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pore-c is interesting - git push lfs issue



Hello,

pore-c has a series of dependencies that are of interest for Debian as a
whole and still missing

python3-pyarrow
         python3-streamz,
         python3-pyranges,
         python3-pairtools,
         python3-ncls,
         python3-intake

The package builds but does not run without these. In an attempt to push
what I have, I ran into

remote: GitLab: LFS objects are missing. Ensure LFS is properly set up
or try a manual "git lfs push --all".
To salsa.debian.org:med-team/pore-c.git
! [remote rejected]master -> master (pre-receive hook declined)
! [remote rejected]pristine-tar -> pristine-tar (pre-receive hook declined)
! [remote rejected]upstream -> upstream (pre-receive hook declined)
error: failed to push some refs to 'salsa.debian.org:med-team/pore-c.git'
$ git lfs push --all
Specify a remote and a remote branch name (`git lfs push origin master`)
$ git lfs push origin master
Locking support detected on remote "origin". Consider enabling it with:
 $ git config
lfs.https://salsa.debian.org/med-team/pore-c.git/info/lfs.locksverify true
LFS upload failed:cts:   0% (0/23), 0 B | 0 B/s
 (missing) tests/data/NlaIII_run01_GRCh38.haplotagged.bam
(1214675dd07b5a072ecbe9bf22ae7513c6f2c6b1435a86c0b8b93e6e85da6293)
 (missing) tests/data/NlaIII_GRCh38.contacts.parquet/part.0.parquet
(94b3ebd6d94f10a2de3093d46473a51c003cd41713c9b3712d56ab30b676e193)
 (missing) tests/data/NlaIII_GRCh38.concatemers.parquet/_metadata
(91d16d1ec1483db8b8080179ba9b485dce5bb625110768c23c348df6bef19e60)
 (missing) tests/data/GM12878_NlaIII_reads.tsv
(7ce4529be82183332f9f3e37fa85f19a0a2aa5afa887f742145016bb2edcca53)
 (missing) tests/data/GRCh38.chromsizes
(50e35247e1305e2a0a1fd1b7c07ff3576cec9389382d611c19eb0055633fc82b)
 (missing) tests/data/GM12878.phased.conf.vcf.gz
(a7efa2fe2641ac2c76c0596ad628f90d9a8531856115f8b840379e95ee0709c8)
 (missing) tests/data/GM12878_NlaIII_reads.fq.gz
(9d722847361b9c2d037d50d7e9cd126c958f5a0f689694fe5dfef37ae3ac1c4a)
 (missing) tests/data/GRCh38.fasta.gz.gzi
(be5698ffc76f644f9483d04b3d58c8c2c7f0ba6a1fd37e78ac5eb99f5901e4f3)
 (missing) tests/data/NlaIII_GRCh38.contacts.parquet/_common_metadata
(950401c687f40c995d415799583fa38ed1e063ceddd500d77c182388dda35d00)
 (missing)
tests/data/NlaIII_run01_GRCh38.align_table.parquet/_common_metadata
(82b94a7abce2fe49c8321de6ce5cb127c832e6de3dd74aa1c0e756098ab26e86)
 (missing) tests/data/NlaIII_GRCh38.vd.fragments.parquet/_metadata
(b97516f9b93688053d27efe7f604fde9573e63444354e42d31507922df8ca3b1)
 (missing) tests/data/GRCh38.fasta.gz.fai
(cbd68404c124a5e3ee4e4335bf907cbd0db00b1a077d695042495260716dfd9b)
 (missing) tests/data/GRCh38.fasta.gz
(79582e1bbeec718000027048849a6413ee576f17c1d9aa877211db1f8d6a7b1b)
 (missing) tests/data/NlaIII_run01_GRCh38.read_sort.bam
(b451a851e775d7c364eb844feafa1a0054939be6035b0e6cfb808d2e13db2f82)
 (missing) tests/data/test_ns.sam
(d9a0a31551e5cec6444e9fbfb6b87f0b644ef5a4ab9bad09329a856eb39160de)
 (missing) tests/data/GM12878.phased.conf.vcf.gz.tbi
(0db1dcb337cfe2d23dd6d2369b49ec1414961ee2305e635ca6af7289aacf16ab)
 (missing) tests/data/NlaIII_GRCh38.contacts.parquet/_metadata
(83aaf5e4f09b9cafa30446bd3f8016164c450d23ba840cbd62bcef55049e3356)
Uploading LFS objects:   0% (0/23), 0 B | 0 B/s, done.
 (missing) tests/data/NlaIII_GRCh38.concatemers.parquet/part.0.parquet
(24ce696c45a21106d36ca97278f49ac707c1d77b97f86c77408ae0ee42c9905f)
 (missing) tests/data/NlaIII_run01_GRCh38.align_table.parquet/_metadata
(42660830367bfa83ef9b4a5a501bdf0e19fd6c3a826210e8098e297443aad04e)
 (missing) tests/data/NlaIII_GRCh38.vd.fragments.parquet/part.0.parquet
(6684beefe4fa555e3ef5ba2dca13769cda043424c08ac8f2b647471d7b587c80)
 (missing)
tests/data/NlaIII_run01_GRCh38.align_table.parquet/part.0.parquet
(8fecdb8434662f0c0892dcdd103078ff2c48c96f40cc3546a9e76638b9c42740)
 (missing)
tests/data/NlaIII_GRCh38.concatemers.parquet/_common_metadata
(ec1a8f121551b7d0bccc8f2eb4097742029b30068313dc15a932b701e4d91b0c)
 (missing)
tests/data/NlaIII_GRCh38.vd.fragments.parquet/_common_metadata
(2902630654ed49ea1ea6648dc21bba0c20b499fa6182a6b2ec6b531b7564cb6e)
hint: Your push was rejected due to missing or corrupt local objects.
hint: You can disable this check with: 'git config
lfs.allowincompletepush true'

