release: v1.7.2

Author: jvanmalder

base/src/main/java/eu/openanalytics/rdepot/base/initializer/RepositoryDataInitializer.java

@@ -74,27 +74,21 @@ public RepositoryDataInitializer(RepositoryService<E> repositoryService,
 	 * @param declaredRepository
 	 * @return
 	 */
-	protected abstract E declaredRepositoryToEntity(R declaredRepository);
+	protected abstract E declaredRepositoryToEntity(R declaredRepository, boolean declarative);
 
 	protected void createRepositoriesFromConfig(List<R> repositories, boolean declarative) {
 		List<E> existingRepositories = repositoryService.findAll(); 
 		for(R declaredRepository : repositories) {
 			logger.debug("Creating declared repository " + declaredRepository + "...");
-			E newRepository = declaredRepositoryToEntity(declaredRepository);
+			E newRepository = declaredRepositoryToEntity(declaredRepository, declarative);
 
 			Optional<E> possiblyExistingRepository = existingRepositories.stream()
 					.filter(r -> r.getName().equals(newRepository.getName())).findFirst();
 			if(possiblyExistingRepository.isPresent()) {
 				E existingRepository = possiblyExistingRepository.get();
 				existingRepositories.remove(existingRepository);
 
-				if(Boolean.valueOf(declarative)) {
-					if(existingRepository.isDeleted() == null) {
-						existingRepository.setDeleted(false);
-					}
-					if(existingRepository.isPublished() == null) {
-						existingRepository.setPublished(true); //TODO: Isn't it safer to set default to true?
-					}
+				if(Boolean.valueOf(declarative)) {					
 					updateRepository(newRepository, existingRepository);
 				} else {
 					logger.warn("We tried to create one of the preconfigured repositories but "					

base/src/main/java/eu/openanalytics/rdepot/base/mirroring/pojos/MirroredRepository.java

@@ -30,22 +30,26 @@ public abstract class MirroredRepository<P extends MirroredPackage, M extends Mi
 	protected String name;
 	protected String publicationUri;
 	protected String serverAddress;
+	protected Boolean deleted;
+	protected Boolean published;
 	protected Set<M> mirrors = new HashSet<>();
 	protected Technology technology;
 
 	public MirroredRepository() {}
 
-	public MirroredRepository(String name, String publicationUri, String serverAddress, 
-			Technology technology) {
-		this(name, publicationUri, serverAddress, new HashSet<>(), technology);
+	public MirroredRepository(String name, String publicationUri, String serverAddress,
+			Boolean deleted, Boolean published,	Technology technology) {
+		this(name, publicationUri, serverAddress, deleted, published, new HashSet<>(), technology);
 	}
 
 	public MirroredRepository(String name, String publicationUri, String serverAddress, 
-			Set<M> mirrors, Technology technology) {
+			Boolean deleted, Boolean published,	Set<M> mirrors, Technology technology) {
 		super();
 		this.name = name;
 		this.publicationUri = publicationUri;
 		this.serverAddress = serverAddress;
+		this.deleted = deleted;
+		this.published = published;
 		this.mirrors = mirrors;
 		this.technology = technology;
 	}
@@ -74,6 +78,22 @@ public void setServerAddress(String serverAddress) {
 		this.serverAddress = serverAddress;
 	}
 
+	public Boolean isDeleted() {
+		return deleted;
+	}
+	
+	public void setDeleted(Boolean deleted) {
+		this.deleted = deleted;
+	}
+	
+	public Boolean isPublished() {
+		return published;
+	}
+	
+	public void setPublished(Boolean published) {
+		this.published = published;
+	}
+	
 	public Set<M> getMirrors() {
 		return mirrors;
 	}

base/src/main/java/eu/openanalytics/rdepot/base/technology/InternalTechnology.java

@@ -46,7 +46,7 @@ public String getName() {
 
 	@Override
 	public String getVersion() {
-		return "1.7.1";
+		return "1.7.2";
 	}
 
 	@Override

build.gradle

@@ -41,7 +41,7 @@ ext.buildTime = {
 }
 
 group = 'eu.openanalytics'
-ext.versionNumber = '1.7.1'
+ext.versionNumber = '1.7.2'
 ext.baseVersion = versionNumber
 version = versionNumber
 description = """rdepot"""

docker-compose.yaml

@@ -31,7 +31,7 @@ services:
     networks:
       - oa-rdepot
   app:
-    image: openanalytics/rdepot-app:1.7.1
+    image: openanalytics/rdepot-app:1.7.2
     restart: unless-stopped
     hostname: oa-rdepot-app
     container_name: oa-rdepot-app
@@ -55,7 +55,7 @@ services:
       timeout: 10s
       retries: 10
   repo:
-    image: openanalytics/rdepot-repo:1.7.1
+    image: openanalytics/rdepot-repo:1.7.2
     restart: unless-stopped
     hostname: oa-rdepot-repo
     container_name: oa-rdepot-repo

docker/build/app-standalone/Dockerfile

@@ -1,3 +1,3 @@
-FROM openanalytics/rdepot-app-it:1.7.1
+FROM openanalytics/rdepot-app-it:1.7.2
 
