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github.com/ome/omero-cli-transfer

An OMERO CLI plugin for creating transfer packets between OMERO servers.
https://github.com/ome/omero-cli-transfer

marking as release candidate

4f1940919df376a70a4d065868fd5a70cbed22e3 authored 11 months ago by Erick Martins Ratamero <[email protected]>
sets action to "published" so it runs on prereleases (#80)

40ee7a7c5458e980638ca5800f1df3a0c4ef59d8 authored 11 months ago by Erick Martins Ratamero <[email protected]>
Changing from negative-id `CommentAnnotations` and `MapAnnotations` to `XMLAnnotations` for non-OME data model info (#74)

* schemas!

* better schemas!

* starting to move towards XML annotations

* creating XML ...

e8fc2809628fecb98c369145b1f382637b60d9e9 authored 11 months ago by Erick Martins Ratamero <[email protected]>
adds a --metadata-only option to pack (#72)

* adds a --server option to pack

* removed black autoformatting

* fix too many blank lines...

97cf7efc718cf58c1e16d53f0d408344f78daa94 authored 11 months ago by Guillaume Gay <[email protected]>
Update infra (#75)

* bump actions/checkout to v4

* use branch

* remove local copy of files from omero-test-in...

009504b7874c6125f01fdb0310ff7bae9d04710f authored 12 months ago by jean-marie burel <[email protected]>
Added plugin interface for external packers (#73)

* added plugin interface for pack

* added usage instructions for plugins to readme and added ...

760b7893877563435adf0d0fe2fcd407a559395d authored about 1 year ago by Christoph Moehl <[email protected]>
migrate to Docker Compose V2 using (#70)

3a1c056fa11048afeb513630bc318b73924e1ca6 authored about 1 year ago by Kiya Govek <[email protected]>
Packing and unpacking figures (#67)

* help text for figure pack/unpack

* added arguments

* stub `populate_figures`

* grabbi...

1f3e8c34802b17ac059a5c5ae98af025fb32ff99 authored about 1 year ago by Erick Martins Ratamero <[email protected]>
Human readable pack (#65)

* scaffold for simple pack

* simple test case working

* new tests, all passing

* improv...

baeb5094430820bf8b0baa499a8faee70e026b09 authored over 1 year ago by Erick Martins Ratamero <[email protected]>
Update setup.py

64e6d9f5b0e081ada14426b43850125992bbe590 authored over 1 year ago by Erick Martins Ratamero <[email protected]>
updated ome-types version (#62)

c78060043d39ef7adfcac8e79d896649a6f31381 authored over 1 year ago by Erick Martins Ratamero <[email protected]>
using relative paths for `--filelist` as well (#61)

* using relative paths for `--filelist` as well

* tests passing

e033ac2e40d9cef0a5b777cd56b6b9016eb8eaaa authored over 1 year ago by Erick Martins Ratamero <[email protected]>
prepare now uses relative paths (#60)

a13e385f079f8c664f4f9e647275a2d7c4706667 authored over 1 year ago by Erick Martins Ratamero <[email protected]>
Fix typo in README.md (forge not force, and single =) (#58)

* Fix typo in README.md (forge not force)

* fix conda install version specification

3ba94d0d5140937d62ca8dcc4f138dbc91479a18 authored over 1 year ago by Peter Sobolewski <[email protected]>
Add `--merge` option to `unpack` (#57)

* bump to new ome-types

* updating things for ome_types=0.4.0

* first try at merge project...

