Update develop submodules

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

Repository: openmicroscopy/bioformats
Updating f247b30..f27f679
Merged PRs (fast-forward):
  # 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..491d96e
Merged PRs (fast-forward):
  # 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..3656f6a
Merged PRs (fast-forward):
  # 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#131 (http://ci.openmicroscopy.org/job/OMERO-5.1-latest-submods/131/)
Merge pull request #2583 from joshmoore/12358-parse-metadata

12358 parse metadata
refactoring duplicates
removing unnecessary configuration
adding link to Django documentation
Merge pull request #2682 from aleksandra-tarkowska/rebased/develop/group_permissions

Group permissions (rebased onto develop)
merge develop -D org: PR 2127 (Working view to email announcements to selected users, groups, email addresses and/or all users)
merge develop -D org: PR 2391 (Imagej omero (rebased onto develop))
merge develop -D org: PR 2411 (Update develop submodules)
merge develop -D org: PR 2435 (cpp: RTypesI: use static locals in place of duplicated globals)
merge develop -D org: PR 2550 (Avoid upscaling of bird's eye image)
merge develop -D org: PR 2560 (for-loop fix removes 'undefined' from reset dialog. See #12301)
merge develop -D org: PR 2612 (Add wsgi.py for OMERO.web (develop))
merge develop -D org: PR 2624 (nginx config template improvement)
merge develop -D org: PR 2684 (Rename don't recreate repos on move (Fix #12355) (rebased onto develop))
merge develop -D org: PR 2686 (clear sessions)
merge develop -D org

Repository: openmicroscopy/openmicroscopy
Excluded PRs:
  # PR 2688 manics 'Use a global HDF5 lock (trac: 10464)' (status: pending)
  # PR 2690 jburel 'Roi clean up develop' (status: failure)
  # PR 2403 aleksandra-tarkowska 'Send email' (label: breaking)
  # PR 2691 jburel 'Tag import (rebased onto develop)' (status: error)
  # PR 2363 dominikl 'Java Gateway API' (label: breaking)
  # PR 2683 sbesson 'Also mark TestTables.testErrorInGet as xfail (rebased onto develop)' (label: exclude)
  # PR 2585 aleksandra-tarkowska 'making time_zone and first_day_of_week configurable' (exclude comment)
  # PR 2182 joshmoore 'Read only flag' (label: exclude)
  # PR 2412 qidane 'Extra annotations' (exclude comment)
Already up-to-date.

Merged PRs:
  # PR 2127 dpwrussell 'Working view to email announcements to selected users, groups, email addresses and/or all users'
  # PR 2391 jburel 'Imagej omero (rebased onto develop)'
  # PR 2411 snoopycrimecop 'Update develop submodules'
  # PR 2435 rleigh-dundee 'cpp: RTypesI: use static locals in place of duplicated globals'
  # PR 2550 dominikl 'Avoid upscaling of bird's eye image'
  # PR 2560 will-moore 'for-loop fix removes 'undefined' from reset dialog. See #12301'
  # PR 2612 chris-allan 'Add wsgi.py for OMERO.web (develop)'
  # PR 2624 aleksandra-tarkowska 'nginx config template improvement'
  # PR 2684 joshmoore 'Rename don't recreate repos on move (Fix #12355) (rebased onto develop)'
  # PR 2686 aleksandra-tarkowska 'clear sessions'

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1162 melissalinkert 'AFI: populate magnification and physical pixel size metadata' (status: failure)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
  # PR 1054 qidane 'Additional annotation points throughout the model' (exclude comment)
  # PR 978 berl 'Add writing of .v3draw format for easy loading with Vaa3D.' (user: berl)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (label: exclude)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 1141 LeeKamentsky 'Reader for Amaris FlowSight .cif format' (label: exclude)
  # PR 1136 melissalinkert 'Add initial support for reading BinaryOnly OME-TIFF datasets (rebased onto develop)' (label: exclude)
Updating f27f679..0f70082
Merged PRs (fast-forward):
  # PR 1175 melissalinkert 'Fix channel count when exporting RGB images in ImageJ'

Merged PRs:
  # PR 983 melissalinkert 'Woolz: make sure the service is initialized when calling openBytes (rebased onto develop)'
  # PR 1123 melissalinkert 'Add a reader that accepts a file containing a file pattern'
  # PR 1154 melissalinkert 'Leica: prevent exception when linking EmissionFilter'
  # PR 1164 melissalinkert 'Add modulo support for LI-FLIM data'
  # PR 1170 rleigh-dundee 'cmake: Enable CMP0042 @rpath usage for MacOSX'
  # PR 1176 rleigh-dundee 'xsd-fu: Use package namespaces throughout and consolidate commands'
  # PR 1178 melissalinkert 'Nikon .nd2 fixes, part 2 (rebased onto develop)'

Repository: ome/scripts
Already up-to-date.

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

Merged PRs:
  # PR 799 manics 'Linux walkthrough (rebased onto develop)'
  # PR 824 sbesson 'OME DCO'
  # PR 827 aleksandra-tarkowska 'Nginx doc'
  # PR 834 aleksandra-tarkowska 'Session engine'

Generated by OMERO-5.1-merge-push#301 (http://ci.openmicroscopy.org/job/OMERO-5.1-merge-push/301/)