Well, kind of curious I did enable it, but could not push --all. After
also pushing upstream, I went for pristine-tar without lsf


$ git push --set-upstream origin pristine-tar
Enumerating objects: 4, done.
Counting objects: 100% (4/4), done.
Delta compression using up to 2 threads
Compressing objects: 100% (3/3), done.
Writing objects: 100% (4/4), 3.11 KiB | 3.11 MiB/s, done.
Total 4 (delta 0), reused 0 (delta 0), pack-reused 0
To salsa.debian.org:med-team/pore-c.git
* [new branch]      pristine-tar -> pristine-tar
Branch 'pristine-tar' set up to track remote branch 'pristine-tar' from
'origin'.
moeller@steffen-laptop-debian:~/git/med-team/pore-c/pore-c$ git checkout
master
Downloading tests/data/GM12878.phased.conf.vcf.gz (516 KB)
Error downloading object: tests/data/GM12878.phased.conf.vcf.gz
(a7efa2f): Smudge error: Error downloading
tests/data/GM12878.phased.conf.vcf.gz (a7efa2fe2641ac2c76c0596ad628f90d9a853
1856115f8b840379e95ee0709c8):
[a7efa2fe2641ac2c76c0596ad628f90d9a8531856115f8b840379e95ee0709c8]
Object does not exist on the server or you don't have permissions to
access it: [404]
Object does not exist on the server or you don't have permissions to
access it

Errors logged to
/home/moeller/git/med-team/pore-c/pore-c/.git/lfs/logs/20200608T030628.335563029.log
Use `git lfs logs last` to view the log.
error: external filter 'git-lfs filter-process' failed
fatal: tests/data/GM12878.phased.conf.vcf.gz: smudge filter lfs failed
moeller@steffen-laptop-debian:~/git/med-team/pore-c/pore-c$ git branch
 master
* pristine-tar
 upstream

Hm. Ok. This is all new to me. I know about the large file support, but
why is this enforced on me when working with a regular tarball that is
not even big (most likely because of those special files pointing to
external data). My immediate response would be to remove the test data
and find other ways to perform the testing.

Steffen



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