581996c21e3591c866759adaffa60284908167a3 authored over 1 year ago by Erick Martins Ratamero <[email protected]>
bump to 0.6.0

2f3c319d12e5176786fdaa7acf68e8ff3be803f9 authored over 1 year ago by Erick Martins Ratamero <[email protected]>
`prepare` can take a filelist instead of folder path (#55)

* added filelist argument

* generating targets from filelist when necessary

* putting init...

b3b89495d17d894440fe34e7cfdf6df00f5168ec authored over 1 year ago by Erick Martins Ratamero <[email protected]>
Update setup.py with version 0.5.0

788222faf26cd590277441b67d6d0c8650fb5972 authored over 1 year ago by Erick Martins Ratamero <[email protected]>
Update setup.py with version 0.5.0

0983eb9b4ebf047edb8dba268392b5dfe4ea7d56 authored over 1 year ago by Erick Martins Ratamero <[email protected]>
EXPERIMENTAL addition of `omero transfer prepare` (#52)

* added help for `omero transfer prepare`

* hooked command into `prepare` function

* next ...

fdcfbaa2f6a4e8a65b52f575a1113f347a66e77f authored over 1 year ago by Erick Martins Ratamero <[email protected]>
using the correct version-agnostic DOI

5780268076519846edc301f355c138a9602c3cf0 authored over 1 year ago by Erick Martins Ratamero <[email protected]>
updated DOI badge for version-agnostic one

a5930b047a391c7e9314ef46e38ba496a060f6cb authored over 1 year ago by Erick Martins Ratamero <[email protected]>
use default python version. 3.7 EOL (June 2023) (#48)

92d4d67e9716ca8ccaa3fd11e3db94d8aedc1cc8 authored over 1 year ago by jean-marie burel <[email protected]>
Merge pull request #47 from erickmartins/licensing

licensing update

ac81c1fa9340af81cec4f4d62813d61980090fb1 authored over 1 year ago by jean-marie burel <[email protected]>
changing repo license and adding simple copyright headers

99760b22218d5a1543ebc55e287e886fae9ac61a authored over 1 year ago by Erick Martins Ratamero <[email protected]>
fix indentation (#46)

617113566e5166d72b7a179d2079ff19b45e8a04 authored over 1 year ago by jean-marie burel <[email protected]>
remove twine (#44)

Moved the "upload to PyPI" GH action to be in line with other OME releases, using a dedicated GH...

3e079f05a7713ad22cc45d39c07667f211f7de0d authored almost 2 years ago by jean-marie burel <[email protected]>
update setup-python to v4

875d2f871c0bf5253377a22e338c71fe1649dbef authored almost 2 years ago by Jean-Marie Burel <[email protected]>
update checkout action to v3

4e0372ba55fe2f18c4dae521f015492f4a3aea71 authored almost 2 years ago by Jean-Marie Burel <[email protected]>
RO-crate support (#42)

* assume fully opaque for `fillColor` without alpha

* skeleton for ro-crate support

* rocr...

9e27ab9fe7bdebade81cbdb57f72b062f4bb1ccc authored almost 2 years ago by Erick Martins Ratamero <[email protected]>
added DOI badge

dd9a736d45d1ad866a0aaa0f613f679bf30e89e7 authored almost 2 years ago by Erick Martins Ratamero <[email protected]>
Roi and plate fixes (#40)

* passing colors/width correctly

* removing debug print

* added provenance metadata for pl...

7442abc0df6f53afaa231777e3a8a2fbc2039ef1 authored almost 2 years ago by Erick Martins Ratamero <[email protected]>
Better tests, fixing "dataset to plate" issue and ROI fill/strokecolors (#37)

* new `test_pack_unpack` test

* plate/screen tests still failing

* all tests passing but p...

8b021b55e2646f038c4199972f5aaf52e22fdd0e authored almost 2 years ago by Erick Martins Ratamero <[email protected]>
Typed functions and bugfixes (#36)

* fixed tests, using non-deprecated zeroc-ice for testing, solved #32

* generate_omero_object...

dd6936318a2d322c16b62b26c6eb2c39f4dee307 authored about 2 years ago by Erick Martins Ratamero <[email protected]>
Fix formatting of <object> etc in README (#34)

9ad9a4b653034ea977954dc5820bed09517d462f authored over 2 years ago by Will Moore <[email protected]>
Adds `--metadata` options to `pack` and `unpack` (#31)

* added `--metadata` argument

* passing metadata to the right place

* metadata argument be...

