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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.4.3]

Fixed or optimized

  • (!1342) [ApiDocs] Fixed link to api-docs on some instances where a "/" was missing from the url.
  • (!1343) [Dashboard] Metric links now correctly redirect to other pages on all instances.

[1.4.2]

Fixed or optimized

  • (!1337) [GlobalUriSearch] Fixed the uri search box not popping up on instances with a unique header.

[1.4.1]

Fixed or optimized

  • (!1331) [Dataverse] Creating a dataset now works again
  • (!1334) [GlobalUriSearch] Blocked access to data details if the user shouldn't be able to see them.
  • (!1335) [Datafile] Added support for tiff format images

[1.4.0]

Warning : upgrading to this new version requires manual operations. Please follow the versioning notes

Changes and new features

  • (!1263) Update RDF4J from 3.7.7 to 5.0.3 version
  • (!1264) Upgrade to java 17 and update internal dependencies
  • (!1275) [GlobalMap] A global map now displays instance sites, outside experiments.
  • (!1276) [Devices] The name of the variables linked to a given device is now displayed. It is possible to sort them or search in the list by name. A button allows the copy of the URI
  • (!1281) [Sites] new interface dedicated to sites management.
  • (!1285) [Organization] Simplify organizations interface.
  • (!1287) [Provenance] The provenance search filter by agent (operator) now allows multiple selection.
  • (!1290) [UriSearch] Added a web-service to search by any URI on the instance. Added a search button to app-header to use this feature.
  • (!1298) [Events] Improvement on events ergonomy, targets can now redirect to concerned element detail page, specific properties URIs can be copie
  • (!1312) [Scientific object] The selector level filter for scientific object search now perform a logical AND instead of an OR when multiple levels are selected, to allow filtering on multiple different factors at once
  • (!1321) [Germplasm] Added sort by name to germplasm list

Fixed or optimized

  • (!1315) [Event] Fixed event template generation from a selection of Scientific Objects or Devices
  • (!1315) [Event] Removed empty target column from Device events
  • (!1310) [VariableGroup] Fixed creating a Group of Variables from a selection of Variables on the Variables page.
  • (!1272) [VariableGroup] A variable selector with filters is now used for Group of variables updating
  • (!1274) [Facility] Repaired the getUsedVariables webservice in Data Module, this was causing the Facility Monitoring page to not work.
  • (!1283) [Facilities] Facilities selectors no longer only display the first 10 results
  • (!1292) [Data] Huge performance optimization on POST addListData service. Fix permissions error when inserting data with a unauthorized target.
  • (!1293) [Ontology] Services GET /uri_labels and GET /uri_types now use the POST method. The URI list is passed as body to allow for more parameters.
  • (!1302) [Site] a warning message is now displayed if a site address can't be geolocated.
  • (!1303) [Selectors] Selected elements on Facility selector and Group selector no longer deselect themselves in function of her URIsd
  • (!1309) Fixed QUDT ontology link
  • (!1309) Fixed the "time interval" field in the variable form
  • (!1312) [Web interface] You can no longer select factors in factor level selectors
  • (!1314) [Web interface] Factor level selector in the scientific object modal selector now works correctly again
  • (!1316) [Germplasm] Germplasm export now works again if additional columns are present
  • (!1318) [Data] The CSV validation process now returns an error message when the "target" column is missing (if no device is specified)
  • (!1326) [Device] Removed some pointless error messages.
  • (!1326) [Device] Fixed duplication of linked variables list on Device details page after a page refresh.

Other

  • (!1267) For developpers, cleaned the build logs by removing unecessary debug info and fixing non-blocking build errors

[1.3.5]

Warning : upgrading to this new version requires to update the ontologies. Please run the following command to make sure they are up-to-date :

# From the directory which contains your OpenSILEX executable .jar file
java -jar opensilex.jar --CONFIG_FILE=<config_file> sparql reset-ontologies

Fixed

  • (!1301) vocabulary:hasGeometry property is now present again in the scientific object export file
  • (!1301) Fixed an error where objects with the exact type vocabulary:ScientificObject were displayed twice in results

[1.3.4]

Fixed

  • (!1289) Deleting data with criteria now works again
  • (!1291) Updating a Facility from the Facility details page now works correctly

[1.3.3]

Fixed

  • (!1262) Fixed Move import template generation, and Move import

[1.3.2]

Fixed

  • (!1260) Fixed the link to swagger for the specific case where a "/" is at the end of server uri in the config file.

