Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

github.com/ome/ome-model

OME model (specification, code generator, implementation)
https://github.com/ome/ome-model

First phase of changes to add optical element to filterset, schema/diagram/transform are all out of sync.

9b0dc662cf24fc185df9eb08c6cfc5d1947430b9 authored over 14 years ago by Andrew J Patterson <[email protected]>
Fixing typo

b89f9693f6c7f0b601114858efac982d7273e984 authored over 14 years ago by Andrew J Patterson <[email protected]>
Removing secondary filters and updating the transform

49011f59777cc4fad0758387e282cfaafe1a96a6 authored over 14 years ago by Andrew J Patterson <[email protected]>
Commented out unused sections of the code and adding trascform for FilterLists

c1e11167a04de9ac7e647a51fa70e879f966d885 authored over 14 years ago by Andrew J Patterson <[email protected]>
#73 Added a long comment to LightEmittingDiode but no real changes to the schema. It did not seem there was a suitable generic solution.

39933b8315946e1add74eae1e6fcb3a9a2ea0287 authored over 14 years ago by Andrew J Patterson <[email protected]>
Ticket #106 - WellSampleCount renamed to MaximumFieldCount

83fed125e0f1d3c4664c7c0e081cdfcdac78256d authored over 14 years ago by Andrew J Patterson <[email protected]>
Filter changes for ticket #63 - Adding LightPath object

9190a72dad9d83207d496da9f3382e6588560272 authored over 14 years ago by Andrew J Patterson <[email protected]>
Updated the transform for 2010-04, now has code to caculate the max number of well samples in the wells of a given plate. Thought I needed this value to get the unique index working, now think it might have been working all along.

7be294dfc6340435b2c6ab523dfe60464bc213ee authored almost 15 years ago by Andrew J Patterson <[email protected]>
Fix various dependency problems exposed by scan-deps.pl.

85faa3e4b6a5e62e58d44650cea122f9496f3012 authored almost 15 years ago by Curtis Rueden <[email protected]>
Realised the XSLT file had the wrong name.

5be18ce86ab2c0f43757b94173d863c2fc7c54ac authored almost 15 years ago by Andrew J Patterson <[email protected]>
Adding more sample file for OMERO trac ticket http://trac.openmicroscopy.org.uk/omero/ticket/1820

00140d406007521e73e09651a2d11ef3ece93909 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Adding more sample files for OMERO trac ticket http://trac.openmicroscopy.org.uk/omero/ticket/1820

76337813b9657996da8d73594bc5434ff0b0096f authored almost 15 years ago by Andrew J Patterson <[email protected]>
Updated the transform for 2010-04, second try at index in WellSample, will now work provided the total number of samples in any given well is less than the total number of wells.

22118cb894a883e406cfc2c43013f717dedfedb3 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Updated the transform for 2010-04, first try at index in WellSample.

1eac181d354209c6379e4ff5d66ff82a9af57042 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Changed OME schema to import from working folder on server not local directory for schema transform testing.

ca6fe6743720daf934a99f1b78e9ff93318873b0 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Removing unused functions from new transform to 2010-04, they can be added back as required

Ticket on omero trac http://trac.openmicroscopy.org.uk/omero/ticket/1897

b9f7228203f7f98401765eb220f55060b9d0867e authored almost 15 years ago by Andrew J Patterson <[email protected]>
Adding two more sample files used to test validation failures of the schema

b6f5abd07116f5176ebd264d535df9c32939a9f8 authored almost 15 years ago by Andrew J Patterson <[email protected]>
New version of tabGenMain that works with the latest schema

22cc9ec863ad985aaefa55f9a75b078c5b8b74eb authored almost 15 years ago by Andrew J Patterson <[email protected]>
Updating EA files I will use to generate DB diagram for FAQ

Ticket on omero trac http://trac.openmicroscopy.org.uk/omero/ticket/1928
Adding more OME samples
...

c8499fe84a5dee0f5861f0e9b2a4eb4bcd08645b authored almost 15 years ago by Andrew J Patterson <[email protected]>
Removed the misleading SamplesPerPixel from Channel generated as part of the update process.

