Commit graph

5081 commits

Author SHA1 Message Date
Brian Lowe
fe09808b1b
Retrieve sitemap profile URLs only after consuming result set in order to avoid transaction errors with TDB. Resolve https://jira.lyrasis.org/browse/VIVO-1910 (#231) 2021-03-30 09:41:24 -06:00
Ralph O'Flinn
d00d7de585
Revert deployment strategy (#230)
* revert deployment changes

* update docker and compose for previous deployment

* minor readme update

* use package instead of install

this avoids exploding war file in tomcat but seems to be missing overlays for VIVO theme

* test docker workflow

* test deploy workflow

* add package profile for home

* skip deploy for installer

* skip installer by profile

* update workflows

* minor readme update

* use app-name for vivo log file name

* Update log4j.properties

Co-authored-by: William Welling <wwelling@library.tamu.edu>
2021-03-24 01:46:24 -05:00
hauschke
47fb4fdc05
Update LICENSE (#226)
Update license year to 2021.
2021-03-12 16:31:39 +02:00
dependabot[bot]
fdda5f0774
Bump junit from 4.11 to 4.13.1 in /api (#195)
Bumps [junit](https://github.com/junit-team/junit4) from 4.11 to 4.13.1.
- [Release notes](https://github.com/junit-team/junit4/releases)
- [Changelog](https://github.com/junit-team/junit4/blob/main/doc/ReleaseNotes4.11.md)
- [Commits](https://github.com/junit-team/junit4/compare/r4.11...r4.13.1)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-02-18 10:11:44 -06:00
dependabot[bot]
0d5049f3b6
Bump junit from 4.12 to 4.13.1 in /selenium (#196)
Bumps [junit](https://github.com/junit-team/junit4) from 4.12 to 4.13.1.
- [Release notes](https://github.com/junit-team/junit4/releases)
- [Changelog](https://github.com/junit-team/junit4/blob/main/doc/ReleaseNotes4.12.md)
- [Commits](https://github.com/junit-team/junit4/compare/r4.12...r4.13.1)

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-02-18 10:11:14 -06:00
William Welling
880ac5b797
VIVO-1963: Initial docker compose (#223)
* initial docker compose

* for docker volume use direct tdb filemode

* runtime properties with solr url configured

* move gitattributes to root to ensure scripts stay valid

* fix VIVO dockerfile command permissions

* use public vivoweb/vivo-solr image

* start script improvements

* pass docker compose env to containers

* generate digest.md5 of existing VIVO home

* add initial readme

* reset docker compose env defaults

* minor readme updates
2021-02-18 10:07:19 -06:00
Andrew Woods
5f6cabc42a
Update example.runtime.properties (#222)
* Update example.runtime.properties

Resolves: https://jira.lyrasis.org/browse/VIVO-1930

Co-authored-by: gneissone <mbgross@wustl.edu>
Co-authored-by: Andrew Woods <awoods@duraspace.org>
2021-02-12 16:42:58 +02:00
gneissone
f15eec19e0 Bugfix for type restriction in search index config 2021-02-11 09:00:22 -05:00
gneissone
2122254cdb Update to google chart library loads 2021-02-10 15:12:37 -05:00
William Welling
a9ce8c7de8
VIVO-1961: GitHub Action to Publish Docker Image (#220)
* simple dockerfile and image publish workflow
* upgrade to v2 of build push action
* provide context and explicit docker file

Resolves: https://jira.lyrasis.org/browse/VIVO-1961
2021-02-10 15:03:29 -05:00
Andrew Woods
268ffa1cd7
Sprint i18n with main (#215)
* Layer uqam updates onto master (minus trailing whitespace)

* Update AddOrganizerRoleToPersonGenerator.java

Removed extraneous whitespace

* My whitespace (#153)

* Update AddPublicationToPersonGenerator.java

* Removed extraneous whitespace AND move RootUserPolicy.java from VIVO to Vitro

* Fixed whitespace in: AddAttendeeRoleToPersonGenerator.java

* Fixed indentations for AddOutreachProviderRoleToPersonGenerator.java

* Fixed indentations

* Removed extraneous whitespace (#158)

* Removed extraneous whitespace

* Fix bug introduced in cleaning up whitespace

* Tagging UQAM comments with the following tags

-Add-Feature
-Optimization
-Linguistic-Management
-Bug-Correction

* Update AddReviewerRoleToPersonGenerator.java

* Added an internationalization correction to be considered in the vivo-i18n-core that was forgotten when sprint-i18n was created.

