commit a26a2eebdf5359cbb8d4195dc4d58ed03bf92536

Author: Simon Li <[email protected]>
Date:   Tue Jan 26 14:03:33 2021 +0000

    Delete intermediate filelist-*.tsv and failures

commit 578bb20275da63c3caa773d81011790f5d71b573
Author: Simon Li <[email protected]>
Date:   Tue Jan 26 10:00:13 2021 +0000

    Remove experimentRETRY

commit bbfadd35223aba85ce28bca95a991538b70b6af3
Author: Simon Li <[email protected]>
Date:   Mon Jan 25 19:32:46 2021 +0000

    Fix Study Experiments Number

commit 2736def
Author: Frances Wong <[email protected]>
Date:   Mon Jan 25 16:38:27 2021 +0000

    Fix Author List

    Fix Author List

commit 586a8c7
Author: Simon Li <[email protected]>
Date:   Mon Jan 25 15:08:17 2021 +0000

    Removed "-updated" from annotation CSV names:

    for e in A B C D E F; do git mv -f experiment$e/idr0071-experiment$e-annotation-updated.csv experiment$e/idr0071-experiment$e-annotation.csv ; done

commit d2cd81d
Author: Simon Li <[email protected]>
Date:   Mon Jan 25 14:54:23 2021 +0000

    Check rendering process

commit f2b50df
Author: Frances Wong <[email protected]>
Date:   Wed Jan 20 16:52:48 2021 +0000

    Update idr0071-study.txt

    Update study file

commit 0c0fa4e
Author: Simon Li <[email protected]>
Date:   Tue Jan 19 16:33:00 2021 +0000

    Update imagelist.json

commit 8a8dbbf
Author: Simon Li <[email protected]>
Date:   Tue Jan 19 16:29:58 2021 +0000

    Rename datasets: remove experiment prefix

commit 34d9c98
Author: Simon Li <[email protected]>
Date:   Tue Jan 19 16:22:12 2021 +0000

    Record retried imports

commit 4dacf95
Author: Simon Li <[email protected]>
Date:   Mon Jan 18 20:47:42 2021 +0000

    Update scripts/render.sh

commit 3b3ebe1
Author: Simon Li <[email protected]>
Date:   Mon Jan 18 16:13:59 2021 +0000

    Remove old renderdefs

commit a6c4448
Author: Simon Li <[email protected]>
Date:   Mon Jan 18 15:37:00 2021 +0000

    Add new renderdefs

    ome/omero-cli-render#52

commit d1fa9a7
Author: Simon Li <[email protected]>
Date:   Mon Jan 18 14:05:59 2021 +0000

    Add single failed experimentA image to experimentRETRY

commit 33baf54
Author: Simon Li <[email protected]>
Date:   Mon Jan 18 14:04:00 2021 +0000

    Copy experimentD/idr0071-experimentD-filelist.tsv ➜ experimentRETRY/idr0071-experimentRETRY-filelist.tsv

commit 0696d9a
Author: Simon Li <[email protected]>
Date:   Wed Jan 13 11:32:15 2021 +0000

    Remove experimentRETRY

commit ddca528
Author: Simon Li <[email protected]>
Date:   Tue Jan 12 15:48:54 2021 +0000

    Move transfer/idr0071-experiment?-filelist-companion.tsv to experiment?/idr0071-experiment?-filelist.tsv

commit 2b8634c
Author: Simon Li <[email protected]>
Date:   Tue Jan 12 15:45:51 2021 +0000

    Update companion file path to /uod/idr/filesets/....

    sed -i 's%/uod/idr/metadata/idr0071-feldman-crisprko/companions/%/uod/idr/filesets/idr0071-feldman-crisprko/20201027-companions/companions/%' *companion.tsv

commit 5deb5f7
Author: Simon Li <[email protected]>
Date:   Mon Jan 11 20:00:33 2021 +0000

    Add renderdefs for processed images

commit 9d0f47c
Author: Simon Li <[email protected]>
Date:   Mon Jan 11 15:15:25 2021 +0000

    Add channel names to annotations for processed files

commit d131be1
Author: Simon Li <[email protected]>
Date:   Thu Dec 17 18:50:38 2020 +0000

    Remove experiment prefix from dataset annotations

commit 8eeb94a
Author: Simon Li <[email protected]>
Date:   Thu Dec 17 16:23:54 2020 +0000

    Script to rename datasets (remove experiment letter prefix)

commit 2e74a27
Author: Simon Li <[email protected]>
Date:   Thu Dec 17 16:05:37 2020 +0000

    Prevent integer float conversion in annotations

commit 61f57c5
Author: Simon Li <[email protected]>
Date:   Wed Dec 16 16:52:41 2020 +0000

    Add scripts/render.sh

commit 5d41cd7
Author: Simon Li <[email protected]>
Date:   Wed Dec 16 11:37:24 2020 +0000

