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Fix north-pacific-gyre hierarchy #1462

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HepoH3
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@HepoH3 HepoH3 commented Sep 6, 2024

After c24e262 Nelle's samples files processed as if they were placed directly in 'north-pacific-gyre' (see listing below), while right now they placed in '2012-07-03' subdirectory. Running this commands will produce an error instead of 18 lines of result.

## Nelle's Pipeline: Checking Files
Nelle has run her samples through the assay machines
and created 17 files in the `north-pacific-gyre` directory described earlier.
As a quick check, starting from the `shell-lesson-data` directory, Nelle types:
```bash
$ cd north-pacific-gyre
$ wc -l *.txt
```
The output is 18 lines that look like this:
```output
300 NENE01729A.txt
300 NENE01729B.txt
300 NENE01736A.txt
300 NENE01751A.txt
300 NENE01751B.txt
300 NENE01812A.txt
... ...

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After c24e262 Nelle's samples files processed as if they were placed
directly in 'north-pacific-gyre', while right now they placed in
'2012-07-03' subdirectory.
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@HepoH3
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HepoH3 commented Sep 6, 2024

I found out that there are two north-pacific-gyre dirs:

  • /shell-lesson-data/north-pacific-gyre
  • /filesystem/Users/nelle/north-pacific-gyre

The first one already contains this files as expected (without 2012-07-03 directory). As I see now, the exercise should be executed using this folder. However, I'm a bit confused: what is the filesystem directory for, then? In order to generate .svg figures? Should it be consistent with the shell-lesson-data directory? If so, this PR still applies.

@bkmgit
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bkmgit commented Sep 7, 2024

Thanks for the pull request. Checking it.

@gcapes
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gcapes commented Sep 9, 2024

There should be a zip file to download, which contains the shell-lesson-data directory. This is what learners should be using to follow the lesson (detailed on the setup page). It looks like there are also some legacy pages left around which could maybe be removed? It doesn't look like the filesystem directory is used for anything(?)

When these lessons moved over to being built with R, it looks like the makefile was deleted but it contained a rule to make the zip file, which was

##
## Shell lesson specific commands
## =================================================

ZIPFILE = data/shell-lesson-data.zip

.PHONY : zip
## zip              : create zip file for learners to download
zip : shell-lesson-data
	zip -r -FS $(ZIPFILE) $<

I've had a quick search through the lesson material and I don't think there's a 2012-07-03 directory mentioned, so I think it's all good how it is?

@HepoH3
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HepoH3 commented Sep 10, 2024

Okay, I think I should close this PR then😅

@HepoH3 HepoH3 closed this Sep 10, 2024
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3 participants