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Princeton-LSI-ResearchComputing / tracebase

Mouse Metabolite Tracing Data Repository for the Rabinowitz Lab
MIT License
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Convert google docs links in TraceBaseDocs to Markdown #757

Open hepcat72 opened 9 months ago

hepcat72 commented 9 months ago

FEATURE REQUEST

Inspiration

I was working on issue #705 and noted that I needed to change information in a google doc that I didn't have permission to edit. However, it seems that this and other google docs linked inside the markdown were not intentionally created. They were assumed to have all been converted to markdown.

Description

Convert all google docs linked in the documentation to markdown saved in the repo (except for links that are to templates and forms that are intended to be used from the tracebase interface.

Alternatives

None

Dependencies

None

Comment

slack

I'm not sure what the document is, but I don't own it. Most of the docs for TraceBase are now at https://princeton-lsi-researchcomputing.github.io/tracebase/ and are generated from the source code

Yes, and this document is linked from that code in step 9 under the Step-by-step instructions (see attached screenshot). Looks like @mneinast is the owner.

how_to_upload_-_tracebase_documentation_720 Should we remove that from the docs?

Looks like something Michael missed when he converted to markdown. I say we just put the contents into the markdown docs.

ISSUE OWNER SECTION

Assumptions

  1. List of assumptions that the code will not explicitly address/check
  2. E.g. We will assume input is correct (explaining why there is no validation)

Limitations

  1. A list of things this work will specifically not do
  2. E.g. This feature will only handle the most frequent use case X

Affected Components

Requirements

DESIGN

Interface Change description

None provided

Code Change Description

None provided

Tests

mneinast commented 9 months ago

ah good catch - i've given you permission to edit that google doc.

I agree that all of these pages should be markdown docs so that any of us can edit them.

hepcat72 commented 9 months ago

I also just noticed that the website is rendering these steps as 2 numbered lists (1-4 and 1-9), whereas it should contain a single 3-member numbed list with nested numbered lists:

  1. Create a Sample Sheet (see also How to label sample information) Copy the TraceBase Animal and Sample Table Template.

    1. Fill in the Animals sheet. Give each mouse in your study a unique ID.
    2. Fill in the Samples sheet. Ensure that each Sample Name matches the sample names in your AccuCor/Isocorr files. If you have a Tissue that is not included in the existing list, please label it as you would like to in the Tissues sheet and tell the developer you have a new Tissue.

    3. Fill in Treatments sheet (optional) with any treatments not captured by other columns (ie Diet). Use no treatment if applicable. Provide a list of treatments used in the study, along with a description of each.

      Note: In general, you should NOT edit your AccuCor files. It's simplest and often best to resolve issues by editing your animal and sample table file.

  2. Upload your data on Google Drive

    1. Create a folder for your study in the TraceBase Study Submission folder on Google Drive
    2. Create a folder with your name (if it doesn't already exist).
    3. Create a new folder for this study.
    4. Copy the Animal and Sample spread sheet and any AccuCor files that should be included in the study

  3. Submit the TraceBase Study Submission form. Complete the following:

    1. Study Name
    2. Link to Google Drive folder with study submission.
    3. Mass Spectrometry Details (see How to label Mass Spec Run Information)
hepcat72 commented 4 months ago

This was fixed by #797, however, the markdown needs to be re-rendered as HTML. I.e. The markdown was updated to remove the google doc links, but the navigable docs need to be re-generated on https://princeton-lsi-researchcomputing.github.io/