Ecosyste.ms: OpenCollective

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

github.com/ome/omero-blitz

Gradle project containing Ice remoting code for OMERO
https://github.com/ome/omero-blitz

Fix: A lot of unit tests didn't run due to wrong import

1bcbba12366f6becf827aa31407c64922affb48d authored about 6 years ago by Dominik Lindner <[email protected]>
Some cleanup (unify, white spaces, etc.)

1985e6ab384e92c87b7bda74b3adb53646308cb3 authored about 6 years ago by Dominik Lindner <[email protected]>
Add method to create multiple mask ROIs from int array

4f29aeb0e4d1715204ab24c25ac055d8ba149bae authored about 6 years ago by Dominik Lindner <[email protected]>
Add a toString method to MaskData to help debugging

aac014f56a0b539045fd252092197fec4decb01f authored about 6 years ago by Dominik Lindner <[email protected]>
Move crop mask methods out of the MaskData into util class

a7c4aeeced5e94f3a75a352220c065bd1132cd83 authored about 6 years ago by Dominik Lindner <[email protected]>
Have import log include specific report of target container.

e73194364bdd549e2a8ef85f87f1c88fb2dc5780 authored about 6 years ago by Mark Carroll <[email protected]>
Have importer-cli more concisely report bad server hostname.

e3abcbd03f521c5294e1f275a8615f125f70b7c8 authored about 6 years ago by Mark Carroll <[email protected]>
Added some convenience methods to MaskData

0db257514b4de8a39705dd694e413ae04650b4a1 authored about 6 years ago by Dominik Lindner <[email protected]>
Replace all usages of DefaultMetadataOptions by DynamicMetadataOptions

The second class is a more generic implementation of the MetadataOptions
allowing support for ke...

0ca3fba2b0360ef9e84686b9d2e19560a54b6f5b authored about 6 years ago by Sebastien Besson <[email protected]>
Added some more tests to ImportCandidatesTest

d984d257a3b2a64432ff1bf436ea59f3742b1abd authored over 6 years ago by Dominik Lindner <[email protected]>
Don't remove files which are still needed by other filesets

d6001abf7776448b52a54bb8da4b653a764b2a2f authored over 6 years ago by Dominik Lindner <[email protected]>
Also test the folder itself

6e47d9d5bc8ce7d5ccc040116cc4be65d8c6088b authored over 6 years ago by Dominik Lindner <[email protected]>
Use artificial NHDR files for the test

8ca9e4db40f472dadffcc70441fff3c3f32cecb0 authored over 6 years ago by Dominik Lindner <[email protected]>
Use Collections2; Improve error output

42b7c8e9a2b8b6eaebbfa7ee3dbec45d7c3f35fc authored over 6 years ago by Dominik Lindner <[email protected]>
Print all failures

1ee0796b43d0fdc7c6ba8b749199ed8736bb2f57 authored over 6 years ago by jmoore <[email protected]>
Added file order test for ImportCandidates

a04a7acfe76c7a80fa39100edc4abeec15fdd161 authored over 6 years ago by Dominik Lindner <[email protected]>
import: add synchronized to ImportLoggingMonitor

a1a34487f2f476b8c44edda7d73d1a8ddfb57657 authored over 6 years ago by jmoore <[email protected]>
import: always include newline for clear logs

The various calls to `System.{out,err}.print()` (no `ln`)
allow multiple different threads to in...

29449c364dd7a5e13ffcc54f43a0fc76b47678bf authored over 6 years ago by jmoore <[email protected]>
import: add --readers flag and unit tests

This is in addition to the short `-l` form.

fc02d1e438e9a3569eaaa6909e527b149fc4ea16 authored over 6 years ago by jmoore <[email protected]>
Merge pull request #5827 from rgozim/update_thumbnail_loading

Updates to ThumbnailLoader and ThumbnailService

ac30f02fe482e2ab8f52d3e0ce0e33af370cfad0 authored over 6 years ago by Josh Moore <[email protected]>
Merge pull request #5839 from joshmoore/background-queue

Add Executor.Priority.BACKGROUND

8b30bf845b4bb68e469e0772182265063e51cbe4 authored over 6 years ago by Josh Moore <[email protected]>
Merge pull request #5828 from mtbc/file-upload-in-parallel

for CLI import add --parallel-{upload,fileset} options

2f749d6716ea67a1b2eb06e2913f3e44dec2e199 authored over 6 years ago by Josh Moore <[email protected]>
Merge pull request #5817 from melissalinkert/trust-bf-colors-develop

ChannelProcessor: do not change color to white if Bio-Formats set a color

177a9d7e79c5c1dbf96e8a171c624d81305026da authored over 6 years ago by Josh Moore <[email protected]>
don't make a larger thread pool than the number of filesets

ebde9bc2064c54591fdb6a6bdceff41a8098a727 authored over 6 years ago by Mark Carroll <[email protected]>
Add Executor.Priority.BACKGROUND

The addition of parallel import has made it quite easy
to use up the omero.db.pool_size number o...

a12d248430dd835962eb42c7121ed76217971a63 authored over 6 years ago by jmoore <[email protected]>
Merge pull request #5826 from mtbc/single-checksum-on-import

have import calculate the uploaded file checksum only once, not twice

ee2f2240d6f665d84bd988bd822d8e9ac1db6f04 authored over 6 years ago by Josh Moore <[email protected]>
adjust wording of error message

We upload files and import images.