    Add renderdefs

    These should be applied with ome/omero-cli-render#50 `omero render batchset Project:<id> experiment<>/renderdefs`

commit 0517fa1
Author: Simon Li <[email protected]>
Date:   Wed Dec 16 11:34:44 2020 +0000

    Add scripts/create_renderdefs.ipynb

commit c44bcf5
Author: Simon Li <[email protected]>
Date:   Wed Dec 16 10:21:11 2020 +0000

    Add scripts/annotate.sh

commit 6cf0207
Author: Simon Li <[email protected]>
Date:   Tue Dec 15 17:41:05 2020 +0000

    Update annotations

commit e68afce
Author: Frances Wong <[email protected]>
Date:   Fri Dec 11 15:59:43 2020 +0000

    Changes to bulkmap config

    Changes to bulkmap config

commit 02594b8
Author: Simon Li <[email protected]>
Date:   Thu Dec 10 17:18:19 2020 +0000

    idr0071-bulkmap-config.yml

commit 137dbd2
Author: Simon Li <[email protected]>
Date:   Thu Nov 26 14:38:22 2020 +0000

    check dataset and image names can be matched with annotations, update csv

commit f9daaa1
Author: Simon Li <[email protected]>
Date:   Tue Nov 10 16:40:00 2020 +0000

    Current state of companion files used for import

commit cae7ab2
Author: Simon Li <[email protected]>
Date:   Thu Aug 20 18:15:13 2020 +0000

    Attempt at importing companion files

commit 63de913
Author: Simon Li <[email protected]>
Date:   Thu Aug 20 17:41:14 2020 +0000

    Update generate-companions.py

commit bd2ffd3
Author: Simon Li <[email protected]>
Date:   Wed Aug 19 10:58:06 2020 +0000

    Extracted dimensions from all images using tifffile

commit 1b63db9
Author: Simon Li <[email protected]>
Date:   Mon Jul 6 21:30:53 2020 +0100

    getsizes-20200706.ipynb include clientpath

commit bfd8a42
Author: Simon Li <[email protected]>
Date:   Mon Jul 6 16:11:08 2020 +0100

    getsizes-20200706.ipynb to investigate incorrect dims

commit 7a82764
Author: Simon Li <[email protected]>
Date:   Tue Jun 23 11:51:31 2020 +0100

    Run exiftool -ImageDescription= on failures

    Output to 20200623-fixes

commit 59029b7
Author: Simon Li <[email protected]>
Date:   Tue Jun 23 11:12:34 2020 +0100

    Forgot to commit failures.txt

commit 97b6bcc
Author: Simon Li <[email protected]>
Date:   Mon Jun 22 19:08:10 2020 +0100

    Move import failures into separate list

    The 32 files which failed to import have been moved from ?/idr0071-experiment?filelist.tsv to experimentRETRY/idr0071-experimentRETRY-filelist.tsv so they can be dealt with later

commit ac9a6b6
Author: Simon Li <[email protected]>
Date:   Mon Jun 22 17:51:28 2020 +0100

    Prefix datasets with experiment letter

    This is required to handle datasets with the same name: ome/omero-blitz#91

commit 38ffdcb
Author: Simon Li <[email protected]>
Date:   Mon Jun 22 17:30:06 2020 +0100

    Add readers.txt loci.formats.in.TiffReader

commit 3a85c74
Author: Frances Wong <[email protected]>
Date:   Mon Jun 22 11:02:39 2020 +0100

    Add annotation csv

    Add annotation csv

commit 9da0915
Author: Simon Li <[email protected]>
Date:   Wed Jun 3 16:21:06 2020 +0100

    Use unrenamed files for import

commit 0dd1a39
Author: Simon Li <[email protected]>
Date:   Wed Jun 3 15:07:08 2020 +0100

    Delete experimentA-sample

commit de24d66
Author: Simon Li <[email protected]>
Date:   Wed Apr 15 15:12:04 2020 +0100

    Add experiment?/idr0071-experiment?-{filelist.tsv,bulk.yml} (A-F)

commit 922e0ed
Author: Simon Li <[email protected]>
Date:   Wed Apr 15 15:10:02 2020 +0100

    notebook: create filelist for ABCDEF

commit cd5941c
Author: Simon Li <[email protected]>
Date:   Tue Apr 7 14:18:12 2020 +0100

    Add process to experimentA/idr0071-experimentA-filelist.tsv

commit 1612ab9
Author: Simon Li <[email protected]>
Date:   Thu Apr 2 18:12:27 2020 +0100

    Experiment a input

commit b8ce263
Author: Simon Li <[email protected]>
Date:   Thu Apr 2 17:42:06 2020 +0100

