cleaning includes (1) inserting a

line break and a bullet point in place of every semicolon (which

separates the topic tags in the collection following querying) and (2)

replacing hyphens with a space. Special cases or substitutions of

cleaning are handled within `index.Rmd` of this ITN\_course\_search

repo, specifically in the `wrangle_data` code chunk.



Within that chunk …



1.  Use title case on the concepts with the `str_to_title()` function

    because the repo topic tags are all lower case.

2.  Ai –> AI (for the AI for Efficient Programming and AI for

    Decision Makers courses)

3.  Ci-Cd –> Continuous Integration/Continuous Deployment (for the

    Containers for Scientists Course)

4.  Nih –> NIH (for the Data Management and Sharing for NIH Proposals

    course)

5.  Hipaa –> HIPAA (for the Ethical Data Handling for Cancer Research

    course)

6.  Llm –> LLM (for the AI for Efficient Programming course)

7.  Phi –> (PHI) (for the Ethical Data Handling for Cancer Research

    course)

8.  Pii –> (PII) (for the Ethical Data Handling for Cancer Research

    course)

9.  Arxiv –> ArXiv (for the Overleaf and LaTeX course)

10. Latex –> LaTeX (for the Overleaf and LaTeX course)

11. And –> & (space saving, used for the Choosing Genomics Tools

    course )

12. Iv –> IV (for the Containers for Scientists course which we

    called Reproducibility Series IV)

13. Iii –> III (for the GitHub Automation for Scientists course which

    we called Reproducibility Series III)

14. Ii –> II (for the Adv Reproducibility course which we called

    Reproducibility Series II)



Add any additional specific changes to the topic tags for cleaning

within that chunk going forward.



### Adding icons



Audience (column is `BroadAudience`), course categories (column is

`Category`), and funding (column is `Funding`) information adds icons to

the data while building the tables. This is done within the

`prep_table()` function of the `format-tables.R` file. If you are

editing or adding a category to any of these, you will need to update

those `mutate` steps there.



## Important files



- `scripts/query_collection.R`: gathers information (audience, funding,

  topics, etc.) about ITN courses from their GitHub repos

- `resources/collection.tsv`: where the collection from

  `query_collection.R` is stored.

- `scripts/format-tables.R`: functions to wrangle course data and format

  course table

- `index.Rmd`: drives building each course specific html page and the

  overall course table

- `chunks/*Rmd` or `chunks/#.md`: chunks that we’ll borrow using

  `ottrpal::borrow_chapter` (from the `base_ottr:dev` container

  specified in `config_automation.yml`) and fill in {SPECIFIC INFO} for

  course (following the example of our cheatsheets repo). Because of

  this approach, a chunk will only inherit specific information if we

  pass it as a tag replacement. In other words, not every piece of

  information in each row/about a specific course will be available to

  the chunks, only the information we specify as a tag replacement).

  - about: `aboutCourse.md` with “{COURSE\_DESCRIPTION}”,

    “{COURSE\_CATEGORY}”, and “{COURSE\_LAUNCH}” to be provided/replaced

  - audience: `audienceCourse.Rmd` with “{FOR\_SLIDE\_LINK}” and

    “{COURSE\_AUDIENCE}” to be provided/replaced

  - format: `formatFullCourse.Rmd` with “{BOOKDOWN\_LINK}”,

    “{GITHUB\_LINK}”, “{COURSERA\_LINK}”, and “{LEANPUB\_LINK}” to be

    filled in

  - funding: `fundingFullCourse.Rmd` with “{hutch\_funded}” to be filled

    in

  - LOs: `loCourse.Rmd` with “{LO\_SLIDE\_LINK}” to be provided/replaced

  - concepts discussed: `conceptsCourse.Rmd` with

    “{CONCEPTS\_SLIDE\_LINK}” tag to be provided/replaced

  - pre-requisites: `prereqsCourse.Rmd` with “{PREREQ\_SLIDE\_LINK}” and

    “{GITHUB\_LINK}” tags to be provided/replaced. If there are

    pre-requisites for a course, and you want to add a direct link to

    them, look at or add to the conditionals in this particular `.Rmd`

- `*_template.Rmd`: the template for driving course specific pages.

  - `single_course_template.Rmd`: layout for building general course

    pages

  - `ai_course_template.Rmd`: layout for AI for Decision Makers course

    page

- `*_coursePage.html`: the output course specific html pages