2d979ad5a25fd9380d4996e7b6a328e49bf5a2f9 authored over 2 years ago by Erick Martins Ratamero <[email protected]>
added import `--skip` options (#30)

c34be8afb9c95a13a3b29051fa00a5ed41103d2f authored over 2 years ago by Erick Martins Ratamero <[email protected]>
fixes imports that autogenerate annotations (#28)

* fixes imports that autogenerate annotations

* flake8 pass

d1d3d983881f721039f6b9dbad9d5bd0811af6cb authored over 2 years ago by Erick Martins Ratamero <[email protected]>
Md5 fix for OOM errors and skipping failed/missing images (#27)

* fixed md5 hashing to not read whole file in memory

* failed imports do not leave data orphaned

5aefdf8c7bda81ad4a9701f4cad01e54b7b80118 authored over 2 years ago by Erick Martins Ratamero <[email protected]>
Bioimage archive export option (#25)

* starting work to generate tsv

* zip file generated with image files in the right places

...

20fd1e25e0130f3c078f6366dc20b8f01406e4f9 authored over 2 years ago by Erick Martins Ratamero <[email protected]>
Extra packing/unpacking options (#23)

* packing/unpacking tar, unpack zip without OOM

* added possibility to pass a folder to unpack

f211f94f944e3da22313cc588e58c2d26c139179 authored over 2 years ago by Erick Martins Ratamero <[email protected]>
Improved testing (#21)

* extra tests

* edited readme, added test for no-file images

* added plate and screen test...

9858d9122e30b334a2dba35ddd278f77c88db73d authored over 2 years ago by Erick Martins Ratamero <[email protected]>
casting ID of non-file image as str for export (#19)

35e34aec73381a382aa26ee86026196e8e154146 authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
adding upload to pypi action and update to readme/setup

2c378d6e378f445bd8df285c81d953f60baa5e35 authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
Screens and plates (#18)

* first try at packing plates/screens

* making sure we are not repeatedly trying to download ...

29310e73decfc07429cc7e424895ca49ccf3d657 authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
Extra annotations (Comments, Ratings, File Annotations) (#17)

* minimal working commit for commentannotations

* LongAnnotations! (i.e. ratings!!!)

* Fil...

4ea501fffdee176d215a20412d85c3102d2a110d authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
Enforcing whole filesets in XML files, filtering destination IDs (#16)

* enforce all images in a fileset to be in the XML

* only getting destination IDs without Map...

527ef210becf1aed5bd4fdfc4ae8570a53bc309b authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
Extended rois (#15)

Using the new ROI types from ezomero 1.0.1 (Polyline, Label) and adding markerStart and markerEn...

7bc5594c2bebb836846db3664e20a682b83c671b authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
Support for multi-file formats (#14)

If an `Image` ID has multiple file paths on the server, indicating that the import required mult...

75df3a71dd9cb8048a3b16e95d574251d7986029 authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
Images without `OriginalFile`s are included in packed zip file

9db2fd3b71a67aa45b143c813bee11f93b407482 authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
Added provenance metadata (#10)

* testing hostname passing

* hostname should be correctly parsed now

* ..and now as a stri...

d09a2ab9dfa9a9f93bc86cba8d2d7977ebe798e0 authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
Testing (#9)

* testing omero_plugin.yml

* pinning requirements

* flake8 pass

* added local testing i...

5fec969b26bc959c01a8c77fa210008ea30fdbe0 authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
removed entry for generate_omero_objects as main

a9ed6e559f6926e609df750e2839f71135cc4f32 authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
minor readme fixes

d1c6c360f73af3daf0f3fec4c8e15aa1d7ae81ab authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
updated readme

b6b168991740666569bbba3a07eecc06bfa9209f authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
added some help text

547f0a00a699a49a35dad7bc841082dbb6d5f6e2 authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
initial commit for new repo

c4d32e4420af4e7a793ef407eaee3b0f23aadf06 authored almost 3 years ago by Erick Martins Ratamero <[email protected]>
Initial commit

d595ab3ad5951db5e11ff858cf7c2875d7b880c2 authored almost 3 years ago by Erick Martins Ratamero <[email protected]>