Bug: OriginalMetadataRequestI non-conversion

[jamoore]

Seen in the orca log file testing for Paris:

2014-06-03 11:05:08,856 WARN  [o.c.f.OriginalMetadataRequestI.@56bdf30a] (2-thread-1) Count not convert to rtype photosensorReading: 1.0
2014-06-03 11:05:08,856 WARN  [o.c.f.OriginalMetadataRequestI.@56bdf30a] (2-thread-1) Count not convert to rtype photosensorReading: 1.0
2014-06-03 11:05:08,856 WARN  [o.c.f.OriginalMetadataRequestI.@56bdf30a] (2-thread-1) Count not convert to rtype photosensorReading: 1.0
2014-06-03 11:05:08,856 WARN  [o.c.f.OriginalMetadataRequestI.@56bdf30a] (2-thread-1) Count not convert to rtype photosensorReading: 1.0
2014-06-03 11:05:08,856 WARN  [o.c.f.OriginalMetadataRequestI.@56bdf30a] (2-thread-1) Count not convert to rtype photosensorReading: 1.0
2014-06-03 11:05:08,856 WARN  [o.c.f.OriginalMetadataRequestI.@56bdf30a] (2-thread-1) Count not convert to rtype photosensorReading: 1.0
2014-06-03 11:05:08,856 WARN  [o.c.f.OriginalMetadataRequestI.@56bdf30a] (2-thread-1) Count not convert to rtype photosensorReading: 1.0
2014-06-03 11:05:08,856 WARN  [o.c.f.OriginalMetadataRequestI.@56bdf30a] (2-thread-1) Count not convert to rtype photosensorReading: 1.0
2014-06-03 11:05:08,864 WARN  [o.c.f.OriginalMetadataRequestI.@56bdf30a] (2-thread-1) Count not convert to rtype photosensorReading: 1.0
2014-06-03 11:05:08,864 WARN  [o.c.f.OriginalMetadataRequestI.@56bdf30a] (2-thread-1) Count not convert to rtype photosensorReading: 1.0
2014-06-03 11:05:08,864 WARN  [o.c.f.OriginalMetadataRequestI.@56bdf30a] (2-thread-1) Count not convert to rtype photosensorReading: 1.0

File to test with: /repositories/OMERO-1/ManagedRepository/ome-team-01_2/2014-06/02/18-53-17.694/P-TRE_13_R3D_D3D.dv

[jamoore]

Increasing the logging this looks like this:

2014-06-03 11:49:58,505 WARN  [o.c.fs.OriginalMetadataRequestI.@be241ff] (2-thread-5) Could not convert to rtype: key=Extended header Z54 W2 T0, value=photosensorReading: 1.0
timeStampSeconds: 290.559
stageXCoord: -6827.92
stageYCoord: -4598.75
stageZCoord: -32.80004
minInten: 179.0
maxInten: 2691.0
expTime: 1.5
ndFilter: 0.0
exWavelen: 555.0
emWavelen: 617.0
intenScaling: 1.0

[jamoore]

PR opened: ​https://github.com/openmicroscopy/openmicroscopy/pull/2583

[jamoore]

All PRs (and rebases) opened. Closing ticket.

[jmoore <josh@…>]

(In [5252bbb9fdd1eaedee68d5ff6440f2861c9c1d62/ome.git] on branch develop) Initial fix for unparsed metadata (See #12358)

This is only a band-aid over the issue of
table values being possibly non-scalar. Either
we will need to provide a getter that flattens
all values, or agree upon some API such as
DVExtHdrFields extending java.util.Map to make
this tractable.

[Snoopy Crime Cop <snoopycrimecop@…>]

(In [d8d2857c4ba79ce9dbd20c640055b075ea61d94e/ome.git] on branch develop) Update develop submodules

Repository: openmicroscopy/openmicroscopy
Already up-to-date.

Repository: openmicroscopy/bioformats
Updating f247b30..3086fd2
Merged PRs (fast-forward):

