---
# System prepended metadata

title: Standup 2021-02-01
tags: [standup, ' temp']

---

---
tags: standup, temp
---

# Standup 2021-02-01

General notes:
- opt/management_tools/utils/standup-scraper
- environment.yml
- VPN or on Dundee machine
- run.sh as an option

## image.sc


`./imagesc.py -d 6`

<li>[???] <a href="https://forum.image.sc/t/48244/2">[sc:bf,matlab] How to in-memorily read multi-file images? (EbolaChan)</a> </li>
<li>[???] <a href="https://forum.image.sc/t/48226/1">[sc:imagej,bf,batch-processing] Convert spider stk files to tiff file in batch? (yongshuo-Z)</a> </li>
<li>[???] <a href="https://forum.image.sc/t/47046/12">[sc:web] Sharing contents (vsnlme108)</a> Solved? Hi @joshmoore Thanks for prompt reply. the file system is xfs. I checked the /O…</li>
<li>[???] <a href="https://forum.image.sc/t/48125/5">[sc:omero,fiji] Omero Tips January edition : Fiji Omero plugin (1/3) - Installation (NicoKiaru)</a> </li>
<li>[???] <a href="https://forum.image.sc/t/47881/14">[sc:omero,wsi] RE: Can't import entire pyramidal WSI file in OMERO (BaxterGarcia)</a> </li>
<li>[???] <a href="https://forum.image.sc/t/47977/5">[sc:bf,python-bioformats] Problems installing python-bioformats (java not found) (u2056710)</a> </li>
<li>[???] <a href="https://forum.image.sc/t/46618/5">[sc:bf] Opening .lvi files (x346x)</a> </li>
<li>[???] <a href="https://forum.image.sc/t/47841/4">[sc:bf,omero,ome-tiff] Converting MRXS to OME-TIFF (brianc)</a> Solved? Thank you both for the input! Unfortunately it seems our size increase is just …</li>


Josh:
<li>[???] <a href="https://forum.image.sc/t/47990/10">[sc:napari,ome,ome-ngff,zarr,ome-zarr] Polygon and other ROI annotations in ome-zarr? (glyg)</a> </li>
<li>[???] <a href="https://forum.image.sc/t/44653/13">[sc:ome-ngff,zarr] Mesh data in ome-zarr (sofroniewn)</a> </li>

Omit: 
<li>[???] <a href="https://forum.image.sc/t/48106/4">[sc:ome-tiff] Color tag in OME-tiff XML (michael_ef)</a> Solved? Perfect, thanks for the fast reply</li>
<li>[???] <a href="https://forum.image.sc/t/47951/3">[sc:bf] What are the specifications(image format,range,bit information ,2D or 3D etc) of images that we got from cell painted assays (9645451493)</a> Solved? Thank you Sir for this information</li>

## QA (requires VPN/SOCKS; password needs settling; see README

<li>[???] <a href="https://www.openmicroscopy.org/qa2/qa/feedback/29996/">[QA 29996]</a>dalia.gala@merton.ox.ac.uk 129.67.80.81  java.lang.Exception: Abnormal terminatio</li>
<li>[???] <a href="https://www.openmicroscopy.org/qa2/qa/feedback/29995/">[QA 29995]</a>irene.lamberti@epfl.ch 128.179.130.65 uploading new data and preview of already uploaded ones on the webpage java.lang.Exception: omero.gateway.excep</li>
<li>[???] <a href="https://www.openmicroscopy.org/qa2/qa/feedback/29994/">[QA 29994]</a>skappelhoff@uni-osnabrueck.de 131.173.45.44  java.lang.Exception: omero.gateway.excep</li>
<li>[???] <a href="https://www.openmicroscopy.org/qa2/qa/feedback/29993/">[QA 29993]</a> 134.158.246.160  ome.conditions.SecurityViolation: User 4</li>


## Emails (complicated setup)

- Notes:
  - Requires authuser
  - creating oauth consent
  - creating credentials
  - adding URL
  - enabling gmail API
  - copying file
  - allowing on first run
  
