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feat: Add generic SODAR ingest command #199

Merged
merged 72 commits into from
Jan 9, 2024
Merged

feat: Add generic SODAR ingest command #199

merged 72 commits into from
Jan 9, 2024

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sellth
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@sellth sellth commented Nov 7, 2023 •
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re do of #168

This adds a generic sodar ingest command which tries to mimic the base functionality of irsync, boosted by the power of using SODAR's API. Features include:

  • no dependency on icommands; uses iinit session file if present, asks for password otherwise

  • multiple source locations, single target collection

  • recursive file matching

  • creation of matched sub-folders in iRODS

  • destination either as iRODS path or SODAR LZ UUID

  • uses SODAR API for UUID destination & for querying LZ collections

  • computes local checksums if missing

  • triggers remote iRODS checksum computation

  • scriptable; all user input can be skipped

  • has a cool progress bar

  • rebase after PR feat: Common functions for interfacing with python-irodsclient #202 is merged.

@sellth
feat: Common functions for interfacing with python-irodsclient
95c76ab
@sellth
fix tests
6b72d9d
@sellth
fix chksum test
2636c8c
@sellth
move all basic irods logic into new class iRODSCommon
779d402
@sellth
adapt tests to new class
1f58f7e
@sellth
iRODSTransfer is now a child of iRODSCommon
da40f44
@sellth
flake8
d8dbbbf
@sellth
custom irods_env_path support; pass along kwargs
064a1e6
@sellth
flake8
7837b2a
@sellth
make internal variables private
32aaa5f
@sellth
cleanup
f36efff
@sellth
improved docstrings
523bc28
@sellth
TransferJob computes file size during init
c62faf1
@sellth
flake8
f66cc42
@sellth
using attrs import instead of attr shadow
e2bda03
@sellth
show file counts in progress bar
9d480c9
@sellth
add recursive put
179aee5
@sellth
use proper context manager
4b0e1d2
@sellth
add sync mode; check for existing files on remote
4bde914
@sellth
do not clean up session too soon
538e9a8
@sellth
prepare TransferJob to also handle gets
41c8e12
@sellth
add get method
5df1d7e
@sellth
restructure session creation; check valid token every time
205c6e4
@sellth
create irods sessions dynamically
27e54da
@sellth
also check for timed out session token
f1e5105
@sellth
make session available as property
78e01a1
@sellth
linting
e1625a8
@sellth
remove irods session context manager and multiple sessions
1a58949
sellth and others added 18 commits December 8, 2023 16:42
@sellth
check for missing API token
d1a599b
@sellth
adjusted docstring
9a6cb90
@sellth
add documentation for sodar ingest command
db872b4
@sellth
check if file already exists in iRODS and skip
4e0ffee
@sellth
moved remote file check to wrapper
2b24a8c
@sellth
Clean exit code when nothing to do.
48d33a5
@sellth
upgrade python-irodsclient version
5650dd8
@sellth
add support for exclude patterns
d3d0312
@sellth
fix excludes
31b6416
@sellth
sort file list for output
35eea47
@sellth
reworked hashsum logic
6b96f59 
- now checks for .md5 file on disk
- loads hash if found
- computes hash if not found and stores on disk
- checks iRODS for existing file using hash
@sellth
increased iRODS session timeout
040bf38
@sellth
don't re-create already existing collections
026d93a
@sellth
re-write of command to use irods_common.py
7ee5eb4
@sellth
fix infinite loop when only 1 collection is present
f179b49
@sellth
increase test coverage
4490dde
@sellth
accomodate final subcollection as target
70908b7
@sellth
transfer jobs as tuple, not set
2fa772c
@sellth sellth changed the title feat: SODAR ingest command based on irods-pythonclient feat: Add generic SODAR ingest command Dec 8, 2023
Nicolai-vKuegelgen
Nicolai-vKuegelgen approved these changes Jan 9, 2024
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@Nicolai-vKuegelgen Nicolai-vKuegelgen left a comment

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LGTM

@sellth sellth enabled auto-merge (squash) January 9, 2024 14:33
@sellth sellth disabled auto-merge January 9, 2024 14:34
@sellth sellth enabled auto-merge (squash) January 9, 2024 14:35
@sellth sellth merged commit 8548c97 into main Jan 9, 2024
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@sellth sellth deleted the ingest branch January 9, 2024 14:37
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@Nicolai-vKuegelgen Nicolai-vKuegelgen Nicolai-vKuegelgen approved these changes

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@sellth @Nicolai-vKuegelgen