 COPY rdepot-app-*application.war /opt/rdepot/rdepot.war

docker/build/repo-standalone/Dockerfile

@@ -1,3 +1,3 @@
-FROM openanalytics/rdepot-repo-it:1.7.1
+FROM openanalytics/rdepot-repo-it:1.7.2
 
 COPY rdepot-repo-*application.jar /opt/repo/rdepot-repo.jar

r-module/src/main/java/eu/openanalytics/rdepot/r/initializer/RRepositoryDataInitializer.java

@@ -78,12 +78,27 @@ public void createRepositoriesFromConfig(boolean declarative) {
 	}
 
 	@Override
-	protected RRepository declaredRepositoryToEntity(MirroredRRepository declaredRepository) {
+	protected RRepository declaredRepositoryToEntity(MirroredRRepository declaredRepository, boolean declarative) {
 		RRepository repository = new RRepository();
 		repository.setName(declaredRepository.getName());
 		repository.setPublicationUri(declaredRepository.getPublicationUri());
 		repository.setServerAddress(declaredRepository.getServerAddress());
 
+		if(declarative) {
+			boolean deleted, published;
+			if(declaredRepository.isDeleted() == null)
+				deleted = false;
+			else
+				deleted = declaredRepository.isDeleted();			
+			if(declaredRepository.isPublished() == null) 
+				published = true;
+			else
+				published = declaredRepository.isPublished();
+			
+			repository.setDeleted(deleted);
+			repository.setPublished(published);
+		}		
+		
 		return repository;
 	}
 

r-module/src/main/java/eu/openanalytics/rdepot/r/mirroring/pojos/MirroredRRepository.java

@@ -33,8 +33,8 @@ public MirroredRRepository() {
 	}
 
 	public MirroredRRepository(String name, String publicationUri, String serverAddress, 
-			Set<CranMirror> mirrors) {
-		super(name, publicationUri, serverAddress, mirrors, RLanguage.instance);
+			Boolean deleted, Boolean published, Set<CranMirror> mirrors) {
+		super(name, publicationUri, serverAddress, deleted, published, mirrors, RLanguage.instance);
 	}
 
 }

src/integration-test/resources/JSONs/declarative/repositories_after_synchronization.json