Closes ticket on omero trac http://trac.openmicroscopy.org.uk/omero/ticket/1954

fdcdc437e6c7f573e10526ac8f287d25aad69509 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Merging cleanup branch back into trunk.

a49cde8514b6dadae3ad6827da5e26fb86a8ce20 authored almost 15 years ago by Melissa Linkert <[email protected]>
Fixed bug with duplicate Channel IDs and bug with no pixels if no AcquiredPixels set. The ChannelID now had the position fo the chanel appended to producing a couter from 1 up. If no AcquiredPixels value is set it now used DefaultPixels instead.

Ticket on opero trac http://trac.openmicroscopy.org.uk/omero/ticket/1954

baca2494243047bcece16e9ba8695664618aa682 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Update to Plate for ticket #106 to add a unique constraint to the index in WellSample on the Plate level.

7ba2437040da2a0067073d58674431ae99845ebc authored almost 15 years ago by Andrew J Patterson <[email protected]>
Update to WellSample for ticket #106 to add a unique but non-sequential index

b4a987b0cc36febb39bc6cfc491451aeb49e259c authored almost 15 years ago by Andrew J Patterson <[email protected]>
Updates to enumerations for ticket #117 and #118 but these may be changed to use full terms not abbreviations.

bc57c1235dc63d5ff285c035fd617331f219299a authored almost 15 years ago by Andrew J Patterson <[email protected]>
Updated Oxygen Project

31e3bb2e61498e83b0ed58241d1bee39439ae7d8 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Move a bunch of Ant junk into its own folder.

e41a7631caf5050de3583e8631813a0cdc009a71 authored almost 15 years ago by Curtis Rueden <[email protected]>
Adding more sample files for OMERO trac ticket http://trac.openmicroscopy.org.uk/omero/ticket/1820 (also suitable for #60 on this trac)

806b5fd4510df984491a18600fb1084e2933d09e authored almost 15 years ago by Andrew J Patterson <[email protected]>
More cleanup of URLs.

ab92207ee6e433363a47f66102effd4a28c7346f authored almost 15 years ago by Curtis Rueden <[email protected]>
Update a bunch of URLs. Still more to be done in various packages though.

4e5ad3a0cc290cdd2267da7e32be6e33c5c3b674 authored almost 15 years ago by Curtis Rueden <[email protected]>
Adding first set of sample files for OMERO trac ticket http://trac.openmicroscopy.org.uk/omero/ticket/1820 (also suitable for #60 on this trac)

7173561bacbf6e479cd2bde0c38427046a306aba authored almost 15 years ago by Andrew J Patterson <[email protected]>
Latest updates for ticket #106 from the EA diagram.

1f905cfc544014c74906d1ba0a9a292bfbfa129b authored almost 15 years ago by Andrew J Patterson <[email protected]>
Adding some samples using StructuredAnnotations under 2009-09 schema.

66e4d0cb30842c62ca49826a090af84d372cad00 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Replace ScreenAcquisition by PlateAcquisition. Added Index to WellSample. #106

19c6bafac6709666cd5db8999d3cd04c1bd9b0a8 authored almost 15 years ago by Andrew J Patterson <[email protected]>
ROI: Namespace now optional #108

fab3c6c45873a7254033565a74d4ccb507b7bb32 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Adding first stab at a transform file from Lica-OME to regular OME. This file is probably not needed at all but may as well store it.