Changes and new features

  • (!1261) You can now fetch a list of moves at once using the new service GET /moves/by_uris

[1.3.1]

Fixed

  • (!1259) Fixed link to swagger and corrected the 1.3.0 migration documentation (the "Known issues" of version 1.3.0 have been fixed).

[1.3.0] - Dizzy Diamond

WARNING : upgrading to this new version requires manual operations. Please see the versioning notes. Also available locally.

Changes and new features

  • (!1128) [GraphQL] Added a WebService to retrieve graph URIs in the triple store. This is used by the Staple API for GraphQL mapping.
  • (!1172) [GraphQL] Rectifying ontologies and adding a list of authorized experiments to the token, as well as adding a web service that returns the base URI. This is used by the GraphQL service to retrieve data and manage authorizations.
  • (!1188) [API] There are now FAIDARE compatible services. Use this service for more information : "/rest/faidare/v1/calls"
  • (!1204) [Visualization] If there are more than 50000 data in the selected time range for visualization a message warns the user that the serie was truncated.
  • (!1211) [Annotation] Added API and DAO tests for opensilex:Annotation

Fixed or optimized

  • (!1200) [Event] In the event creation form, if there is a URI error in the "targets" field, error messages are now displayed.
  • (!1206) [Moves] fixed pagination for tabs returning a list of positions. The first page of results is no longer the only one available.
  • (!1214) [Data] fixed number of elements and totalcount rendered on datalist, improve interface
  • (!1224) [Data] operator and device filters for data searches now work.
  • (!1229) [Facility] Optimization of the Facilities page
  • (!1233) [Interface] Allows redirection to the different sections from the dashboard metrics information. When changing the selected period, the metrics only display a loader instead of the entire dashboard. Fix missing global header for variables after clicking on a variable property and being redirected to the global section. Fix of the "showMoreResult" message at the end of the list of selectors, which could disappear depending on the searches although there are more results
  • (!1242) [Germplasm] Germplasm POST service with checkOnly now returns valid metadata instead of null
  • (!1246) [Account] Optimization of account and group services, display is now faster
  • (!1255) [Metrics] Metrics querying has been optimized

[1.2.7]

Fixed or optimized

  • (!1220) Updating custom relations of SO and devices now works correctly (the "Kown issue" of version 1.2.6 has been fixed).

[1.2.6]

Fixed or optimized

  • (!1219) Fixed display of custom relations in forms when both incoming and outgoing relations are defined.

Known issue

  • Self-referencing custom properties (i.e. properties that reference the same type as the object they are declared on, e.g. a Device property that targets another Device) are not stable when declared in chain for Scientific Objects and Devices, meaning that they can be removed by the system when trying to update one of the resource of the chain. By "chain", we mean three or more resources that are linked together by the same property.

    For example, a property "contains" declared on scientific objects A, B and C such as "A contains B" and "B contains C" may be removed when trying to update A, B or C.

    We are actively working on fixing this issue, but for the moment you should avoid declaring this kind of property chain.

[1.2.5]

Fixed or optimized

  • (!1218) Service "all_facilities" now correctly returns all results

[1.2.4]

Fixed or optimized

  • (!1212) Device filter no longer ignored during data export.
  • (!1213) A wrong error message is no longer displayed on the visualization page of a device with no associated scientific object

[1.2.3]

⚠️ WARNING : upgrading to this new version require manual operations. Please see the versioning notes.

Highlight

  • Some data-related pages and services have been greatly optimized, especially for OpenSILEX instances where a lot of data are declared (> 10M).
  • You can now configure a custom notification banner that will be displayed at the top of the web interface. This can be used to inform your users of maintenances, changes, etc. See the configuration instructions.