@@ -1 +1 @@
-[{"id":2,"version":1,"publicationUri":"http://localhost/repo/A","name":"A","serverAddress":"http://oa-rdepot-repo:8080/A","deleted":false,"published":false,"packages":[],"repositoryMaintainers":[]},{"id":7,"version":4,"publicationUri":"http://localhost/repo/D","name":"D","serverAddress":"http://oa-rdepot-repo:8080/D","deleted":false,"published":false,"packages":[{"id":5,"version":"1.68.0","repository":{"id":7,"name":"D","publicationUri":"http://localhost/repo/D"},"submission":{"deleted":false,"changes":null,"accepted":true,"id":5},"name":"annotate","description":"Using R enviroments for annotation.","author":"R. Gentleman","depends":"R (>= 2.10), AnnotationDbi (>= 1.27.5), XML","imports":"Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr","suggests":"hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit,","systemRequirements":null,"license":"Artistic-2.0","title":"Annotation for microarrays","url":null,"source":"/opt/rdepot/new/26971548/annotate_1.68.0.tar.gz","md5sum":"c06830f9bcfc0ae87023bfe03acb319e","active":false,"deleted":false,"user":{"id":4,"login":"einstein","name":"Albert Einstein","email":"einstein@ldap.forumsys.com"}},{"id":4,"version":"1.80.0","repository":{"id":7,"name":"D","publicationUri":"http://localhost/repo/D"},"submission":{"deleted":false,"changes":null,"accepted":true,"id":4},"name":"genefilter","description":"Some basic functions for filtering genes.","author":"Robert Gentleman, Vincent J. Carey, Wolfgang Huber, Florian Hahne","depends":null,"imports":"BiocGenerics, AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices","suggests":"class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr","systemRequirements":null,"license":"Artistic-2.0","title":"genefilter: methods for filtering genes from high-throughput experiments","url":null,"source":"/opt/rdepot/new/47794045/genefilter_1.80.0.tar.gz","md5sum":"8586fdf3f5bd2c66a09d7324c05a200a","active":false,"deleted":false,"user":{"id":4,"login":"einstein","name":"Albert Einstein","email":"einstein@ldap.forumsys.com"}},{"id":2,"version":"3.3.2","repository":{"id":7,"name":"D","publicationUri":"http://localhost/repo/D"},"submission":{"deleted":false,"changes":null,"accepted":true,"id":2},"name":"ggplot2","description":"A system for 'declaratively' creating graphics, based on \"The Grammar of Graphics\". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.","author":"Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),","depends":"R (>= 3.2)","imports":"digest, glue, grDevices, grid, gtable (>= 0.1.1), isoband, MASS, mgcv, rlang (>= 0.3.0), scales (>= 0.5.0), stats, tibble, withr (>= 2.0.0)","suggests":"covr, dplyr, ggplot2movies, hexbin, Hmisc, knitr, lattice, mapproj, maps, maptools, multcomp, munsell, nlme, profvis, quantreg, RColorBrewer, rgeos, rmarkdown, rpart, sf (>= 0.7-3), svglite (>= 1.2.0.9001), testthat (>= 2.1.0), vdiffr (>= 0.3.0)","systemRequirements":null,"license":"GPL-2 | file LICENSE","title":"Create Elegant Data Visualisations Using the Grammar of Graphics","url":"http://ggplot2.tidyverse.org, https://github.com/tidyverse/ggplot2","source":"/opt/rdepot/new/17512975/ggplot2_3.3.2.tar.gz","md5sum":"02d87290852410924eb816c2d4788afa","active":false,"deleted":false,"user":{"id":4,"login":"einstein","name":"Albert Einstein","email":"einstein@ldap.forumsys.com"}},{"id":3,"version":"4.10.1","repository":{"id":7,"name":"D","publicationUri":"http://localhost/repo/D"},"submission":{"deleted":false,"changes":null,"accepted":true,"id":3},"name":"plotly","description":"Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.","author":"Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Chris Parmer [aut], Toby Hocking [aut], Scott Chamberlain [aut], Karthik Ram [aut],","depends":"R (>= 3.2.0), ggplot2 (>= 3.0.0)","imports":"tools, scales, httr (>= 1.3.0), jsonlite (>= 1.6), magrittr, digest, viridisLite, base64enc, htmltools (>= 0.3.6), htmlwidgets (>= 1.5.2.9001), tidyr (>= 1.0.0), RColorBrewer, dplyr, vctrs, tibble, lazyeval (>= 0.2.0), rlang (>= 0.4.10), crosstalk, purrr, data.table, promises","suggests":"MASS, maps, hexbin, ggthemes, GGally, ggalluvial, testthat, knitr, devtools, shiny (>= 1.1.0), shinytest (>= 1.3.0), curl, rmarkdown, Cairo, broom, webshot, listviewer, dendextend, maptools, rgeos, sf, png, IRdisplay, processx, plotlyGeoAssets, forcats, palmerpenguins, rversions, reticulate, rsvg","systemRequirements":null,"license":"MIT + file LICENSE","title":"Create Interactive Web Graphics via 'plotly.js'","url":"https://plotly-r.com, https://github.com/plotly/plotly.R,","source":"/opt/rdepot/new/41972207/plotly_4.10.1.tar.gz","md5sum":"56c437fe24025831b5367747e4a341ff","active":false,"deleted":false,"user":{"id":4,"login":"einstein","name":"Albert Einstein","email":"einstein@ldap.forumsys.com"}}],"repositoryMaintainers":[]}]