0471fea80cef95c264a94798d90198dc5c70f0c5 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Changing dates for copyright and release 2010-04. First part of #115

ca1f9ca9985ab95c551bfc29fc34c6c145d6d0ff authored almost 15 years ago by Andrew J Patterson <[email protected]>
Removing Custom Attributes (CA/STD) & Analysis (AC/AM/MLI/CLI/DH) for schema clean up #113

fe5765b24e96f46195d1800f0c7a0a2abb7ccb61 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Adding missing units for #81 to ROI schema. Reworking ROI schema for #108

8643a4e9b28e882fc2189c9c448596f5bfd5ee84 authored almost 15 years ago by Andrew J Patterson <[email protected]>
Adding final missing units for #81 to OME schema

a901f3c69e8a3319d3ebe73ff876b446136c297b authored almost 15 years ago by Andrew J Patterson <[email protected]>
Adding units for #81 to OME schema

5b41d95bbcf86b50564ed9a70fa11aa2c6788973 authored almost 15 years ago by Andrew J Patterson <[email protected]>
* Tweaked pixel type enumeration to allow the "double" type.

* Fixed a bug in loci.formats.tiff.IFD that caused double data to be incorrectly identified.

b32889f51d08f262d4f5f5d4ae1da5717b9ffc1e authored almost 15 years ago by Melissa Linkert <[email protected]>
Enough changes to the ROI schema to get code generation for ROI types working correctly. (#108)

0e56b46d02932e013ceb74a4d676b109372e7112 authored about 15 years ago by Chris Allan <[email protected]>
Fixed choice max occurances support

b9a8934c3f60094101e80f0754e2416c3f02c537 authored about 15 years ago by Chris Allan <[email protected]>
* xsd:appinfo support

* abstract type support
* fixed issues with cardinality resolution in an xsd:choice

1c226a3320a98eba42c3246a06707856d3db3a39 authored about 15 years ago by Chris Allan <[email protected]>
Fix OSGi version numbers to match latest 4.1.0 release.

3f3b5a8992a1d85e79116e28f4349d15b0d5b408 authored about 15 years ago by Curtis Rueden <[email protected]>
Ignore case and trailing whitespace when looking for an enumeration.

723d33e32111aae9137e448fbfb71b1b3b82d29b authored about 15 years ago by Melissa Linkert <[email protected]>
A few template fix-ups to make enumerations and their handlers work more nicely with a class hierarchy.

bfd1c93acda14b17698ad13a8db1b0d0fa4229a0 authored about 15 years ago by Chris Allan <[email protected]>
Enumeration handlers now import the corresponding enumeration class.

18754a3b084bfab3958da482655448aea2b1bc0a authored about 15 years ago by Melissa Linkert <[email protected]>
Enumeration handler initial template.

83957aaf8b4ccfc0639cab1ade46054b2b37be0c authored about 15 years ago by Chris Allan <[email protected]>
Correct name handling for enumerations with "-" or leading digits.

b699b95f0142077f239fdb73fb32bbad8d188e4d authored about 15 years ago by Chris Allan <[email protected]>
Added appinfo element marking Shape and LightSource as abstract types

60e69b53844e48f52fa5ed83c15294f4f519cbd0 authored about 15 years ago by Andrew J Patterson <[email protected]>
Fix setter bracket count across metadata templates.

81a64bda8b44462760e11a63a55121932bf3ba07 authored about 15 years ago by Chris Allan <[email protected]>
Fix typo in metadata store template.

4dfc500a6aff44bf6187ac3dfb7c0466d5cb878d authored about 15 years ago by Chris Allan <[email protected]>
Better and more pervasive type resolution for enumerations.

f2cd02d7f8a30976365404d6e9c69bb621f00d71 authored about 15 years ago by Chris Allan <[email protected]>
Adding some missing docs to the 2009-09 schema - no change to the structure on the docs.

cd3745fc72344f21f1f51cd3dac25870bfa885d8 authored about 15 years ago by Andrew J Patterson <[email protected]>
Adding a version of the released 2009-09 schema for the validator

and other tools to run against.

915c14277efbf20e3a07268997c50474580ef113 authored about 15 years ago by Andrew J Patterson <[email protected]>
Multiple schema support for Java class generation.

25e8ae33be3ee890ddb7b8386372f04c3d0cbae9 authored about 15 years ago by Chris Allan <[email protected]>
Multiple schema support.