Changes and new features

  • (!1167) Changed type of publication date and last modification date from Integer to Date when it wasn't already the case. This improves
    uniformity and client support.
    • Concerned services :
      • Data
      • Provenance
      • Datafile
  • (!1168) Improvement on the "move" type event declaration.
    • Additional information for the user in the form.
    • Dynamic attribute required for location fields.
    • An error message is now returned if the move is incorrectly declared, even though nothing was indicated and nothing happened before.
  • (!1175) Added a message notification system to users.
    • Message can be translated into different languages.
    • Possibility of adding HTML tags in the message.
    • Several color themes available.
    • Possibility of defining an end date for display.
    • See the configuration instructions.
  • (!1178) You can no longer select an end date that is earlier than the start date during Event creation. The target column of the Event list now redirects to the resource in question upon click.
  • (!1180) The Event import system now works the same way as ScientificObjects and Devices, the headers of columns are now short uris instead of labels.
  • (!1185) Replaced simple germplasm selector in the ScientificObjects tab of Experiments with a pop-up one.
  • (!1186) Creation of a new default order for ontology properties : properties from higher up in the hierarchy get shown first, all the way down to properties from the lowest domain in the hierarchy. Within the sublist of properties from a single domain, they are ordered alphabetically (by name).
    • Usage of this new order, if no order has ever been defined for CSV template generation.
    • Usage of this new order, if no order has ever been defined for Ontology based forms.
  • (!1195) Germplasm and Germplasm Group filter no longer treated as a logical OR with the targets filter
  • (!1203) The details tab is now the first and default tab for facilities instead of monitoring

Fixed or optimized

  • (!1166) Fix concerning the dates of an event.
    • If the event is instantaneous, the end date is now required.
    • If it is on a time interval, at least one of the two fields (start / end) is required.
  • (!1169) Fix concerning the data import. If the standard provenance is not created, it is no longer possible to insert data by selecting it, a specific error message is returned to the user in this scenario.
  • (!1183) Visibility of areas and devices on the map is now stable
  • (!1190) Data and datafile table pages now render correctly when every data or datafile in the table has an undefined target
  • (!1194) In the create germplasm view, when loading a heavy CSV file, the table is now filled in less than 2 seconds and is showing a loader.
  • (!1197) Optimisation of data search.
    • A new optimized searchDataListByTargets service is available. This service no longer compute the totalCount of data and just indicate if a next page exists.
    • All data search service no longer return detailed information about data publisher (only the publisher URI is returned).
    • Two new MongoDB indexes are created on data experiment and data provenance URI.
  • (!1198) fixed a bug that prevented Move from being declared if no position information was provided
  • (!1207) Inserting scientific objects in an experiment, when they were already present in another experiment, using an import file now works correctly again.

[1.2.2]

Fixed

  • [Doc] Changelog and versioning notes was changed to avoid deployment and configuration issues

[1.2.1]

Fixed

  • [Map] When we open the "map" module, the focus is now on the correct extent of the scientific objects of the experiment.
  • [Experiment] Scientific objects are now displayed in a hierarchy again by default, instead of a flat table. Flatten display will now only trigger when searching using certain filters, such as data criteria.

[1.2.0] - Caramelized Crystal

WARNING : upgrading to this new version requires manual operations. Please see the versioning notes. Also available locally.

Highlight

  • [General] Every resource now has associated metadata linking to its creator (account), its date of creation and its last update date. This metadata is usually displayed in the detailed view of a resource. -> bf721199
  • [Scientific Object] You can now search scientific objects by applying mathematical filters on their associated data. For example, you can search "all scientific objects with recorded data for the variable 'air_temperature' where the value is between 10°C and 20°C". -> b4d06f44
  • [Person] You can now create a person based on an existing ORCID account. All relevant data will be automatically fetched to fill the person's info. -> 3361a1c8
  • [RGPD] You can now display your RGPD file as a PDF in the web interface. See configuration instructions -> cc2a416b

