Move GEO metadata script to this repo

Turns out that merging an entire repo into another repo (and preserving history) is easier than (1) moving a directory from one repo into another, which is easier than (2) moving an individual file from one repo to another...

Here are the steps I used to copy a Python file from another repo: https://github.com/CRI-iAtlas/synapse-utils/blob/master/python/data_manifest.py

... into the scripts folder of this repo.

(Might be worth turning into a script at some point. @kdaily might have better ideas how to do this.)

Starting in the folder for this repo, move up to the parent directory and create a temp folder; cd into that folder.

jaeddy:~/code/github/projects/syndccutils$ cd ..
jaeddy:~/code/github/projects$ mkdir temp
jaeddy:~/code/github/projects$ cd temp/

Clone the CRI-iAtlas/synapse-utils repo into a new local folder under temp; cd into synapse-utils.

jaeddy:~/code/github/projects/temp$ git clone https://github.com/CRI-iAtlas/synapse-utils
Cloning into 'synapse-utils'...
remote: Counting objects: 35, done.
remote: Total 35 (delta 0), reused 0 (delta 0), pack-reused 35
Unpacking objects: 100% (35/35), done.
jaeddy:~/code/github/projects/temp$ cd synapse-utils/

Locate the file I want to move (python/data_manifest.py).

jaeddy:~/code/github/projects/temp/synapse-utils$ ls
README.md            nbs/                 python/              synapse-utils.Rproj
jaeddy:~/code/github/projects/temp/synapse-utils$ ls python/
data_manifest.py

Filter the branch to only keep files matching the one I want to move (this is where things get ugly...); note: good to remove the origin remote to avoid accidentally pushing changes to the CRI-iAtlas/synapse-utils repo.


jaeddy:~/code/github/projects/temp/synapse-utils$ git remote rm origin # 4 safety
jaeddy:~/code/github/projects/temp/synapse-utils$ git filter-branch --index-filter 'git read-tree --empty; git reset $GIT_COMMIT -- python/data_manifest.py' -- --all -- python/data_manifest.py
Rewrite cd06a2e77d805cf151ebb7a766fd2b20557e2d76 (1/3) (0 seconds passed, remaining 0 predicted)    Unstaged changes after reset:
D   python/data_manifest.py
Rewrite 4e5451395b5c5b79c00442a0620b0c785a6b56ec (2/3) (1 seconds passed, remaining 0 predicted)    Unstaged changes after reset:
D   python/data_manifest.py
Rewrite 1efbede4c9ece810514436d220dbf6638e1cc52e (2/3) (1 seconds passed, remaining 0 predicted)    Unstaged changes after reset:
D   python/data_manifest.py

Ref 'refs/heads/master' was rewritten Ref 'refs/remotes/origin/master' was rewritten WARNING: Ref 'refs/remotes/origin/master' is unchanged


5. Check the results... File is still within the `python` folder; let's fix that too.
```console
jaeddy:~/code/github/projects/temp/synapse-utils$ ls
python/

Filter again: only keep files (just one because of step 4) in the python folder and move them to top level.

jaeddy:~/code/github/projects/temp/synapse-utils$ git filter-branch -f --subdirectory-filter python/ -- --all
Rewrite 504cc9d7cf40321c19c25f0732f4abaf242896c7 (3/3) (0 seconds passed, remaining 0 predicted)
Ref 'refs/heads/master' was rewritten
Ref 'refs/remotes/origin/master' was rewritten
WARNING: Ref 'refs/remotes/origin/master' is unchanged

Check results... Success!

jaeddy:~/code/github/projects/temp/synapse-utils$ ls
data_manifest.py

Switch back to the syndccutils folder.

jaeddy:~/code/github/projects/temp/synapse-utils$ cd ../../syndccutils/

Set up a remote named temp pointing to the relative path of synapse-utils; fetch the remote.

jaeddy:~/code/github/projects/syndccutils$ git remote add temp ../temp/synapse-utils/
jaeddy:~/code/github/projects/syndccutils$ git fetch temp
warning: no common commits
remote: Counting objects: 9, done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 9 (delta 2), reused 0 (delta 0)
Unpacking objects: 100% (9/9), done.
From ../temp/synapse-utils
+ fed86c7...8bcae2e master     -> temp/master  (forced update)

Create a new branch named temp that tracks our new remote "repo".

jaeddy:~/code/github/projects/syndccutils$ git branch temp remotes/temp/master
Branch temp set up to track remote branch master from temp.

Merge the temp branch into `master.

jaeddy:~/code/github/projects/syndccutils$ git merge --allow-unrelated-histories temp
Merge made by the 'recursive' strategy.
data_manifest.py | 123 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 123 insertions(+)
create mode 100644 data_manifest.py

Check results... Success!

jaeddy:~/code/github/projects/syndccutils$ ls
DESCRIPTION           README.md             data/                 mock_datatable_files/ scripts/
NAMESPACE             Rmd/                  data_manifest.py      portal-dashboard/     syndccutils.Rproj
R/                    config/               mock_chart_files/     python/               tests/
~/code/github/projects/syndccutils$ git status
On branch master
Your branch is ahead of 'origin/master' by 4 commits.
(use "git push" to publish your local commits)

Move the new file to the scripts folder and push changes.

jaeddy:~/code/github/projects/syndccutils$ mv data_manifest.py scripts/
jaeddy:~/code/github/projects/syndccutils$ git add scripts/data_manifest.py
jaeddy:~/code/github/projects/syndccutils$ git commit -m "stash data_manifest.py in scripts dir"
[master 7be09c2] stash data_manifest.py in scripts dir
1 file changed, 123 insertions(+)
create mode 100644 scripts/data_manifest.py
jaeddy:~/code/github/projects/syndccutils$ git push
Counting objects: 14, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (11/11), done.
Writing objects: 100% (14/14), 2.83 KiB | 966.00 KiB/s, done.
Total 14 (delta 4), reused 0 (delta 0)
remote: Resolving deltas: 100% (4/4), completed with 1 local object.
To https://github.com/Sage-Bionetworks/syndccutils
cfa7e2b..7be09c2  master -> master

Clean up: remove the temp remote.

jaeddy:~/code/github/projects/syndccutils$ git remote rm temp

Sage-Bionetworks / syndccutils

Move GEO metadata script to this repo #58