# PR 1181 sbesson 'bfsave: metadata improvements (rebased onto develop)'
# PR 1190 hflynn 'Fixing imaris file spec FAQ link (rebased onto develop)'
# PR 1162 melissalinkert 'AFI: populate magnification and physical pixel size metadata'
# PR 1185 hflynn 'Fixing imglib scifio github link (rebased onto develop)'
# PR 1176 rleigh-dundee 'xsd-fu: Use package namespaces throughout and consolidate commands'
# PR 1170 rleigh-dundee 'cmake: Enable CMP0042 @rpath usage for MacOSX'
# PR 1175 melissalinkert 'Fix channel count when exporting RGB images in ImageJ'
# PR 1174 melissalinkert 'CZI: prevent AIOOB exception when populating position metadata (rebased onto develop)'
# PR 1155 joshmoore 'Memoizer errs (rebased onto develop)'
# PR 981 melissalinkert 'Ignore namespaces when filling in an XMLAnnotation's Value'
# PR 1138 melissalinkert 'Lots of Zeiss CZI fixes (rebased onto develop)'
# PR 1169 melissalinkert 'ImportProcess?: remove UI-level exception reporting'
# PR 1168 melissalinkert 'Inveon: ignore the absolute path to the image file'
# PR 1165 melissalinkert 'First round of Nikon ND2 fixes (rebased onto develop)'
# PR 1163 melissalinkert 'Fix for BH .Sdt meas mode 0 & 1 single pixel files & (unrelated) problem with dividing by increment count. (rebased onto develop)'
# PR 1166 mtbc 'assist #12385: use ArrayList? instead of Vector'
# PR 1108 melissalinkert 'MRC: fix handling of mode 16 data (rebased onto develop)'
# PR 1116 rleigh-dundee 'cpp: Add TIFF support (1)'
# PR 1145 joshmoore 'Make private class in DV reader public (see #12358)'
# PR 1156 sbesson 'Updating Zeiss links (rebased onto develop)'
# PR 1158 hflynn 'Removing dead link from Minolta-MRW format page (rebased onto develop)'
# PR 1110 sbesson 'BF docs: Jenkins cleanup (rebased onto develop)'
# PR 1147 rleigh-dundee 'cpp: bioformats: PixelProperties? supports pixel types of different endianness'
# PR 1152 hflynn 'Comstat2 link (rebased onto develop)'
# PR 1149 sbesson 'Add prefix to zip file produced by dist-bftools target (rebased onto develop)'
# PR 1106 melissalinkert 'Imaris HDF: make sure that all resolutions have the same ZCT sizes (rebased onto develop)'
# PR 1097 melissalinkert 'CellSens?: fix off-by-ones in subresolution tile calculations (rebased onto develop)'
# PR 1070 melissalinkert 'DICOM: expand sequence reading to include known sequences (rebased onto develop)'
# PR 1060 melissalinkert 'Allow dist-matlab to run on Windows'
# PR 1049 melissalinkert 'DICOM: fix file grouping so that path names are normalized (rebased onto develop)'
# PR 1028 melissalinkert 'Large fileset performance improvements (rebased onto develop)'
# PR 1135 joshmoore 'Update native-lib-loader to 2.0.1 release (rebased onto develop)'
# PR 1142 hflynn 'Add 'show and edit on Github' to docs side menu (rebased onto develop)'
# PR 1137 melissalinkert 'Update version history for 5.0.2 (rebased onto develop)'
# PR 1103 melissalinkert 'Flex: fix support for new file naming scheme (rebased onto develop)'
# PR 1092 sbesson 'Allow for a >1 count increment in B&H .sdt Files. (rebased onto develop)'
# PR 1101 melissalinkert 'QuickTime?: fix header/footer parsing bug (rebased onto develop)'
# PR 1127 sbesson 'CI logging improvements (rebased onto develop)'
# PR 1102 melissalinkert 'Metamorph .nd performance improvements (rebased onto develop)'
# PR 1109 melissalinkert 'Fix memo file path creation on Windows (rebased onto develop)'
# PR 1100 melissalinkert 'Fix single plane ND2 line scan (rebased onto develop)'
# PR 1096 melissalinkert 'Fix 5D Imspector support (rebased onto develop)'
# PR 1098 melissalinkert 'Gatan metadata fixes (rebased onto develop)'
# PR 1082 rleigh-dundee 'C++: Add support for integers of different endianness'
# PR 1120 rleigh-dundee 'cpp: ome-bioformats: Use std::complex for complex pixel types'
# PR 1118 joshmoore 'LogbackTools?: silence ClassCastException? traces (rebased onto develop)'
# PR 1128 hflynn 'Update auto-generated documentation on develop'
# PR 1119 hflynn 'User docs tidying (rebased onto develop)'
# PR 1099 melissalinkert 'Disable file grouping in ImageJ remote import plugin (rebased onto develop)'
# PR 1107 melissalinkert 'Exclude log4j and packages from target-test-runner (rebased onto develop)'
# PR 1121 sbesson 'Fix bfGetPlane tile input check (rebased onto develop)'
# PR 1117 rleigh-dundee 'cpp: Minor doxygen fixes'
# PR 1126 hflynn 'Leica link (rebased onto develop)'
# PR 1083 rleigh-dundee 'make: Convert variables to ant properties'
# PR 1075 hflynn 'Remove dead bitmap link (rebased onto develop)'
# PR 1076 hflynn 'Adding CONTRIBUTING file to BF repo (rebased onto develop)'
# PR 1073 rleigh-dundee 'docs: Delegate all sphinx Makefile targets to ant'