* Fix typo in AddReviewerRoleToPersonGenerator

Resolves: https://jira.lyrasis.org/browse/VIVO-1774

* Fix typo in AddOutreachProviderRoleToPersonGenerator

Resolves: https://jira.lyrasis.org/browse/VIVO-1775

* Include language dependencies in build all of the time (#168)

Move "LocaleSelectionSetup" higher in the startup list so that the Vitro:RDFFilesLoader has the locale info available on its startup

Part of resolution to: https://jira.lyrasis.org/browse/VIVO-1836

Co-authored-by: Andrew Woods <awoods@duraspace.org>

* Made modifications to publicationToPersonUtils.js so that multilangua… (#170)

* Made modifications to publicationToPersonUtils.js so that multilanguage support will not break the javascript functionalty.

Co-authored-by: root <root@vivo-development.hs-mittweida.de>

Resolves: https://jira.lyrasis.org/browse/VIVO-1739

* Feature language en_CA (#169)

* Changing ontology extensions for n3 & assigning a base IRI to each
ontology

Co-authored-by: michelheonuqam <heon.michel@uqam.ca>
Co-authored-by: michelheon <heon@videotorn.ca>

Partial resolution of: https://jira.lyrasis.org/browse/VIVO-1862

* i18n: title tag and headings in capability map are in english in french version (#173)

* added multi-language support for ticket VIVO-1846

* fixed swapped properties, added Capability map title to i18n

Partial resolution to: https://jira.lyrasis.org/browse/VIVO-1847

* Added i18n support for Capability Map control buttons, JIRA ticket VIVO-1846

* removed redundat files which are now available via Vitro- and VIVO-languages

* added i18n support for the capability map, ticket vivo-1892

* Revert non-function RDF changes (#180)

Related to: https://jira.lyrasis.org/browse/VIVO-1905

Co-authored-by: Andrew Woods <awoods@duraspace.org>

* Ensure 'other' in Individual->Teaching->advisees->type is translated

Partial resolution to: https://jira.lyrasis.org/browse/VIVO-1881

* [VIVO-1842] i18n: Added function js_string at i18n variables to handle quotes properly (#181)

* added js_string at i18n strings to handle quotes properly, ticket vivo-1842

Partial resolution for: https://jira.lyrasis.org/browse/VIVO-1842

* replace static headings with i18n values (#183)

Partial resolution of: https://jira.lyrasis.org/browse/VIVO-1844

* added empty check for getCountry, fixing bug with spanish label (es), ticket vivo-1900 (#182)

Partial resolution to: https://jira.lyrasis.org/browse/VIVO-1900

* Issue/vivo 1908 (#185)

* Provide fallback language in language-filtered webpage SPARQL query and use existing RDFService-based filtering for ConstantFieldOptions

Resolves: https://jira.lyrasis.org/browse/VIVO-1906

* Fix bug of missing toString() (#187)

Related to: https://jira.lyrasis.org/browse/VIVO-1906

Co-authored-by: Andrew Woods <awoods@duraspace.org>

* Remove files replicated in i18n (#186)

Related to: https://jira.lyrasis.org/browse/VIVO-1917

* removed redundant vitroAnnotations, now in VIVO-languages, ticket vivo-1821

* Removed key.png from the template and replaced it with css sprite and… (#184)

* Removed key.png from the template and replaced it with css sprite and descriptions in plain text.
* * adding height to background images, hopefully fixing issues

Partial resolution for: https://jira.lyrasis.org/browse/VIVO-1902

* [VIVO-1915] i18n - removing language select for label management for individuals (#190)

* removed the language select for managing multi language labels fpr individuals, ticket vivo-1915

* modified ManageLabelsForPersonGenerator so that you can only add an langauge label if it is not already set, ticket vivo-1915

Partial resolution to: https://jira.lyrasis.org/browse/VIVO-1915

* - added i18n() to hardcoded values

* added i18n support to person's domain in capability map, ticket 1867

* [VIVO-1946] - Update ResearcherID description in vivo.owl (#188)

* Update ResearcherID description in vivo.owl

Partial resolution to: https://jira.lyrasis.org/browse/VIVO-1946

* [VIVO-1936] i18n: updated the language comment in runtime.properties (#203)

