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Update handling and parsing of acquisition metadata #75

Merged
merged 2 commits into from
Jun 7, 2024
Merged

Update handling and parsing of acquisition metadata #75

merged 2 commits into from
Jun 7, 2024

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dgault
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@dgault dgault commented Jan 11, 2024

This was originally driven by an exception seen in IDR/idr-metadata#683 (comment)

The stack trace is as below and is caused by attempting to cast acquisition start time to String when it should be Integer as per the spec (https://github.com/ome/ngff/blob/main/0.4/schemas/plate.schema#L35)

Caused by: java.lang.ClassCastException: class java.lang.Long cannot be cast to class java.lang.String (java.lang.Long and java.lang.String are in module java.base of loader 'bootstrap')
        at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:755)
        at loci.formats.in.ZarrReader.initFile(ZarrReader.java:353)
        at loci.formats.FormatReader.setId(FormatReader.java:1443)
        at loci.formats.ImageReader.setId(ImageReader.java:849)
        at ome.io.nio.PixelsService$3.setId(PixelsService.java:869)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
        at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
        at loci.formats.Memoizer.setId(Memoizer.java:690)
        at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:52)
        at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:73)
        ... 82 common frames omitted

When reviewing the spec for acquisition I have also added parsing for endTime and description as well as setting all of the acquisition values on the metadataStore.

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dgault commented Jun 7, 2024

Merging this for release as it has been tested by IDR for a number of months now

@dgault dgault merged commit cc97439 into ome:main Jun 7, 2024
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dgault added a commit to dgault/ZarrReader that referenced this pull request Jun 7, 2024
@dgault
ChangeLog: Add missing entry for PR ome#75
2ec9e5d
dgault added a commit that referenced this pull request Jun 7, 2024
@dgault
Merge pull request #84 from dgault/changelog-75
1805e1e 
ChangeLog: Add missing entry for PR #75
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 8, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
7ee1f6e 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#95 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/95/)
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 9, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
bb9264d 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#96 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/96/)
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 10, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
06750fd 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#97 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/97/)
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 11, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
fdf82d7 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/98/)
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 12, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
ab85004 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#99 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/99/)
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 13, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
2088a38 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#100 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/100/)
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 14, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
9457fdf 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#101 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/101/)
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 15, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
3852980 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#102 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/102/)
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 16, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
96f6690 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#103 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/103/)
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 17, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
f65312c 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#104 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/104/)
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 18, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
21535b4 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#105 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/105/)
snoopycrimecop added a commit to snoopycrimecop/ZarrReader that referenced this pull request Jun 19, 2024
@snoopycrimecop
merge master -Dorg -Ssuccess-only
3851c2d 
Repository: ome/ZarrReader
Excluded PRs:
  - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
Updating 31e9353..9a9e662
Previously merged:
  - PR 90 dgault 'Bump version to 0.5.2-SNAPSHOT'
  - PR 89 dgault 'Bump version to 0.5.1'
  - PR 88 dgault 'Add Change Log for 0.5.1'
  - PR 87 dgault 'Bump formats-api version to 7.3.0'
  - PR 86 dgault 'Bumping version to 0.5.1-SNAPSHOT'
  - PR 85 dgault 'Bump version to 0.5.0'
  - PR 84 dgault 'ChangeLog: Add missing entry for PR ome#75'
  - PR 75 dgault 'Update handling and parsing of acquisition metadata'
  - PR 73 dgault 'Update ReadMe and Change Log'
  - PR 82 dgault 'Reintroduce S3FileSystemStore'

Generated by BIOFORMATS-push#106 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/106/)
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