Changes and new features

  • [Person] Enhanced the ergonomy of the "phone number" field for the person form. -> c9238820
  • [Data] You can now search data by the germplasm group of their target. -> 500c2f9e
  • [Ergonomy] You can now choose the number of results displayed in search result tables. -> 26158449
  • [Ergonomy] In selectors, you can now expand the displayed results that were previously capped at 10 items. -> 3ccabae5
  • [Security] There are now credentials to manage accounts. -> 0865dd7c
  • [Device] You can now filter the data in the device graphs by target. -> 22462def
  • [Graphs] The default visualization date for data has been adjusted. -> 89c02765
    • For devices, variables or scientific objects graphs, the default beginning date is now 15 days before the current date.
    • In the case of a finished experiment, the default dates are those of the experiment.
  • [Analytics] You can now configure an OpenSILEX instance to send analytics data to a Matomo server. -> 90177a11
  • [Germplasm] The germplasm model now supports 3 additional properties, has_parent, has_parent_m and has_parent_f. You can also search germplasms using these properties as filters. -> 1f107ee0
  • [Dashboard] You can now configure your dashboard to display a custom title to your graph. See configuration instructions -> a1e37f00
  • [Map] You can now export elements from the map in the GeoJSON format. -> da13f442
  • [Documentation] The installation documentation was updated. -> 9368839e

Fixed or optimized

  • [Ergonomy] When going back to a previously visited list, the pagination is kept. -> 62a6fb26
  • [Metrics] The metrics service now returns correctly the variable names. -> 4ab1fa1a
  • [Variable group] The "variable group" selector now works correctly for multiple selection. -> 40dfd0fc
  • [BrAPI] Missing mappings for BrAPI 1.3 were added, and other mappings that returned an incorrect format were fixed. -> 3721ad9f
  • [Table list] In table lists where items can be selected, the selection count is now correct even when a selected item is deleted. -> a45111a7
  • [Germplasm] You can now correctly import multiple germplasms with the same name using a CSV file. -> 16228e14
  • [Data] Importing data when the target column is the last column now works correctly. -> fded1f4d
  • [Site] The link to a hosted organization from a site now redirects correctly. -> b2c8ef07
  • [Account] You can no longer delete an account while it is associated to other data. -> 3abe2506

Versions changes

Java 8 to Java 11

  • [WARNING] This requires to have an installed JRE with a version >= 11 on the server host which run OpenSILEX

  • Ensures that the JRE is well installed before upgrading your OpenSILEX version

  • You can check the documentation here if your need more information or contact our team for support.

Docker mongodb

Technical changes

  • [GraphQL] A service wa added to generate a Staple API configuration file. -> 73b2d8ad

Updated Dependencies

Maven plugins

Dependency Old version New version Notes
deploy 3.0.0 3.1.1
install 3.0.0 3.1.1
enforcer 3.0.0 3.1.1
surefire 3.0.0 3.1.1
failsafe 3.0.0 3.1.1
site 3.8.2 3.12.1
version 2.7 2.16.0
plugin-api 3.6.0 3.9.0 Maven plugin in swagger module

Others Dependencies

Dependency Old version New version Notes
caffeine 3.1.1 3.1.8
bcrypt 0.9.0 0.10.2
jwt 3.11.0 4.4.0
picocli 4.6.3 4.7.5
jena.query.builder 4.5.0 4.9.0
bytebuddy 1.10.18 4.9.0
httpcore 4.4.14 4.4.16
httpclient 4.5.13 4.5.14
apache-tika 2.3.0 2.9.1
apache-commons-io 2.11.0 2.13.0
mongodb-driver-sync 4.5.0 4.11.0
mongodb-embed (for-test) 3.4.2 3.5.4 Update mongo test version 5.0.6 to 6.0.2
glassfish-jersey* 2.3.5 2.3.7
swagger.jersey2.jaxrs 1.6.2 1.6.5
git-commit-id-plugin 4.0.0 4.0.5
tomcat-embed-core 9.0.39 9.0.82
jackson* 2.13 2.15.3
janino 3.1.6 3.1.9
awaitility 4.1.1 4.2.0
logstash-encoder 7.0.1 7.4

Removed dependencies

Name Note
medeia-validator-jackson

[1.1.0] - Blazing Basalt

⚠️ WARNING : upgrading to this new version require manual operations. Please see the versioning notes. Also available here