Partial resolution of: https://jira.lyrasis.org/browse/VIVO-1936

Co-authored-by: Kampe <Benjamin.Kampe@tib.eu>

* [VIVO-1924] i18n: @en i18n properties are not loaded during first site startup. (#204)

* rearranged startup-listeners fixing bug with language files, ticket VIVO-1924

* Added a comment to prevent future bugs like this, ticket VIVO-1924

* fixed previous comment, ticket VIVO-1924

* Remove duplicate text from dropdown menus

* Minor checkstyle correction following: VIVO-1936 (#206)

Follow-on to: https://jira.lyrasis.org/browse/VIVO-1936

Co-authored-by: Andrew Woods <awoods@duraspace.org>

* follow-up on vivo-1936 - restore default values in example-settings.xml (#210)

Co-authored-by: gneissone <mbgross@wustl.edu>

* [VIVO-1798] - Internationalize first and last name validation (#207)

* Internationalize first and last name validation

Partial resolution to: https://jira.lyrasis.org/browse/VIVO-1798

* adding collections process terms (#165)

* adding collections process terms

No JIRA :(

* Non-functional change to comment in example.applicationSetup.n3

Related to: https://jira.lyrasis.org/browse/VIVO-1741

* Update orcidConfirm.ftl (#199)

Fix i18n property used on ORCID confirmation step 2 button.
Related to https://jira.lyrasis.org/browse/VIVO-1945

* Fix external AGROVOC service URL

* URL fix for LCSH service

* Remove unnecessary pom.xml 'profile'

- Also, uncomment language overlays
   - Noting that this is not actually necessary, as any 'war' Maven dependencies are automatically overlayed:
   - https://maven.apache.org/plugins/maven-war-plugin/overlays.html

Co-authored-by: Andrew Woods <awoods@duraspace.org>
Co-authored-by: Nicolas D <46490666+nicalico@users.noreply.github.com>
Co-authored-by: UQAM-VIVO <heon.michel@uqam.ca>
Co-authored-by: matthiasluehr <60263380+matthiasluehr@users.noreply.github.com>
Co-authored-by: Michel Heon <heon@videotron.ca>
Co-authored-by: dofeldsc <dofeldsc@uos.de>
Co-authored-by: William Welling <wwelling@library.tamu.edu>
Co-authored-by: Brian Lowe <brianjlowe@gmail.com>
Co-authored-by: Matthias Lühr <luehr@hs-mittweida.de>
Co-authored-by: Ben <mbgross@wustl.edu>
Co-authored-by: Benjamin Kampe <benjamin@fehrmanns.net>
Co-authored-by: Kampe <Benjamin.Kampe@tib.eu>
Co-authored-by: Gross, Benjamin <benjamin.gross@clarivate.com>
Co-authored-by: diatomsRcool <annethessen@gmail.com>
Co-authored-by: L.O <53535673+lb-ov@users.noreply.github.com>
2021-02-10 11:02:20 -06:00
William Welling
f97972e5aa
VIVO-1960: GitHub Actions Continued (#218)
* add build workflow
* remove travis
* remove unnecessary vitro cache
* update readme badge
* run tests during CI build
* build CI use java 11
* add repositories to distribution management
* deploy from main branch and update readme

Follow-on to: https://jira.lyrasis.org/browse/VIVO-1960
2021-02-09 17:46:21 -05:00
William Welling
6dbc31cc9d
VIVO-1960: GitHub Build Action (#217)
* add build workflow
* remove travis
* update readme badge

Partially resolves: https://jira.lyrasis.org/browse/VIVO-1960
2021-02-09 15:01:29 -05:00
Andrew Woods
01776ee692
Enable war deployment model (#197)
* Add 'home' files into build war artifact

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Disable copying exploded war to Tomcat dir

- hardcode vivo.all.log file name
- must now set system property: -Dvivo-dir=/opt/vivo/home/

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Ensure build does not remove and re-add VIVO_HOME/rdf

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Remove unnecessary profile from installer/pom.xml

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Rename example config files to have 'default' prefix

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Require common properties to be in JNDI

Properties include:
- vitro/home
- vitro/appName
- vitro/rootUserAddress
- vitro/defaultNamespace

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* VIVO-1443: app name (#2)