3729ee521ecdb1813642d0b91f15d13dab2758e5 authored over 6 years ago by Mark Carroll <[email protected]>
reindent code, whitespace only

249805720af59cbde8db811dce513a47ed54a308 authored over 6 years ago by Mark Carroll <[email protected]>
for import load container target only within fileset thread

6a519b4c5fdfeefe0e6276e27ea3e6d18526d8e1 authored over 6 years ago by Mark Carroll <[email protected]>
catch failure to retrieve hash of imported file

393623ed65beabcfef033e2902bdd85506e1ae71 authored over 6 years ago by Mark Carroll <[email protected]>
Merge pull request #5835 from mtbc/template-path

for import fix prefix template path expansion bug

4ff391d7c445376cb7dcf3032bf1aed873291d05 authored over 6 years ago by Josh Moore <[email protected]>
cancel fileset's upload threads if one was interrupted

07325657df73e17ab3f5ef69b9171e97871c4555 authored over 6 years ago by Mark Carroll <[email protected]>
if file upload fails then cancel fileset's other uploads

54774cec34420be00639a6d2661f811750a65263 authored over 6 years ago by Mark Carroll <[email protected]>
switch parallel import to use ExecutorCompletionService

Provides earlier warning of failures.

e2bfd353cf8453f655cca90b45fa2d4cd7123a65 authored over 6 years ago by Mark Carroll <[email protected]>
remove unused variable: total

c7fa995b7a431dfdbc0de276dd8cf4e8dde0b1cd authored over 6 years ago by Mark Carroll <[email protected]>
use all-groups context to query for hash of uploaded file

56410e95b21778e918c63d523ac4782c0255c5e4 authored over 6 years ago by Mark Carroll <[email protected]>
Merge pull request #5833 from mtbc/thread-dir

add %thread% expansion option for omero.fs.repo.path

752db7708921fbda00fb85f485797c28429e8eda authored over 6 years ago by Josh Moore <[email protected]>
for import fix prefix template path expansion bug

28d2cb5a113188272d535609d777699ddc1bbe55 authored over 6 years ago by Mark Carroll <[email protected]>
Merge remote-tracking branch 'origin/develop' into single-checksum-on-import

f88883860a52302603f3016b2509857271774539 authored over 6 years ago by Mark Carroll <[email protected]>
can try to stop import threads when earlier one fails

5526711ed1142e3af85b5788afacf4302896a52a authored over 6 years ago by Mark Carroll <[email protected]>
reindent code, whitespace only

1784b1e2bb6e7d1141de2c251a3f851b6a3730ea authored over 6 years ago by Mark Carroll <[email protected]>
import candidates in parallel using fileset thread pool

57e5c5469bfed7c7eea1063728a376f9009b78aa authored over 6 years ago by Mark Carroll <[email protected]>
remove unused variable: numDone

161cbf587167c036116362df4edc0f6af45ae920 authored over 6 years ago by Mark Carroll <[email protected]>
have importImage use upload thread pool from importCandidates

7de16497f52ae88b8bc39e2f671822f191e109de authored over 6 years ago by Mark Carroll <[email protected]>
reindent code, whitespace only

8131a7c11a93b0dbbf09667fc16257f5a9af8fdf authored over 6 years ago by Mark Carroll <[email protected]>
have importCandidates create fileset & upload thread pools

a5f40f65392b83bdd4924f593c993dfce09f6652 authored over 6 years ago by Mark Carroll <[email protected]>
note in a variable the number of import containers

0214a72f5b41f4523c72d830bb83ab5c988027bb authored over 6 years ago by Mark Carroll <[email protected]>
introduce new --parallel-fileset option to Java import config

10ed8cb09d15714a8af8b3b683f3f69b41241e2e authored over 6 years ago by Mark Carroll <[email protected]>
Merge pull request #5821 from joshmoore/import-perf4j

perf4j: log import timings in import log

a3840cae37b87dd00c2de6cdc72d1c655d37b021 authored over 6 years ago by Josh Moore <[email protected]>
perf4j: Minor fixes suggesed by Mark

