Hotfix 1.31.13 #1342

arteymix · 2025-03-15T06:15:52Z

No description provided.

Fix crash in BatchConfoundUtils when a sample is missing a value. Make the code for computing batch effect clearer by using entities instead of their IDs. Make the date batch confound plot resilient to missing values.

HANCESTRO_0575 --> AfPO_0000105 due to obsolete ontology term

Same as last change, added Yoruban as a string to match for new cases

Since biological sex is a common one, we can at least be consistent.

Make parsing of XML much more robust by adding utilities to check that the node lists have expected sizes, text content are non-null, etc.

…nto hotfix-1.31.13

…know when we're done

Make search and retrieval of GEO records two separate operations such that we can reuse the same search query. Make filling of GEO records more configurable and add a detailed preset. For the CLI, we want to exclude certain things like characteristics and sources which are very expensive.

…searched

…ages Improved ontology pages

These scripts make deploying the CLI and Web application consistent. They work both for local or remote deployment (via SSH). Use those scripts in IntelliJ configuration and Jenkins.

Pubpeer for 1.31.13

Proactively exclude bundles and node_modules in the WAR archive.

Bump patch version for Gemma REST to 2.8.5.

Replace all usages of FutureTask with ExecutorService.submit().

If both gemma.python.exe and python.exe are passed as system properties, prefer the first one.

Avoid the overhead of calling System.getProperty() systematically.

…ion.properties

arteymix and others added 30 commits October 18, 2024 15:46

Update versions for hotfix

4283d36

Fix #1261

35e57f0

Fix crash in BatchConfoundUtils when a sample is missing a value. Make the code for computing batch effect clearer by using entities instead of their IDs. Make the date batch confound plot resilient to missing values.

Minor cleanup

675712a

Remove outdated link to Spring 3 docs

4cc7d0f

fixup! Remove outdated link to Spring 3 docs

492da51

Update dependencies

c179300

Include a dependency check report in SonarQube analysis

ed0b5bc

Update valueStringToOntologyTermMappings.txt

22677b4

HANCESTRO_0575 --> AfPO_0000105 due to obsolete ontology term

Update valueStringToOntologyTermMappings.txt

a28ea9b

Same as last change, added Yoruban as a string to match for new cases

Update pavlab-starter-parent to 1.2.17

306a2f5

Ignore terms from AFPO in the GEO replacement validation

18fcf47

replace some occurrences of "probe" in the UI.

83026e2

throw an exception if dfPrior is invalid

51a6bde

partially address #1290

728f829

Since biological sex is a common one, we can at least be consistent.

Fix NPE error on the homepage when a Taxon common name is null

c7030ab

replace more Probe for Element strings

0ab0857

check valid miniML more rigorously

92c867f

fix

275eb8f

Fix seeking point calculation

cae6107

Few improvements for messages and options in listGEOData

abb6ca7

Make sure that the expected number of records is produced

8e6f4e8

Make parsing of XML much more robust by adding utilities to check that the node lists have expected sizes, text content are non-null, etc.

Make sure that the expected number of records is produced

bea6a18

Make parsing of XML much more robust by adding utilities to check that the node lists have expected sizes, text content are non-null, etc.

Merge branch 'hotfix-1.31.13' of https://github.com/ppavlidis/Gemma i…

6aee9a1

…nto hotfix-1.31.13

Fix expected records when searching beyond the count

545c96b

Use a binary search for finding the -startdate and total elements to …

6239f9f

…know when we're done

Use count from the search to assess the number of expected records

ad6d85b

Ignore SocketTimeoutException in assumeThatResourceIsAvailable()

8f560f5

Make GeoBrowser more agnostic of the type of record being browsed or …

af063f3

…searched

Update edpendency-check-maven to 11.1.1 and ignore yarn analyzer

1429ab6

arteymix and others added 29 commits January 31, 2025 10:08

Merge pull request #1324 from PavlidisLab/feature-improved-ontology-p…

af995ef

…ages Improved ontology pages

Align all audit event types with the single-cell branch

0d0a6b2

Rename 1.31.11 migration

82df00d

Fix BuildInfoTest when running in a different TZ than America/Vancouver

c6b2c3b

Fix ABA test when remote is not available

cbfe81e

Add deployment scripts for Web and CLI

38857b3

These scripts make deploying the CLI and Web application consistent. They work both for local or remote deployment (via SSH). Use those scripts in IntelliJ configuration and Jenkins.

Don't make it an error to deploy a CLI that already exists

25bbb2f

merge pubpeer fix

a6d8e19

exclude pubpeer comments from the css

5fb60ba

Fix usage of headings in FilterArg javadocs

61832cd

add PMID to citations. possibly fixing #1283

dbf3de4

exclude pubpeer comments from the css

d8950e5

Merge pull request #1340 from PavlidisLab/pubpeer-for-1.31.13

0b7da98

Pubpeer for 1.31.13

Improve statement rendering (fix #1341)

6dc407d

Slim down the test JAR and WAR archives

f7d26d8

Proactively exclude bundles and node_modules in the WAR archive.

Use 200 as a default response code (fix #1272)

d0c5449

Bump patch version for Gemma REST to 2.8.5.

Fix tests for loading VO by characteristics

dcafbe1

Remove unused media type in OntologyController.getTerm()

e5b7029

Use Future.get() instead of Thread.sleep() to wait for a download

e27bb63

More replacements of Thread.sleep() with Future.get()

3379442

Replace all usages of FutureTask with ExecutorService.submit().

Favour prefixed properties when they are present

3175a70

If both gemma.python.exe and python.exe are passed as system properties, prefer the first one.

Only query system property once

c38f34b

Avoid the overhead of calling System.getProperty() systematically.

Use Log4j JUL handler to redirect JUL usages in Gemma Web

e428e33

Make sure that deployed artifacts are group-writable

53b9b61

Allow for selecting a specific Maven when generating completion scripts

a8d1135

Honor the preferred Maven executable when suggesting to generate vers…

04cb4a6

…ion.properties

Drop redundant default javadoc report

c26def7

Add PubMed 2025 DTD

1af81d9

Update dependencies

acd293b

arteymix merged commit acd293b into master Mar 27, 2025
3 of 6 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Hotfix 1.31.13 #1342

Hotfix 1.31.13 #1342

arteymix commented Mar 15, 2025

Hotfix 1.31.13 #1342

Hotfix 1.31.13 #1342

Conversation

arteymix commented Mar 15, 2025