Repository: ome/scripts
Updating 31f89c4..9f8a7a0
Merged PRs (fast-forward):

# PR 85 hflynn 'Update batch image export tutorial link'
# PR 76 will-moore 'Fix 'No permissions' error in Make_Movie.py. See #12227'
# PR 81 will-moore 'Make movie format time 12254 (rebased onto develop)'
# PR 84 sbesson 'Get inputs all scripts (rebased onto develop)'
# PR 79 sbesson 'Travis fix (rebased onto develop)'

Repository: openmicroscopy/ome-documentation
Updating be161c6..81205bb
Merged PRs (fast-forward):

# PR 837 joshmoore 'Add mention of 'Protocol' failure for IPv6 (rebased onto develop)'
# PR 832 sbesson 'Fix minor points on the Cpp page (rebased onto develop)'
# PR 833 sbesson 'Restore build system on the main developers documentation index (rebased onto develop)'
# PR 828 sbesson 'Search page tidying up (rebased onto develop)'
# PR 829 sbesson 'OMERO Developer doc tidying (rebased onto develop)'
# PR 823 joshmoore 'Add deploy downstream: 'merge-maven
# PR 825 hflynn 'Contributing section update'
# PR 822 hflynn 'Schema links develop'
# PR 817 ximenesuk 'Update DropBox? documentation (rebased onto develop)'
# PR 812 sbesson 'Remaining changes post 5.0.x job migration'
# PR 816 will-moore 'Webgateway mip 5150 (rebased onto develop)'
# PR 814 bpindelski 'Add LDAP error message explanation.'
# PR 806 aleksandra-tarkowska 'Webstart template (rebased onto develop)'
# PR 807 aleksandra-tarkowska 'ldap over ssl instruction improvement (rebased onto develop)'
# PR 805 hflynn 'Adding contributing doc link & Zeiss link update'
# PR 810 hflynn 'Adding example server setup page (rebased onto develop)'
# PR 743 sbesson 'Propose redesign of OMERO and Bio-Formats 5.0 CI jobs'
# PR 809 sbesson 'Travis fix (rebased onto develop)'
# PR 802 snoopycrimecop 'Update index.txt'
# PR 801 sbesson 'Add Edit on Github button (rebased onto develop)'
# PR 783 mtbc 'document new separator in omero.fs.repo.path (rebased from dev_5_0)'
# PR 782 will-moore 'Custom web login 11961 (rebased onto develop)'
# PR 795 manics 'Root password reset command (rebased onto develop)'
# PR 786 mtbc 'warn that in-place ln_s can be slower for HCS (rebased from dev_5_0)'
# PR 797 ximenesuk 'Add DropBox? Windows requirements'
# PR 793 hflynn 'Ice35 support for Windows (rebased to develop)'
# PR 791 hflynn 'Limitations update for 5.0.2 (rebased onto develop)'
# PR 792 bpindelski 'Remove repetition of the word "files" (rebased onto develop)'
# PR 787 manics 'Add code-signing documentation (rebased onto develop)'
# PR 776 sbesson 'Remove all references to CI jobs in the official documentation'
# PR 772 rleigh-dundee 'make: Convert variables to ant properties'
# PR 771 hflynn 'Adding pyramid generation data duplication warning to in-place import (rebased onto develop)'
# PR 760 rleigh-dundee 'Make Ice 3.4 the minimum supported version'
# PR 768 hflynn 'Rephrasing CONTRIBUTING re: branch for PRs (rebased onto develop)'
# PR 769 hflynn 'Making API doc links point at release version (rebased onto develop)'
# PR 766 rleigh-dundee 'ant: Default all properties and handle empty vars in conf.py'
# PR 758 hflynn 'Adding API doc links to OMERO docs front page (rebased onto develop)'
# PR 759 hflynn 'ticket 10030 fix - contributing file for docs repo (rebased onto develop)'
# PR 761 rleigh-dundee 'Delegate all Makefile targets to ant'

Generated by OMERO-5.1-latest-submods#135 (​http://ci.openmicroscopy.org/job/OMERO-5.1-latest-submods/135/)