Comments (3)
I ran the following commands:
# https://rtyley.github.io/bfg-repo-cleaner/
# https://confluence.atlassian.com/bitbucket/use-bfg-to-migrate-a-repo-to-git-lfs-834233484.html
# Outside of original repository
git clone --mirror [email protected]:hetio/hetionet.git hetionet-bfg.git
java -jar ~/Downloads/bfg-1.13.0.jar \
--convert-to-git-lfs "*.{bz2,gz,xz,zip}" \
hetionet-bfg.git
cd hetionet-bfg.git
git reflog expire --expire=now --all && git gc --prune=now --aggressive
git lfs fetch --all
git lfs push --all origin master
# From within original repository
git checkout -b master-bfg
git remote add bfg /home/dhimmel/Desktop/hetionet-bfg.git
git fetch bfg
git reset --hard bfg/master
git push --set-upstream origin master-bfg
The bfg command produced the following output:
Using repo : /home/dhimmel/Desktop/hetionet-bfg.git
Found 44 objects to protect
Found 9 commit-pointing refs : HEAD, refs/heads/master, refs/heads/matrix, ...
Protected commits
-----------------
These are your protected commits, and so their contents will NOT be altered:
* commit 23f6117c (protected by 'HEAD')
Cleaning
--------
Found 70 commits
Cleaning commits: 100% (70/70)
Cleaning commits completed in 3,231 ms.
Updating 8 Refs
---------------
Ref Before After
------------------------------------------
refs/heads/master | 23f6117c | 3cf25f2c
refs/heads/matrix | 3a09715e | f7190594
refs/heads/neo4j-2.3 | 7eec671b | ec10b0a4
refs/heads/neo4j-3.0 | 7d3d257c | 95818820
refs/heads/pre-lfs | 23f6117c | 3cf25f2c
refs/pull/11/head | 3a09715e | f7190594
refs/pull/11/merge | caaedf26 | 5af06766
refs/tags/v1.0.0 | 4933ca17 | 3bbc130a
Updating references: 100% (8/8)
...Ref update completed in 33 ms.
Commit Tree-Dirt History
------------------------
Earliest Latest
| |
DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDmmmm
D = dirty commits (file tree fixed)
m = modified commits (commit message or parents changed)
. = clean commits (no changes to file tree)
Before After
-------------------------------------------
First modified commit | 0009918a | 38873689
Last dirty commit | 9f214ab7 | ff4f2eef
Changed files
-------------
Filename Before & After
--------------------------------------------------------------------------
hetionet-v1.0-edges.sif.gz | 81f59db4 ⇒ 90dc2b88
hetionet-v1.0-perm-1.db.tar.bz2 | f55f7c4d ⇒ 3459eedb
hetionet-v1.0-perm-1.json.bz2 | 735791b0 ⇒ 430b6f3e
hetionet-v1.0-perm-2.db.tar.bz2 | a49c15dc ⇒ 76303e92
hetionet-v1.0-perm-2.json.bz2 | d92bd3d6 ⇒ 928c919d
hetionet-v1.0-perm-3.db.tar.bz2 | d27169c3 ⇒ ae4716bb
hetionet-v1.0-perm-3.json.bz2 | 5ecba96e ⇒ 1e420742
hetionet-v1.0-perm-4.db.tar.bz2 | 3bbf56d4 ⇒ a832f8b9
hetionet-v1.0-perm-4.json.bz2 | 2b5ca7b0 ⇒ cbeb6364
hetionet-v1.0-perm-5.db.tar.bz2 | f0df2d09 ⇒ 381b0472
hetionet-v1.0-perm-5.json.bz2 | c51dcd1e ⇒ d18d6af3
hetionet-v1.0.db.tar.bz2 | 152c7796 ⇒ 76141ba3, 36ae082b ⇒ df19a5fc
hetionet-v1.0.json.bz2 | 54177a6a ⇒ ce8ba918
In total, 267 object ids were changed. Full details are logged here:
/home/dhimmel/Desktop/hetionet-bfg.git.bfg-report/2018-11-07/11-21-52
BFG run is complete! When ready, run: git reflog expire --expire=now --all && git gc --prune=now --aggressive
hetionet-bfg.git.bfg-report/2018-11-07/11-21-52
contains the three text files:
When running git push --set-upstream origin master-bfg
I kept getting
open /home/dhimmel/Documents/serg/rephetio/hetionet/hetnet/permuted/neo4j/hetionet-v1.0-perm-1.db.tar.bz2: no such file or directory
error: failed to push some refs to '[email protected]:hetio/hetionet.git'
I added --no-verify
, which made the upload work. Hopefully, this isn't too dangerous!.
So this repo now has a master-bfg
branch, which I will switch to master
.
from hetionet.
The master
branch prior to the BFG rewrite is available at https://github.com/hetio/hetionet/tree/pre-lfs
from hetionet.
I have decided to undo this, but keep the BFG rewrite around in a bfg-lfs-rewrite
branch. I decided it was too risky for too little benefit. The repo size is not too big at the moment. Specifically, I was having issues migrating #11 to be based on the rewritten master
. I tried cherry-picking, checking out individual files, and rebasing... none which worked. I also got errors during the rebase:
Encountered 5 file(s) that should have been pointers, but weren't:
hetnet/permuted/neo4j/hetionet-v1.0-perm-1.db.tar.bz2
hetnet/permuted/neo4j/hetionet-v1.0-perm-2.db.tar.bz2
hetnet/permuted/neo4j/hetionet-v1.0-perm-3.db.tar.bz2
hetnet/permuted/neo4j/hetionet-v1.0-perm-4.db.tar.bz2
hetnet/permuted/neo4j/hetionet-v1.0-perm-5.db.tar.bz2
So I'm going back!
from hetionet.
Related Issues (20)
- Local files HOT 2
- Multiple Match Queries Not Working HOT 2
- Question About Hetionet's Dictionary HOT 3
- How to add new disease and anatomy nodes HOT 2
- Providing a dump version of Hetionet HOT 11
- http://neo4j.het.io/browser/ time out HOT 4
- Neo4J instance down (?) HOT 7
- Updated TSV version HOT 6
- graph.db database offline in neo4j HOT 3
- neo4j website down HOT 6
- Hetionet Browser is down HOT 4
- Mapping to original databases HOT 2
- Cannot map non-existing file HOT 5
- Do any relations imply another relation? HOT 1
- Connectivity Search Automated Query Question HOT 8
- Docker compatibility question HOT 4
- Question on metrics HOT 1
- What does it mean if something up regulates a disease in this context? HOT 3
- Speeding up data import to Neo4j v5 and CSV format data HOT 2
- Inquiry about metapaths from 2017 Paper "Systematic Integration of Biomedical Knowledge Prioritizes Drugs for Repurposing" HOT 7
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hetionet.