diff --git a/CHANGELOG b/CHANGELOG index 5dd515dad4136d9f58c0d4ef8a726e97a251a206..c3f89ecd532c541b63f977af20ceeca48bed1dbe 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,3 +1,9 @@ +minerva (17.0.2) stable; urgency=medium + * Bugfix (backward incompatibility): default permissions when adding new user + are copied from guest account (#2029) + + -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 18 Apr 2024 10:00:00 +0200 + minerva (17.0.1) stable; urgency=medium * Bug fix: remove references to stitch and string annotators from miriam data (#2017,#2018,#2019,#2020) @@ -398,7 +404,7 @@ minerva (16.1.0) stable; urgency=medium stimulation", "absolute inhibition" (#1624) * Small improvement: additional annotations are supported: ExAC Gene, ExAC Transcript, ExAC Variant, LINCS Protein, LINCS Cell, GWAS Central Marker, - GWAS Central Phentoype, GWAS Central Study, Cooperative Patent + GWAS Central Phenotype, GWAS Central Study, Cooperative Patent Classification, USPTO, Google Patents, MIRIAM Registry collection, ICD, PIRSF, Nucleotide Sequence Database, Wormpep, PROSITE, arXiv, ArrayExpress, SABIO-RK Reaction, Transport Classification Database, UniParc, MINT, @@ -608,7 +614,7 @@ minerva (16.0.1) stable; urgency=medium on reaction) * Bug fix: speed of searching by coordinates improved * Bug fix: speed of exporting as map/image improved - * Bug fix: unexpected error hungs uploading of the project (#1576) + * Bug fix: unexpected error hangs uploading of the project (#1576) * Bug fix: too many projects opened inside one domain caused issues with storing session data (#1575, #1566) * Bug fix: drug with target without defined type caused an issue (#1578) @@ -899,7 +905,7 @@ minerva (15.0.0) stable; urgency=medium * Improvement: API allows to merge files (#1208) * Improvement: export to SBGN/SBML/GPML format provides popup with list of warnings occurred in the translation process (#713) - * Improvement: support for rendering colors in SBGNML added (#1009) + * Improvement: support for rendering colors in SBGN-ML added (#1009) * Small improvement: compartments in not layouted SBML file are more scattered (#326) * Small improvement: when downloading a map results in too big file (>1MB) @@ -971,7 +977,7 @@ minerva (15.0.0) stable; urgency=medium * Bug fix: modifiers joined by operator were exported to SBML without line corresponding to the operator (#1199) * Bug fix: first state variable that does not match modification residue is - translated to structural state when importing from SBGNML (#1088) + translated to structural state when importing from SBGN-ML (#1088) * Bug fix: exported SBML was not compliant with the standard when element name was empty (#1147) * Bug fix: invalid data overlays in uploaded zip file created "valid" project @@ -999,7 +1005,7 @@ minerva (15.0.0) stable; urgency=medium * Bug fix: import from CellDesigner rounded alias dimension to integer * Bug fix: compartments limited by corner (left-top corner compartment, etc) are parsed properly from CellDesigner files - * Bug fix: structural states of proteins are imported properly from SBGNML PD + * Bug fix: structural states of proteins are imported properly from SBGN-ML PD (#995) * Bug fix: export to CellDesigner names with new line is properly handled (#930) @@ -1008,7 +1014,7 @@ minerva (15.0.0) stable; urgency=medium * Bug fix: unknown catalysis boolean gate modifiers in CellDesigner are visualized with proper line type across all included modifiers (#957) * Bug fix: dimension of the modifications is the same as in minerva when - exporting to SBGNML-PD (#554) + exporting to SBGN-ML-PD (#554) * Bug fix: position of structural state is preserved on upload CellDesigner file (#671) * Bug fix: problematic notes doesn't crash CellDesigner upload (#968) @@ -1308,7 +1314,7 @@ minerva (14.0.0) stable; urgency=medium loaded plugins (#885) * Bug fix: export to CellDesigner of reaction with two modifiers connected with boolean operator resulted was skipping some layout information - * Bug fix: reaction in SBGNML file containing two products was improperly + * Bug fix: reaction in SBGN-ML file containing two products was improperly drawn * Bug fix: color handling in CellDesigner did not work properly for modifiers inside boolean gateway @@ -1436,7 +1442,7 @@ minerva (13.1.0) stable; urgency=medium * Bug fix: invisible layer shouldn't be shown on the map (#813) * Bug fix: list of available annotators is sorted alphabetically (#815) * Bug fix: redirect url from export panel is fixed (#819) - * Bug fix: allow to reupload the same file without closing add overlay dialog + * Bug fix: allow to re-upload the same file without closing add overlay dialog (#833) * Bug fix: gene_name column is allowed only in the genetic variant data overlay @@ -1460,7 +1466,7 @@ minerva (13.1.0) stable; urgency=medium list of genomes (#761) * Bug fix: fixing situation when MolArt started with variation overlay not having the a change information - * Bug fix: plugin contect element width is adjusted when link to tabs are + * Bug fix: plugin content element width is adjusted when link to tabs are wrapped in more than one line (#758) * Bug fix: export to CellDesigner preserve font size (#798) * Bug fix: layout data