1695576b83d7467075b5d5467f80c6935beece1d authored about 15 years ago by Chris Allan <[email protected]>
Proper object name handling.

8efed16dcce021637eeb703ff61fdd7c92f62337 authored about 15 years ago by Chris Allan <[email protected]>
Initial version of the enumeration classes (#75).

703575509d1912e3194a1ec1d4a0ec501a6a4496 authored about 15 years ago by Chris Allan <[email protected]>
Release of Data Model 2009-09 Schema

9e9db42f68d6eb4410163ff8e25dc41f9a67082f authored about 15 years ago by Andrew J Patterson <[email protected]>
Adding autogenerated docs for 2009-09 schema.

37834751d9b758c4bacfe046dd25c8783e221a27 authored about 15 years ago by Andrew J Patterson <[email protected]>
Use Double instead of Float for all floating point OME metadata.

276bbb971b747c8d0bea66b2415fea5bb6eee2a1 authored about 15 years ago by Curtis Rueden <[email protected]>
Remove obsolete test class.

7538736cfa47b966444e9c45b761f8dfd33d43d1 authored about 15 years ago by Curtis Rueden <[email protected]>
Use Double instead of Float for xsd:float type.

ca28ba5176f61797c051322a7ad81c9b0420c034 authored about 15 years ago by Curtis Rueden <[email protected]>
Adding some docs

cd7b5581dfdd05badb9e4557824d823f41e5e4d9 authored about 15 years ago by Andrew J Patterson <[email protected]>
Added code to create the SA AnnotationLinks

d80a1a98aefd93e9a84943fa96ae605f8647250e authored over 15 years ago by Andrew J Patterson <[email protected]>
Fix up Ant build system; add OSGi bundle export to JAR production.

5b3088d16b13f4109df0fb4f0af3abb4c30f9d72 authored over 15 years ago by Curtis Rueden <[email protected]>
* Better bounds checking in FlexReader.getSeriesUsedFiles.

* Fixed a few more bugs exposed by the test suite.

684612752fc7a5eb87502f06d3d16dac3c84ef9c authored over 15 years ago by Melissa Linkert <[email protected]>
File re-indented and comment out code removed.

ec46b140c685f806335479f338831fb6d2b90666 authored over 15 years ago by Andrew J Patterson <[email protected]>
Reworking of SA and ROI for new schema changes. Links need added to SA.

c972ac1c3a1fd534b666fe7b23eb081924bcaed9 authored over 15 years ago by Andrew J Patterson <[email protected]>
Fixes to ROI and assorted namespace issues.

42c91da7af41653a72ba3988f4fb423b9dc3d7c0 authored over 15 years ago by Andrew J Patterson <[email protected]>
Removing older transforms that did not match new naming.

a9a87bc84043cb3362d7318c9cd1319b43a4b7aa authored over 15 years ago by Andrew J Patterson <[email protected]>
* Added enumeration checking to OME-XML MetadataStore implementations.

* Fixed a bunch of bugs exposed by automated tests.

7622962d216dc29b5adc5226baec320f408b0a0f authored over 15 years ago by Melissa Linkert <[email protected]>
* Changed signatures of MetadataStore.setMaskPixelsBinData and MetadataRetrieve.getMaskPixelsBinData to operate on a byte array instead of a String.

* OME-XML MetadataStore implementations handle Base64 compression/decompression of MaskPixels.Bin...

80f21cc4914ae4eea8fd3de6c5324f76c12566af authored over 15 years ago by Melissa Linkert <[email protected]>
Adding in Will changes to docs

113302f9bd4e01496aee21266025343b5fefbd28 authored over 15 years ago by Andrew J Patterson <[email protected]>
Adding in Will changes to docs

624bd0576c0e37119b12593a4bd888ad79d3f3cb authored over 15 years ago by Andrew J Patterson <[email protected]>
Adding full URL to the script and stylesheet links.