* Non-functional change to comment in example.applicationSetup.n3

Related to: https://jira.lyrasis.org/browse/VIVO-1741

* Update orcidConfirm.ftl (#199)

* remove example-settings.xml
* simplify war name and afford override during build
* default app name to vivo and pass into context.xml

Co-authored-by: Andrew Woods <awoods@duraspace.org>
Co-authored-by: L.O <53535673+lb-ov@users.noreply.github.com>

Co-authored-by: Andrew Woods <awoods@duraspace.org>
Co-authored-by: William Welling <wwelling@library.tamu.edu>
Co-authored-by: L.O <53535673+lb-ov@users.noreply.github.com>
2021-02-05 10:56:50 -06:00
L.O
c54f8a105b
Update orcidConfirm.ftl (#199)
Fix i18n property used on ORCID confirmation step 2 button.
Related to https://jira.lyrasis.org/browse/VIVO-1945
2021-01-06 22:31:09 +02:00
Andrew Woods
17dd020835 Non-functional change to comment in example.applicationSetup.n3
Related to: https://jira.lyrasis.org/browse/VIVO-1741
2020-09-30 17:56:58 -04:00
diatomsRcool
f585d90c0e
adding collections process terms (#165)
* adding collections process terms

No JIRA :(
2020-09-23 11:03:25 -04:00
Andrew Woods
df7165e994
Remove 'legacy' directory (#149)
Partial resolution to: https://jira.lyrasis.org/browse/VIVO-1753

Co-authored-by: Andrew Woods <awoods@duraspace.org>
2020-03-24 12:45:26 -06:00
hauschke
c15f5e5cc5
Added citation information for JOSS paper (#148)
* Added citation information for JOSS paper

Added JOSS citation as text and as BibTeX.

Resolves: https://jira.lyrasis.org/browse/VIVO-1754
2020-03-19 14:36:14 -04:00
Mike Conlon
94c06ebec0
Add CollectionProcess and CurationProcess (#141)
* Add CollectionProcess and CurationProcess

Resolves: 
- https://jira.lyrasis.org/browse/VIVO-1699 and
- https://jira.lyrasis.org/browse/VIVO-1700
2020-03-17 19:54:26 -04:00
Ralph O'Flinn
a75dc3802a
Merge pull request #147 from vivo-project/rel-1.11.1-maint
post-1.11.1 pom.xml updates
2020-03-16 09:51:35 -05:00
Ralph O'Flinn
96e9f507c5 [maven-scm-plugin] prepare development vivo-1.11.2-SNAPSHOT 2020-03-07 10:46:41 -06:00
Ralph O'Flinn
cad6a66f39 [maven-scm-plugin] prepare release vivo-1.11.1 2020-03-07 10:45:36 -06:00
Ralph O'Flinn
300072b544 new file: rc_script.sh 2020-03-07 10:33:50 -06:00
Ralph O'Flinn
6fe665781b
Merge pull request #145 from awoods/vivo-1747
Update puppycrawl dependency to 8.29
2020-03-07 07:08:20 -06:00
Andrew Woods
702dd75164 Update puppycrawl dependency to 8.29
Resolves: https://jira.lyrasis.org/browse/VIVO-1747
2020-03-04 16:21:45 -05:00
Ralph O'Flinn
7fdcd6e264
Merge pull request #144 from awoods/vivo-1741
Update example default triple store from SDB to TDB
2020-02-25 08:53:31 -06:00
Andrew Woods
9b97bcd98c code review 2020-02-24 18:41:36 -05:00
Andrew Woods
56d2ee130f Update example default triple store from SDB to TDB
Resolves: https://jira.lyrasis.org/browse/VIVO-1741
2020-02-24 17:05:40 -05:00
Graham Triggs
d9571cbcce [VIVO-1737] Update Error Prone (#142)
Resolves: https://jira.lyrasis.org/browse/VIVO-1737
2020-01-23 13:14:29 -05:00
gneissone
6481558597 Co-author visualization: Change cursor type when hovering over link 2019-11-19 12:09:57 -05:00
gneissone
e80efb863a Fix visualization tool css selector 2019-11-19 12:08:36 -05:00
gneissone
14b5c82698 Fix unbound research area query 2019-11-01 18:27:08 -04:00
Ralph O'Flinn
4b18675112 [maven-scm-plugin] prepare development vivo-1.11.1-SNAPSHOT 2019-10-21 04:38:26 -05:00
Ralph O'Flinn
f0d3a70fba [maven-scm-plugin] prepare release vivo-1.11.0 2019-10-21 04:35:52 -05:00
Graham Triggs
d3b377b3a7 [VIVO-1670] ORCID - Disable Step 2 and Internationalization (#130)
* Internationalize ORCiD add an iD
* ORCID Internationalization, allow Step 2 to be disabled if only a public API key