49692a40f77accf8b04a66ce5bc128e7c39f0f4f authored over 6 years ago by jmoore <[email protected]>
add %thread% expansion option for omero.fs.repo.path

b63d269456f12b49cb40185e20f84df12ed37626 authored over 6 years ago by Mark Carroll <[email protected]>
explicitly shut down fixed thread pool once upload finishes

989b1b55b55ea113ae63c1187dfbc36c60465a84 authored over 6 years ago by Mark Carroll <[email protected]>
Rework finalization to 'cleaning up import'

c21ff9714c3c15538af994525bc738d76f206e82 authored over 6 years ago by jmoore <[email protected]>
deprecate importer option useFullPath / userFullPath

unused for a long time

116d59717e19b5f6d238f6d8bc0915795b798032 authored over 6 years ago by Mark Carroll <[email protected]>
Add empty implementation to Destroyable

584c10c91bcae6d7f2f242bf38266e9e1f0edfa2 authored over 6 years ago by Dominik Lindner <[email protected]>
fix typo in option text

50f8bb0dbaffc7654ab91826a9f1807ef202785f authored over 6 years ago by Mark Carroll <[email protected]>
have ImportLibrary.importImage do multi-threaded file upload

74d5d893f0019b9419a117698dc432daedf93fb5 authored over 6 years ago by Mark Carroll <[email protected]>
make time estimator thread-safe

561c6bdc16afd92296204db078e6080fc121fd53 authored over 6 years ago by Mark Carroll <[email protected]>
in time estimator split stats mgmt code from stopwatch ops

bb229928fcdd896be347e6e99f39880e17d238cc authored over 6 years ago by Mark Carroll <[email protected]>
introduce new --parallel-upload option to Java import config

7564e484bb8cedba5528f15e709daf6dd3a02f92 authored over 6 years ago by Mark Carroll <[email protected]>
Updates to ThumbnailLoader and ThumbnailService

ThumbnailLoader calls new API, checks if image has pyramids and can determine what state a thumbn...

58cda67df7c9f6742fc656da5a34e62920d7a141 authored over 6 years ago by Riad Gozim <[email protected]>
use filename to identify correct used file in fileset

41e6376744e085b662b16270f613dc2a5f0fc8ae authored over 6 years ago by Mark Carroll <[email protected]>
on import, verify by file bean checksum, do not recalculate

b217bbecb9c4370bc0fcf355d21a1fb0e2f9fc38 authored over 6 years ago by Mark Carroll <[email protected]>
Remove Java8'isms

1fa4fc346b32c75b5328d955c6826f086f3cec1b authored over 6 years ago by jmoore <[email protected]>
perf4j: capture other service calls in log

579370a915fdcfdf32bd5b5082065043603d69d2 authored over 6 years ago by jmoore <[email protected]>
Merge pull request #5820 from mtbc/static-final

adjust ordering of Java "static" "final" modifier keywords

482b99d8624558adeb5f81ddb028a331cd91d9e5 authored over 6 years ago by Josh Moore <[email protected]>
perf4j: also add import request times

6d9e89d7088452e2909185d623a0f8fc870dca36 authored over 6 years ago by jmoore <[email protected]>
perf4j: log import timings in client log

By adding use of Slf4J's MDC to ManagedImportProcessI and
ManagedRepositoryI, we are able to get...

4c308531b25d237499711d4ad43feb20e3d056df authored over 6 years ago by jmoore <[email protected]>
switch modifiers to customary order in API docs

ce5fd1d16b8371654612ce45260403662b0f95d0 authored over 6 years ago by Mark Carroll <[email protected]>
switch modifiers to customary order in omero.* codegen

fc230d368a7167582a5e4ae6c7c7e2666e9ce3ba authored over 6 years ago by Mark Carroll <[email protected]>
quote "[" in Slice as not introducing a link

618dc9cfce29798b4f7f8111dd7786a20137da3f authored over 6 years ago by Mark Carroll <[email protected]>
trim useless header comment lines

2f8308fcccca3642a19631d984e13a3bce079e12 authored over 6 years ago by Mark Carroll <[email protected]>
ChannelProcessor: do not change color to white if Bio-Formats set a color

Channels with no emission wavelength data are typically candidates for
having their colors reset...