    Add local filelists

commit f406163
Author: Simon Li <[email protected]>
Date:   Thu Apr 2 12:14:58 2020 +0100

    notebook: add move ext in summary

commit 9e45c17
Author: Simon Li <[email protected]>
Date:   Thu Apr 2 12:10:40 2020 +0100

    notebook: add ext to summary

commit 778b3eb
Author: Simon Li <[email protected]>
Date:   Thu Apr 2 12:02:39 2020 +0100

    notebook: add summary of file counts  / experiment-cycle-tag

commit 29f06d9
Author: Simon Li <[email protected]>
Date:   Wed Apr 1 19:45:59 2020 +0100

    Notebook to summarise counts of files

commit a437a04
Author: Simon Li <[email protected]>
Date:   Wed Apr 1 18:32:41 2020 +0100

    Add idr0071-study.txt from submitter (2019-10-30)

commit 42614b7
Author: Simon Li <[email protected]>
Date:   Wed Apr 1 18:28:26 2020 +0100

    Add IDR_transfer_files.20191027_235752.csv.gz IDR_transfer_file_summary.20191027_235152.xlsx from submitter 2010-10-30

commit 67efe59
Author: Simon Li <[email protected]>
Date:   Wed Apr 1 16:15:08 2020 +0100

    Add idr0000-experiment-tables.zip from submitter 2019-11-01

commit 85eb349
Author: Simon Li <[email protected]>
Date:   Wed Apr 1 18:34:42 2020 +0100

    Move experimentA → experimentA-sample

commit acdc4be
Author: Simon Li <[email protected]>
Date:   Thu Oct 17 16:36:13 2019 +0100

    Add bulkmap config

commit 28c601f
Author: Simon Li <[email protected]>
Date:   Thu Oct 17 14:43:31 2019 +0100

    Set Dataset Name in idrXXXX-experimentA-assays.csv

commit 3efa58f
Author: Simon Li <[email protected]>
Date:   Thu Oct 17 14:10:46 2019 +0100

    Replace idrXXXX-experimentA-assays.txt with idrXXXX-experimentA-assays.csv from Frances

commit ee9932d
Author: Simon Li <[email protected]>
Date:   Mon Oct 14 15:16:17 2019 +0100

    import config for feldman sample data

commit e39ab5e
Merge: 66f4959 a12cb8b
Author: Sébastien Besson <[email protected]>
Date:   Tue Mar 12 13:19:57 2019 +0000

    Merge pull request #11 from manics/cc-by

    Preferred license is CC-BY

commit a12cb8b
Author: Simon Li <[email protected]>
Date:   Tue Mar 12 12:15:32 2019 +0000

    Preferred license is CC-BY

commit 66f4959
Merge: fae69d9 2981738
Author: Sébastien Besson <[email protected]>
Date:   Tue Mar 5 16:44:40 2019 +0000

    Merge pull request #10 from sbesson/accession

    Unify Accession keys: drop Number suffix

commit 2981738
Author: Sebastien Besson <[email protected]>
Date:   Tue Mar 5 13:21:21 2019 +0000

    Unify Accession keys (drop Number suffix)

commit fae69d9
Merge: f001201 afc9779
Author: francesw <[email protected]>
Date:   Thu Dec 6 09:47:59 2018 +0000

    Merge pull request #8 from sbesson/copyright

    Add study copyright to the metadata templates

commit afc9779
Author: Sebastien Besson <[email protected]>
Date:   Tue Aug 28 15:46:06 2018 +0100

    Add study copyright to the metadata templates

    Also ask to fill in the study license

commit f001201
Merge: 771b5c5 c5658cc
Author: Sébastien Besson <[email protected]>
Date:   Tue Jul 31 10:20:55 2018 +0100

    Merge pull request #7 from manics/patch-1

    Clarify the two types of submission

commit c5658cc
Author: Josh Moore <[email protected]>
Date:   Tue Jul 31 11:17:57 2018 +0200

    Clarify A vs B naming

commit 60a75c4
Author: Simon Li <[email protected]>
Date:   Mon Jul 30 16:12:58 2018 +0100

    Clarify the two types of submission

commit 771b5c5
Merge: 50b9fd4 4f9f3e4
Author: Sébastien Besson <[email protected]>
Date:   Fri Jul 6 13:39:09 2018 +0100

    Merge pull request #6 from IDR/joshmoore-patch-1

    Add "Technology" to HCS Type line

commit 4f9f3e4
Author: Josh Moore <[email protected]>
Date:   Fri Jun 29 14:04:56 2018 +0200

    Add "Technology" to HCS Type line

    We have multiple lines with the same key. I'm not positive, but this seems incorrect.

commit 50b9fd4
Merge: 4b4bd41 60903e5
Author: Sébastien Besson <[email protected]>
Date:   Thu May 3 10:55:23 2018 +0100