+[{"id":2,"version":1,"publicationUri":"http://localhost/repo/A","name":"A","serverAddress":"http://oa-rdepot-repo:8080/A","deleted":false,"published":true,"packages":[],"repositoryMaintainers":[]},{"id":7,"version":4,"publicationUri":"http://localhost/repo/D","name":"D","serverAddress":"http://oa-rdepot-repo:8080/D","deleted":false,"published":false,"packages":[{"id":5,"version":"1.68.0","repository":{"id":7,"name":"D","publicationUri":"http://localhost/repo/D"},"submission":{"deleted":false,"changes":null,"accepted":true,"id":5},"name":"annotate","description":"Using R enviroments for annotation.","author":"R. Gentleman","depends":"R (>= 2.10), AnnotationDbi (>= 1.27.5), XML","imports":"Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr","suggests":"hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit,","systemRequirements":null,"license":"Artistic-2.0","title":"Annotation for microarrays","url":null,"source":"/opt/rdepot/new/26971548/annotate_1.68.0.tar.gz","md5sum":"c06830f9bcfc0ae87023bfe03acb319e","active":false,"deleted":false,"user":{"id":4,"login":"einstein","name":"Albert Einstein","email":"einstein@ldap.forumsys.com"}},{"id":4,"version":"1.80.0","repository":{"id":7,"name":"D","publicationUri":"http://localhost/repo/D"},"submission":{"deleted":false,"changes":null,"accepted":true,"id":4},"name":"genefilter","description":"Some basic functions for filtering genes.","author":"Robert Gentleman, Vincent J. Carey, Wolfgang Huber, Florian Hahne","depends":null,"imports":"BiocGenerics, AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices","suggests":"class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr","systemRequirements":null,"license":"Artistic-2.0","title":"genefilter: methods for filtering genes from high-throughput experiments","url":null,"source":"/opt/rdepot/new/47794045/genefilter_1.80.0.tar.gz","md5sum":"8586fdf3f5bd2c66a09d7324c05a200a","active":false,"deleted":false,"user":{"id":4,"login":"einstein","name":"Albert Einstein","email":"einstein@ldap.forumsys.com"}},{"id":2,"version":"3.3.2","repository":{"id":7,"name":"D","publicationUri":"http://localhost/repo/D"},"submission":{"deleted":false,"changes":null,"accepted":true,"id":2},"name":"ggplot2","description":"A system for 'declaratively' creating graphics, based on \"The Grammar of Graphics\". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.","author":"Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),","depends":"R (>= 3.2)","imports":"digest, glue, grDevices, grid, gtable (>= 0.1.1), isoband, MASS, mgcv, rlang (>= 0.3.0), scales (>= 0.5.0), stats, tibble, withr (>= 2.0.0)","suggests":"covr, dplyr, ggplot2movies, hexbin, Hmisc, knitr, lattice, mapproj, maps, maptools, multcomp, munsell, nlme, profvis, quantreg, RColorBrewer, rgeos, rmarkdown, rpart, sf (>= 0.7-3), svglite (>= 1.2.0.9001), testthat (>= 2.1.0), vdiffr (>= 0.3.0)","systemRequirements":null,"license":"GPL-2 | file LICENSE","title":"Create Elegant Data Visualisations Using the Grammar of Graphics","url":"http://ggplot2.tidyverse.org, https://github.com/tidyverse/ggplot2","source":"/opt/rdepot/new/17512975/ggplot2_3.3.2.tar.gz","md5sum":"02d87290852410924eb816c2d4788afa","active":false,"deleted":false,"user":{"id":4,"login":"einstein","name":"Albert Einstein","email":"einstein@ldap.forumsys.com"}},{"id":3,"version":"4.10.1","repository":{"id":7,"name":"D","publicationUri":"http://localhost/repo/D"},"submission":{"deleted":false,"changes":null,"accepted":true,"id":3},"name":"plotly","description":"Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.","author":"Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Chris Parmer [aut], Toby Hocking [aut], Scott Chamberlain [aut], Karthik Ram [aut],","depends":"R (>= 3.2.0), ggplot2 (>= 3.0.0)","imports":"tools, scales, httr (>= 1.3.0), jsonlite (>= 1.6), magrittr, digest, viridisLite, base64enc, htmltools (>= 0.3.6), htmlwidgets (>= 1.5.2.9001), tidyr (>= 1.0.0), RColorBrewer, dplyr, vctrs, tibble, lazyeval (>= 0.2.0), rlang (>= 0.4.10), crosstalk, purrr, data.table, promises","suggests":"MASS, maps, hexbin, ggthemes, GGally, ggalluvial, testthat, knitr, devtools, shiny (>= 1.1.0), shinytest (>= 1.3.0), curl, rmarkdown, Cairo, broom, webshot, listviewer, dendextend, maptools, rgeos, sf, png, IRdisplay, processx, plotlyGeoAssets, forcats, palmerpenguins, rversions, reticulate, rsvg","systemRequirements":null,"license":"MIT + file LICENSE","title":"Create Interactive Web Graphics via 'plotly.js'","url":"https://plotly-r.com, https://github.com/plotly/plotly.R,","source":"/opt/rdepot/new/41972207/plotly_4.10.1.tar.gz","md5sum":"56c437fe24025831b5367747e4a341ff","active":false,"deleted":false,"user":{"id":4,"login":"einstein","name":"Albert Einstein","email":"einstein@ldap.forumsys.com"}}],"repositoryMaintainers":[]}]