... alternatively, https://groups.google.com/u/2/my-groups

```
    "    'demo-support',\n",
    "    'idr',\n",
    "    'idr-support',\n",
    "    'nightshade-support',\n",
    "    'security',\n",
    "    'learning-support',\n",
    "    'training-support',\n",
```
[idr]
- [Submission of 3D-SIM data](https://groups.google.com/u/0/a/openmicroscopy.org/g/idr/c/9O6NFTndhRc) filled the template with the metadata
- [Submission of a dataset](https://groups.google.com/u/0/a/openmicroscopy.org/g/idr/c/-EbCuDRyIY8) error in credentials ?
- [submitting image to IDR](https://groups.google.com/u/0/a/openmicroscopy.org/g/idr/c/Mi2fe3UBCSA) let the upload run over weekend
- [OMERO Leiden DB](https://groups.google.com/u/0/a/openmicroscopy.org/g/idr/c/iYz3V96Dz0U) data packaging during the last meeting


## Jobs (x3)

./jobs merge-ci --failing
OR failingbuilds.py

Petr: ./jobs merge-ci --failing does not work - not sure where to start it from, there is only ./job in the dir

Petr: failingbuilds.py works


<li>[???] <a href="https://ci.openmicroscopy.org/view/Failing/job/OME-internal-merge-docs/2660/">OME-internal-merge-docs</a>&nbsp;<ul><li><code>Collecting six (from scc)</code></pre>
<li><code>  Cache entry deserialization failed, entry ignored</code></pre>
<li><code>  Using cached https://files.pythonhosted.org/packages/ee/ff/48bde5c0f013094d729fe4b0316ba2a24774b3ff1c52d924a8a4cb04078a/six-1.15.0-py2.py3-none-any.whl</code></pre>
<li><code>Collecting argparse (from scc)</code></pre>
<li><code>  Using cached https://files.pythonhosted.org/packages/f2/94/3af39d34be01a24a6e65433d19e107099374224905f1e0cc6bbe1fd22a2f/argparse-1.4.0-py2.py3-none-any.whl</code></pre></ul></li>


But see: https://ci.openmicroscopy.org/view/Failing/job/OME-internal-merge-docs/2660/console


<li>[???] <a href="https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-test-repo/671/">[merge-ci] BIOFORMATS-test-repo</a>&nbsp;<ul><li><code>[Pipeline] }</code></pre>
<li><code>Failed in branch handling /uod/idr/repos/curated/samples</code></pre>
<li><code>Starting building: BIOFORMATS-test-folder #106944</code></pre>
<li><code>[Pipeline] }</code></pre>
<li><code>Starting building: BIOFORMATS-test-folder #106945</code></pre></ul></li>
<li>[???] <a href="https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-linkcheck/201/">[latest-ci] BIOFORMATS-linkcheck</a>&nbsp;<ul><li><code>(line   21) -ignored- https://github.com/ome/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/SpiderReader.java</code></pre>
<li><code>(line   32) broken    https://spider.wadsworth.org/spider_doc/spider/docs/image_doc.html - HTTPSConnectionPool(host='spider.wadsworth.org', port=443): Max retries exceeded with url: /spider_doc/spider/docs/image_doc.html (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1056)')))</code></pre>
<li><code>(line    9) broken    https://spider.wadsworth.org/spider_doc/spider/docs/spider.html - HTTPSConnectionPool(host='spider.wadsworth.org', port=443): Max retries exceeded with url: /spider_doc/spider/docs/spider.html (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1056)')))</code></pre>
<li><code>(line   26) broken    https://spider.wadsworth.org/spider_doc/spider/docs/spider.html - HTTPSConnectionPool(host='spider.wadsworth.org', port=443): Max retries exceeded with url: /spider_doc/spider/docs/spider.html (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1056)')))</code></pre>


## PRs/Issues

scc issues --external --by-date ome

### 2021-01
 - [???] [\[ansible-role-iptables-raw\] Feature Request: remove word ansible from iptables name comment ](https://github.com/ome/ansible-role-iptables-raw/issues/5) (Helios-23)
 - [???] [\[bioformats\] Illegal reflective access by kryo ](https://github.com/ome/bioformats/issues/3659) (juliangilbey)
 - [???] [\[bioformats\] VSI->TIF converted images with JPEG compression throws errors in GIMP ](https://github.com/ome/bioformats/issues/3372) (ebremer)
 - [???] [\[omero-gallery\] Add "clear/reset filter" button or link ](https://github.com/ome/omero-gallery/issues/76) (abhamacher)
 - [???] [\[omero-guide-ilastik\] Add note about `channel_priority=strict` to docs ](https://github.com/ome/omero-guide-ilastik/issues/28) (tlambert03)
 - [???] [\[omero-rois\] Adding shape classes ](https://github.com/ome/omero-rois/issues/9) (juliomateoslangerak)

## Twitter

https://twitter.com/search?q=openmicroscopy&src=typed_query etc.