was ignored for some reactions when importing from @@ -1773,7 +1779,7 @@ minerva (12.0.4) stable; urgency=medium * Bug fix: Removing of guest (anonymous) account is forbidden - system is unstable after removing such user * Bug fix: Tair database moved to https - * Bug fix: Taxnomy database changed html output that resulted in problems + * Bug fix: Taxonomy database changed html output that resulted in problems with resolving species name to the id -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 12 Sep 2018 17:00:00 +0200 @@ -1897,7 +1903,7 @@ minerva (11.1.2) stable; urgency=medium minerva (11.1.1) stable; urgency=medium * Bug fix: Updating privileges takes much less time - * Bug fix: Concurent update on privileges shouldn't crash anymore + * Bug fix: Concurrent update on privileges shouldn't crash anymore * Bug fix: Search by element id crashed when submaps were available * Bug fix: GO connector uses new API, because the old one was turned off and stopped working diff --git a/CellDesigner-plugin/pom.xml b/CellDesigner-plugin/pom.xml index 194f960f9335abea66dda2a39c04827d011bb4b6..001af6a8511efea0047bf9a901b3cc32604d92fb 100644 --- a/CellDesigner-plugin/pom.xml +++ b/CellDesigner-plugin/pom.xml @@ -5,7 +5,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>CellDesigner-plugin</artifactId> <!-- dependency from the MapViewer model --> @@ -50,19 +50,19 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>commons</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-CellDesigner</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> diff --git a/annotation/pom.xml b/annotation/pom.xml index 9633a9393d81d01de36aa5230dee24e9e46655cb..da2ed379d9c6bde86a0abb9abcd4cbeb9ccd0e5a 100644 --- a/annotation/pom.xml +++ b/annotation/pom.xml @@ -5,7 +5,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>annotation</artifactId> <name>Annotation module</name> @@ -19,7 +19,7 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- dependency from the MapViewer dao --> @@ -27,7 +27,7 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>persist</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- dependency from the MapViewer cell designer parser (we need access @@ -35,13 +35,13 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-CellDesigner</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- Log4J2 --> diff --git a/commons/pom.xml b/commons/pom.xml index 83025f509ef02f07b13d9d558ea066e446bd57e4..89cfcc8d16f5693a81fc1bab338085d3cce558de 100644 --- a/commons/pom.xml +++ b/commons/pom.xml @@ -5,7 +5,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>commons</artifactId> <name>Mapviewer commons</name> diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml index cbc7aa4d034c764abab4fe5c9273491e2a61513a..3cccff81d9474b532dc6de0cfc095435cf02ed25 100644 --- a/converter-CellDesigner/pom.xml +++ b/converter-CellDesigner/pom.xml @@ -5,7 +5,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>converter-CellDesigner</artifactId> <name>CellDesigner converter</name> @@ -17,13 +17,13 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- Log4J2 --> diff --git a/converter-SBGNML/pom.xml b/converter-SBGNML/pom.xml index d0a09ccefdad1944b8d95ceca2cb99af069cc07b..16247b13908db62b37e9303842bf37c1a09673b2 100644 --- a/converter-SBGNML/pom.xml +++ b/converter-SBGNML/pom.xml @@ -5,7 +5,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>converter-SBGNML</artifactId> @@ -20,26 +20,26 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>persist</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> <scope>test</scope> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-CellDesigner</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-graphics</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> diff --git a/converter-graphics/pom.xml b/converter-graphics/pom.xml index ad68bd41aef965ca4f33e0a6231fb8f0937efc9f..8a2ccea28b2b5118c62789eedca185f4f9f829ce 100644 --- a/converter-graphics/pom.xml +++ b/converter-graphics/pom.xml @@ -5,7 +5,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>converter-graphics</artifactId> <name>MapViewer graphics converter</name> @@ -18,13 +18,13 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model-command</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- Log4J2 --> diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml index 9a3808be88f1834430c32018e0893cc077be9664..234749f0d27bd8943ffa9acdb347499f6dec33dc 100644 --- a/converter-sbml/pom.xml +++ b/converter-sbml/pom.xml @@ -7,7 +7,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>converter-sbml</artifactId> <name>converter-sbml</name> @@ -40,22 +40,22 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model-command</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-CellDesigner</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- Log4J2 --> @@ -167,7 +167,7 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-graphics</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> <scope>test</scope> </dependency> diff --git a/converter/pom.xml b/converter/pom.xml index 6e3b2b6444aa4aad429274c815d723e685c8d098..3e3f82648b6c6f9a87f5ba088fa9830c167c3e6c 100644 --- a/converter/pom.xml +++ b/converter/pom.xml @@ -5,7 +5,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>converter</artifactId> @@ -15,7 +15,7 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>xerces</groupId> diff --git a/frontend-js/pom.xml b/frontend-js/pom.xml index 4805044e7ce1bd88eda547a96b4b29855e9bb1cf..248c741ed61387984ae7a6a7fed396665de8a63f 100644 --- a/frontend-js/pom.xml +++ b/frontend-js/pom.xml @@ -7,7 +7,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>frontend-js</artifactId> <name>frontend-js</name> diff --git a/model-command/pom.xml b/model-command/pom.xml index 0f3bd20ad5322542bb57913938d29ddf242d7057..44c70d92bec214d43a4826b5af1b57a3a9b5719e 100644 --- a/model-command/pom.xml +++ b/model-command/pom.xml @@ -3,7 +3,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>model-command</artifactId> <name>Model commands</name> @@ -16,7 +16,7 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> @@ -24,7 +24,7 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-CellDesigner</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- Log4J2--> diff --git a/model/pom.xml b/model/pom.xml index d6afc006c5ec7bcaefcdf072ed4cd07842887a39..178a6fd0c3e486a6b258caf48831741303701e6e 100644 --- a/model/pom.xml +++ b/model/pom.xml @@ -5,7 +5,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>model</artifactId> <name>model MapViewer</name> @@ -15,7 +15,7 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>commons</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- Java xml serialization --> diff --git a/pathvisio/pom.xml b/pathvisio/pom.xml index 81a184142ae0a4e7da21fe1b944e7de7b447294b..bd0f7783870e39390cf94d21bedb92dfeb4927eb 100644 --- a/pathvisio/pom.xml +++ b/pathvisio/pom.xml @@ -5,7 +5,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>pathvisio</artifactId> <name>Pathvisio plugin</name> @@ -77,26 +77,26 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-CellDesigner</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-graphics</artifactId> <scope>test</scope> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model-command</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- Log4J2 --> diff --git a/persist/pom.xml b/persist/pom.xml index d87b1a079952fcce467e98f30ee48279fa94cbd5..a670ae0e57d76ce176b65cd2de4676224327d1fd 100644 --- a/persist/pom.xml +++ b/persist/pom.xml @@ -6,7 +6,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>persist</artifactId> @@ -26,7 +26,7 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- Hibernate --> diff --git a/pom.xml b/pom.xml index f331fdbbce2dc6b9ba0c23f5c91f864ad684cad1..97b422be783fc88b889be72915cc0b9873eef436 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> <packaging>pom</packaging> <name>parent MapViewer</name> diff --git a/rest-api/pom.xml b/rest-api/pom.xml index 6aeb6508794b2bdfb98b2d1e191e5e7eeeefb3e8..feb1ccacc454aeaf0f51cd961ecdfeae03743dcc 100644 --- a/rest-api/pom.xml +++ b/rest-api/pom.xml @@ -7,7 +7,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>rest-api</artifactId> <name>rest-api</name> @@ -19,19 +19,19 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>service</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>pathvisio</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> diff --git a/service/pom.xml b/service/pom.xml index d751b2dbc7b034387e1639e2661833ed10815f48..52a08f784b181ebd6f0fac59537eba032509f138 100644 --- a/service/pom.xml +++ b/service/pom.xml @@ -6,7 +6,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>service</artifactId> @@ -19,7 +19,7 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- dependency from the MapViewer dao --> @@ -27,47 +27,47 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>persist</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>model-command</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>annotation</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- dependency from the MapViewer cell designer parser --> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-CellDesigner</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- dependency from the MapViewer SBGN-ML parser --> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-SBGNML</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- dependency from the MapViewer graphics converter --> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-graphics</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- dependency from the SBML parser --> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>converter-sbml</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <!-- Log4J2 --> diff --git a/web/pom.xml b/web/pom.xml index 18132372c934fb08704f600afb7a74f4d1854981..82b48047bf6e3450c04fff065fdc8539f0d862c3 100644 --- a/web/pom.xml +++ b/web/pom.xml @@ -6,7 +6,7 @@ <parent> <groupId>lcsb.mapviewer</groupId> <artifactId>parent</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </parent> <artifactId>web</artifactId> <packaging>jar</packaging> @@ -36,19 +36,19 @@ <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>service</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>rest-api</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency> <groupId>lcsb.mapviewer</groupId> <artifactId>frontend-js</artifactId> - <version>17.0.1</version> + <version>17.0.2</version> </dependency> <dependency>