69baf059159c8912bda97dea84f4fb9666703fa4 authored over 15 years ago by Andrew J Patterson <[email protected]>
Pending release of the 2009-09 schema.

b5f57501f730e5645d9fd700b70f647f6e927b0a authored over 15 years ago by Andrew J Patterson <[email protected]>
Comment Changes

e9202bd6b20c798670f9891db8b28ce80c25cf78 authored over 15 years ago by Andrew J Patterson <[email protected]>
Comment Changes

b5eb33c3d352f371c3a03790d62a0a81988ff470 authored over 15 years ago by Andrew J Patterson <[email protected]>
Comment Changes

8395e2d0ed041b657a8d4fc545921dd27128718a authored over 15 years ago by Andrew J Patterson <[email protected]>
Fixed node caching problem.

189069700b5091ac2407b925e9b5fa7ff57cc5e8 authored over 15 years ago by Melissa Linkert <[email protected]>
Version of 2007-06 to 2008-09 that runs from Java.

c93178769749aff163e779ed65c70e78c1af9796 authored over 15 years ago by Andrew J Patterson <[email protected]>
Versions of 2003-FC and 2008-02 to 2008-09 that runs from Java.

6151e8e7fedd7bde39bac16a5569c45a14488c93 authored over 15 years ago by Andrew J Patterson <[email protected]>
Version of 2008-09 to 2009-09 that runs from Java. Still needs some update work.

2e73c6cc6893505594dc83bc62f5c86531b002cf authored over 15 years ago by Andrew J Patterson <[email protected]>
Now with fixes from Curtis and a fix for the namespace that should work for Bio-Formats but may not be as general.

adcaca581d20ae5f24ae9009e0f0f958bdb20763 authored over 15 years ago by Andrew J Patterson <[email protected]>
Cleaned up options for NamingConvention for the Plate row and columns.

df43383d7f0b8e7e004baa332aa2603b190b8bc9 authored over 15 years ago by Andrew J Patterson <[email protected]>
Moved ShapeDisplayOptions from OMERO.xsd to Shape in ROI.xsd

3607c9e94efdfc76027ab27296171204637f88f4 authored over 15 years ago by Andrew J Patterson <[email protected]>
Removed the AnalysisModule fromthe schema

e3f273d3b7706472e3c3ce9c227e25c29cc1c538 authored over 15 years ago by Andrew J Patterson <[email protected]>
Removed the processing of AnalysisModule

35a12d344af255279b8002c18a75ad0561c20437 authored over 15 years ago by Andrew J Patterson <[email protected]>
Fix toplevel Findbugs target.

0330b900f84be0a3a3b6833ca497ba0877e18c91 authored over 15 years ago by Curtis Rueden <[email protected]>
Mode Annotation changes.

d6679204e6d38eaefbf747930330edc85030f71c authored over 15 years ago by Andrew J Patterson <[email protected]>
* Significantly better MetadataRetrieve and AggregateMetadata support.

* Various updates to XsdFu generic functionality.

83bb3730c984c5cfb5789402884d600dc24a6932 authored over 15 years ago by Chris Allan <[email protected]>
StructuredAnnotations elements changed to AnnotationRef and made 0 to Many

488c5f20adfeb1dff020ab8ac621871676f08b8f authored over 15 years ago by Andrew J Patterson <[email protected]>
Changing back to using web site for schema imports after validation checked.

5cc229a0e379958bf66b7d436e68c41415281b65 authored over 15 years ago by Andrew J Patterson <[email protected]>
StructuredAnnotations element added at appropriate points in the model but StructuredAnnotations not yet restructured internally.

77250894698e3f9a8aa92a1d45771cecec69a546 authored over 15 years ago by Andrew J Patterson <[email protected]>
Added key for Shape ID

e289d603c4d7e9b400d4eaf18bf5db2f30a42156 authored over 15 years ago by Andrew J Patterson <[email protected]>
Remove redundant WaveStart and WaveIncrement attributes of Pixels

c6109be45f6217e9c5fcd83558bcd2d1b69527c9 authored over 15 years ago by Andrew J Patterson <[email protected]>