145b792f3b0cfc654c26a50a70acddfbca31945f authored over 6 years ago by Melissa Linkert <[email protected]>
Fix 2018-SV1, 2018-SV2 and 2018-SV3

26476dd6318c44c195ab0a460b1943bfc027b343 authored over 6 years ago by Jean-Marie Burel <[email protected]>
Merge pull request #5761 from dominikl/shapedata_bugfix

Shapedata bugfix

5a807727ab99e7455c8c7a6b955a41051e53f125 authored over 6 years ago by Josh Moore <[email protected]>
Some cosmetic changes

6d632fb3567306f9617387e659c7f9ecd8a6af75 authored over 6 years ago by Dominik Lindner <[email protected]>
Fixed getShapes issue and added unit test

4452c62b14c07ca56dc228bcc5ba70145eeda79a authored over 6 years ago by Dominik Lindner <[email protected]>
Another null check

b978df593a99830d588ab94adc5aa1742c676fa5 authored over 6 years ago by Dominik Lindner <[email protected]>
Add some null tests

3f78d3a1efea1a2f0d9b72ae6bd51613a7b5e3d5 authored over 6 years ago by Dominik Lindner <[email protected]>
Merge pull request #5765 from mtbc/gateway-all-groups

address all-groups-context issue for gateway queries

3615de59f5bb4601ac3fb2c03b7ccf11285ac77d authored over 6 years ago by Josh Moore <[email protected]>
Use example url

0c3520ddb97e63665fa9d51701e7575802a76d1c authored over 6 years ago by Jean-Marie Burel <[email protected]>
Do not use QA url

96462d5b82975887459a925795e6e1c57d4a4770 authored over 6 years ago by Jean-Marie Burel <[email protected]>
Remove -- when not necessary

090d41ef21d1f8fa8e0e5f2d433be27aa510bce1 authored over 6 years ago by Jean-Marie Burel <[email protected]>
Add unit test for Shapes dirty flag

a70f99deae2708879438da3261d895a30c29e2e7 authored over 6 years ago by Dominik Lindner <[email protected]>
Just removed comment

88195337d9135656869b710fac1bd7fd7300bfd5 authored over 6 years ago by Dominik Lindner <[email protected]>
Make sure to set dirty flag on any change

a67da5e7dec3d4a4fa1a47574d6ce922e43a8f4e authored over 6 years ago by Dominik Lindner <[email protected]>
have Java Gateway reject SecurityContext(-1)

Ignoring SecurityContext(-1) fools clients into thinking it may
have useful effect. This will br...

39860b61c186e75544de9a75b57d01e2b9de509a authored over 6 years ago by Mark Carroll <[email protected]>
Update javadoc of ROICoordinate

2c24c54ab89d15103d16a3c9766b3fe71611c3cb authored over 6 years ago by Dominik Lindner <[email protected]>
Only deprecated methods which have issues with zct==-1 for now

1971fe47f8aa50ed8abfa991df6c9397f03686f3 authored over 6 years ago by Dominik Lindner <[email protected]>
Also check ZCT when saving/loading ROI

09036d7cd7efa89adb0e9ec268ed886574a0ff6c authored over 6 years ago by Dominik Lindner <[email protected]>
Add unit test for ROICoordinate

The hashcode and equals methods looked a bit unusual,
thought it might be better to have a unit ...

b0f268ca7bad6b2b7914366b7b0af13dedcdafba authored over 6 years ago by Dominik Lindner <[email protected]>
Make ROIData work with zct < 0

3a341d4703b38edb07f895d412ec0cba25ee8736 authored over 6 years ago by Dominik Lindner <[email protected]>
Fixed ZCT getters/setters bug in ShapeData

3f8682bd148287a54ce4ac8043b0515cb00c7759 authored over 6 years ago by Dominik Lindner <[email protected]>
Merge pull request #5754 from mtbc/OMEROImportFixture-deprecation

deprecate OMEROImportFixture

4ce6ab2a1c1b0520af4bda1e96e5430a230d59a3 authored over 6 years ago by jean-marie burel <[email protected]>
deprecate OMEROImportFixture

to be moved to components/blitz/test/ in due course

989ed6fc284a29280036b9660ef2037bceea34df authored over 6 years ago by Mark Carroll <[email protected]>
add ternary canCreate to gateways to check read-only status

150a03ae49f3fd3907175c8b62196dadeee0c5f9 authored over 6 years ago by Mark Carroll <[email protected]>
Merge pull request #5727 from mtbc/copyright-Glencoe-C++

fix copyright year range typo on C++ unit tests

fd218f1207e47c1c56e4d026782da9c27c0d08b3 authored over 6 years ago by Josh Moore <[email protected]>
Merge pull request #5733 from mtbc/fix-read-only-session-query

current sessions request should ignore unloaded sessions

991dd1a89aad1ccbe9452429fbabd59fcb45594d authored over 6 years ago by Josh Moore <[email protected]>
ignore unloaded sessions from in-memory session provider

The proxy cleanup filter unloads those that the Hibernate-based security
would have filtered out...

d70bbe4bcd72d62f6c3c3674252d431e24d0d546 authored over 6 years ago by Mark Carroll <[email protected]>
make punctuation in Copyright comment fit others

28633aa5fb11d27b8a2cfcfa43b6869c647c9be0 authored over 6 years ago by Mark Carroll <[email protected]>