    Merge pull request #5 from sbesson/orcids

    Add ORCID field to the study template files

commit 60903e5
Author: Sebastien Besson <[email protected]>
Date:   Wed May 2 16:53:08 2018 +0100

    Add ORCID field to the study template files

commit 4b4bd41
Merge: cd6dd0d e207be2
Author: Sébastien Besson <[email protected]>
Date:   Sun Jan 21 20:22:02 2018 +0000

    Merge pull request #3 from eleanorwilliams/studyfilefixes

    Study File Fixes

commit e207be2
Author: eleanorwilliams <[email protected]>
Date:   Fri Jan 12 09:26:50 2018 +0000

    changed last line to refer to assay file rather than library file

commit 10e228e
Author: eleanorwilliams <[email protected]>
Date:   Fri Jan 12 09:23:42 2018 +0000

    removed mac line endings in nonHCS study file

commit 5e0d346
Author: eleanorwilliams <[email protected]>
Date:   Fri Jan 12 09:22:18 2018 +0000

    removed mac line endings in HCS study file

commit cd6dd0d
Merge: 9e9e4e4 1be9022
Author: Sébastien Besson <[email protected]>
Date:   Thu Jan 4 15:55:48 2018 +0000

    Merge pull request #2 from sbesson/assays_template

    Fix assays file header to match the latest layout

commit 1be9022
Author: Sebastien Besson <[email protected]>
Date:   Thu Jan 4 14:48:39 2018 +0000

    Add Eleanor's suggestions

commit c8da543
Author: Sebastien Besson <[email protected]>
Date:   Thu Jan 4 09:54:14 2018 +0000

    Also use non-demo HTTPS URL

commit 73f88d0
Author: Sebastien Besson <[email protected]>
Date:   Thu Jan 4 09:53:05 2018 +0000

    Remove Image dimensions comment and convert to tabs

commit 592b09d
Author: Sebastien Besson <[email protected]>
Date:   Wed Jan 3 13:59:00 2018 +0000

    Fix typo 2

commit 1cd6e02
Author: Sebastien Besson <[email protected]>
Date:   Wed Jan 3 13:57:48 2018 +0000

    Add newline

commit 7bf4b36
Author: Sebastien Besson <[email protected]>
Date:   Wed Jan 3 13:57:39 2018 +0000

    Fix typo

commit 3e00421
Author: Sebastien Besson <[email protected]>
Date:   Wed Jan 3 13:53:59 2018 +0000

    Fix assays file header to match the latest layout

    - Move Image File Path as a comment
    - Add Image Dimensions comment
    - Use LF

commit 9e9e4e4
Author: jmoore <[email protected]>
Date:   Wed Mar 15 17:41:10 2017 +0100

    New first sentence

commit 910159c
Author: jmoore <[email protected]>
Date:   Wed Mar 15 17:40:14 2017 +0100

    Re-indent

commit ddc988e
Author: jmoore <[email protected]>
Date:   Wed Mar 15 17:33:33 2017 +0100

    Add 'tab-delimited' note

commit 408cef7
Author: jmoore <[email protected]>
Date:   Tue Mar 14 12:02:04 2017 +0100

    Use 'study' rather than 'dataset'

commit 6bfd7ff
Author: jmoore <[email protected]>
Date:   Tue Mar 14 11:58:22 2017 +0100

    Add .gitignore

commit 86d953a
Author: jmoore <[email protected]>
Date:   Tue Mar 14 11:55:59 2017 +0100

    Use txt for README for downloads

commit aaad6a7
Author: jmoore <[email protected]>
Date:   Tue Mar 14 11:55:47 2017 +0100

    Migrate files from Google Drive

commit 7827a1f
Author: jmoore <[email protected]>
Date:   Mon Mar 13 18:41:54 2017 +0100

    First commit

.gitignore

@@ -0,0 +1 @@
+.*~

bulk.yml

@@ -0,0 +1,16 @@
+---
+continue: true
+transfer: "ln_s"
+exclude: "clientpath"
+skip:
+  - checksum
+  - minmax
+columns:
+  - target
+  - path
+  - name
+
+logprefix: "logs/"
+output: "yaml"
+parallel_upload: "10"
+parallel_fileset: "10"

environment.yml

@@ -0,0 +1,15 @@
+name: omero
+channels:
+  - ome
+  - defaults
+dependencies:
+  - jupyterlab=2.2.6
+  - notebook=6.1.4
+  - numpy=1.19.1
+  - omero-py=5.8.2
+  - pandas=1.1.2
+  - pip=20.2.3
+  - python=3.8.5
+  - tifffile=2020.9.22
+  - pip:
+    - ome-model==6.2.1

experimentA/idr0071-experimentA-bulk.yml

@@ -0,0 +1,3 @@
+---
+include: "../bulk.yml"
+path: "idr0071-experimentA-filelist.tsv"