Resolves: https://jira.duraspace.org/browse/VIVO-1670
2019-08-09 09:29:00 -04:00
Don Elsborg
06d266ea94 Vivo 1287 (#137)
Remove five subclass axioms from five classes that had been subclass of skos:Concept; add subClassOf(DateTimeValuePrecision, Quality)

Resolves VIVO-1287
https://jira.duraspace.org/browse/VIVO-1287
2019-08-09 15:14:31 +03:00
Graham Triggs
f597b7ee42 [VIVO-1415] Add publication claiming from PubMed and CrossRef (#129)
* Claiming interface for DOI and PMID
* Allow http://doi.org urls in the claim process
* Make button i18n compliant
* Check Editor already claimed, error for no citation, PUMCIDs fixed
* Fixed gnarly DOI containing semi-colon (removed semi-colon as separator), match more DOI formats internally, improve AUTH restrictions
* Add Wilma themes
* Add permissions to allow proxy editors
* Update DOI resolver URI for content negotiation
* CSS changes to prevent layout problems in admin pages
* Add selectable list of publication types on import

Resolves to https://jira.duraspace.org/browse/VIVO-1415
2019-08-08 10:15:17 -04:00
Ralph O'Flinn
0a08c2890d VIVO-1614 - Update to allow the TPF API to be toggled via the runtime.properties. (#136)
* Update to allow the TPF API to be toggled via the runtime.properties.

Resolves: https://jira.duraspace.org/browse/VIVO-1614
2019-08-02 13:20:31 -04:00
Andrew Woods
c0ad14b734 Create initial format style enforcement (#127)
- All rules are initially suppressed

Resolves: https://jira.duraspace.org/browse/VIVO-1692
2019-07-25 13:49:59 +03:00
Arfon Smith
89bdf16008 Update paper.bib (#134) 2019-07-24 12:15:48 -04:00
Brian Lowe
cfd154b9b6
Merge pull request #135 from vivo-project/dev-search
dev-search
2019-07-24 17:12:19 +03:00
hauschke
05ba04df9e Update paper.bib (#133)
deleted comma
2019-07-15 12:20:22 -04:00
hauschke
3d08253c47 Update paper.bib (#132)
Added dates to websites according the respective website, checked links, updated urldates, added "author = {VIVO Project}" to the references of "About Vitro" and "VIVO-ISF-Ontology", changes "Vivo-isf-ontology" to "VIVO-ISF-Ontology".
2019-07-15 10:28:53 -04:00
hauschke
abc152cfec Paper revision (#131)
* minor fix in Acknowledgement

* Added references

* Added 2 ORCIDs
2019-07-12 23:40:52 -04:00
Ben
1e487a8238 Set Tenderfoot pub chart height (#125) 2019-07-09 11:03:33 -04:00
Ralph O'Flinn
27cb119918 fixing merge error 2019-06-24 08:43:28 -05:00
Ralph O'Flinn
92d0fe98c5 Merge branch 'sprint-search' into dev-search
# Conflicts:
#	installer/solr/src/main/webResources/WEB-INF/classes/log4j.properties
#	webapp/src/main/webapp/WEB-INF/resources/startup_listeners.txt
2019-06-21 09:50:40 -05:00
Graham Triggs
06726e0979 [VIVO-1656] Extension mechansim for passing properties to templates (#128)
* [VIVO-1656] Extension mechansim for passing properties to templates for Individuals

* [VIVO-1656] Extension mechansim for passing properties to templates for Individuals
2019-06-07 13:02:07 -04:00
Ben
87092cec9c [VIVO-1690] - Remove trailing whitespace throughout project (#126)
* Remove trailing whitespace throughout project

Resolves: https://jira.duraspace.org/browse/VIVO-1690
** Along with: https://github.com/vivo-project/Vitro/pull/117
2019-05-03 12:51:00 -04:00