Changes and new features

  • [Map] You can now visualize data in a chart by selecting an object in the map view
  • [Person] You can now search persons by their ORCID
  • [User] The User API is now deprecated
  • [Account] The form for creating accounts has been simplified
  • [Experiment] Associated facilities are now part of the available facilities for scientific objects of the experiments
  • [Experiment] The "Visualization" tab of a scientific object in an experiment has been removed
  • [Experiment] Scientific object count is now displayed on the scientific objects tab
  • [Germplasm group] Added documentation that you can read by hovering the question mark

Fixed or optimized

  • [Front] Minor visual fixes
  • [Experiment] On the "Data" page of an experiment, targets are now always correctly displayed
  • [Data] Importing multiple variables in one CSV no longer duplicates devices in provenance
  • [Data] Adding annotation during data import now uses the correct date and time
  • [Map] Fixed some issues with the zoom
  • [Organization] Fixed an issue where you had to click twice on "create organization" or "create site" to perform the action
  • [Facility] Tweaked the "Monitoring" page of a facility for better ergonomy
  • [Charts] Tweaked the display of graphs with multi-scale axis for better ergonomy
  • [Charts] Fixed a bug where data with the value 0 where sometimes displayed as undefined
  • [Charts] Charts no longer aggregate data points
  • [PHIS] PHIS logo is now displayed if the dashboard chart is not configured

[1.0.1] - Ambitious Amber

Fixed or optimized

API

  • [Person/User] Removed User and Person delete web services

Web client

  • [Person/Account] Removed Account and Person delete buttons
  • [Profiles] Added translation for Dataverse credentials menu

[1.0.0] - Ambitious Amber

WARNING : upgrading to this new version require manual operations. Please. See the versioning notes. Also available here.

New features

  • [MongoDB] You can now specify credentials to connect to a MongoDB server -> d02b3c8d
  • [Facility] Environmental data can be visualized in the facility detail page, including mean and median graphs -> d9a705bf
  • [Data] Added new filters for data search : devices, facilities, operators -> ea0cc36b
  • [Data] Scientific objects can now be annotated during data import by adding an "annotation" column in the CSV -> 816f5ecf
  • [Map] Various enhancements -> 89ce4fa6
  • [Map] Scientific objects can now be exported as Shapefiles with the selected properties -> fa9fb97e
  • [Germplasm] Germplasm groups can be created to manage a set of germplasms at the same type -> bc29624d
  • [User / Person / Account] The web interface now reflects the changes in the API, where the User concept was split in two Person and Account concepts -> b8457f7b
  • [Person] A person can now have an ORCID, a phone number and an organization -> 0718f5e5
  • [Person] Several links to Users are replaced by links to Persons (for projects, experiments, provenances and devices)
  • [Variable] Added a "not included in group" filter for searching variables -> 98fde231
  • [Experiment] Added a germplasm filter for searching scientific objects in an experiment -> 25f5c93f
  • [API] All resources now have a publisher, publication date and last update date -> 2a3140bd
  • [Dashboard] You can now display a media in the dashboard if the graph component is not configured -> d1aa16ef
  • [Recherche Data Gouv] Added the possibility to create a Dataset draft on Recherche Data Gouv from OpenSILEX -> 63251bc2

Fixed or optimized

API

  • [Data] Fixed export when sending too many parameters (e.g. a variable URI list) -> 1bc02a68
  • [Data] Exporting data with a "long" format without selecting a variable first now correctly works -> 1bc02a68
  • [API] Services returning a paginated list now only returns the list once -> e1b01648
  • [Event] When importing a CSV file containing events, the beginning and end date are now checked to be coherent -> 94cf74db
  • [Organization] Organization and site search now uses an internal cache to improve performance -> 2f077837
  • [Variable] SKOS references are now included in detailed export -> aa969f05
  • [Variable] Fixed some errors when using variables from a shared resource instance -> b18d55fd, cd848c61
  • [SPARQL] Namespaces defined in the triple store are now taken into account by the app -> 2df69a7e
  • [Facility] Facilities can now have a custom geometry -> 152efe01
  • [Ontology] The GET /uri_label service new returns a 404 when the URI or label is not found -> 4c664cdf

Web client

  • Multiple ergonomic changes -> 05162e38, 2bc8dce7, b4f72a5a

  • [Experiment] Fixed "isPartOf" relation when creating a Scientific Object with the "+" button in experiment -> 46211dbc

  • [Visualization] Graphs now display even if the data series contains only NaN values -> 4e1ce841

  • [Forms] Date selectors now checks that the end date is after the beginning date -> 2d8c1da0

  • [Details] Incoming custom properties are now clearly displayed in a distinct section (for scientific objects and facilities) -> 167130fb

  • [Variable] Changing the source instance now reloads all the filters correctly -> e5997c5d

  • [Data] Added an indication to the CSV template to specify the expected format when using a boolean variable -> e318a0ea

  • [Datafile] Image datafiles can now be visualized without problems -> 28c38f05

  • [Map] When zooming out, scientific objects are grouped into clusters to enhance performance and visibility -> c394c7fc

  • [Person] Enhanced display of persons of contact (for accounts, projects, experiments, devices and provenances) -> 70daab17

  • [Germplasm] Searching a germplasm by URI now works correctly -> aad496dc

[1.0.0-rc+7]

WARNING : upgrading to this new version require manual operations. Please see the versioning notes. Also available here

New features

  • [Dashboard] Add a dashboard functionality for visualizing data, scientific objects, devices and germplasm statistics -> 38970ef6
  • [Variables] Allow to browse and import variables from a remote instance ("shared resource instance") -> 5aa3e0482
  • [UI] Indication of elements number in tabs -> 5eb24aac4
  • [UI] Enter Key press no longer necessary in auto-complet fields -> 7dc8ff333
  • [UI] Add an OpenSILEX neutral UI theme -> fd2706c1
  • [Germplasm] Append search by attribute values on front -> a1425b118
  • [Position] Display the Devices/OS LastPosition on detail and map page -> 3cf14f8e2
  • [Facilities] Sites can now be associated to a facility from the facility creation or update form -> 845f3d1d
  • [Data/Image] : Visualization of Images associated to the data since from experiment -> 169cbc31d
  • [Users] Data model has been changed, old users are now split into accounts and persons -> 8ed0303a
  • [Users] Add a command for creating a guest account -> fd2706c1

Fixed or optimized

  • [Ontology] move some subclass and properties from oeso-ext ontology (phis) to oeso-core ontology -> ac1a451c3
  • [Data] Fix bad redirection of scientific object inside experimental context. Fix display error in case of data with no target defined -> d9830177d
  • [Experiment/Visualisation] Fix graphic visualizations in experiment module -> 43dbfe29d
  • [Provenance] Fix creation of provenance with an operator -> abd7ba2a9
  • [Event] Append Fertilization event french translation -> 2dd981f06
  • [Scientific Object] fix storage/search of name composed only of digit in global graph -> 3268a4bf3
  • [Scientific Object] fix germplasm and custom properties export -> 0ede9443d
  • [Move/Location] Enhance OS positions historic -> 89553d5e0
  • [Scientific Object] new rooting for SO tabs / fix links redirect -> c37bc6273
  • [Scientific Objects] Fix SO form if it contains subtype properties -> 4d8b93899
  • [FileSystem] Fix import from local files to mongodb import -> 9436ce94d
  • [Scientific Object] fix no display of object name for each experiment (if name are equals in global and experimental context) -> 1eeff0fcd
  • [Germplasm] Fix search by attributes and attributes list display -> 7b71920d
  • [Scientific Object] Fix form if it contains custom/subtype properties -> 4d8b9389
  • [FileSystem] Fix import from local files to MongoDB import -> 9436ce94
  • [Germplasm] Fix search by attributes and attributes list display -> 7b71920d
  • [Document] Fix error on Document creation when using a fixed URI -> 6e766fbe
  • [Facility] Fix display of associated device -> 465c364f
  • [User/Account] Extract Account and Person from User -> 8ed0303a
  • [Facility] Add tabs for facility view -> 2239fb02
  • [Germplasm] Allow duplicate names for accessions -> 42399304
  • [Organizations] The "create facility" button on site details now works as expected -> 845f3d1d

[1.0.0-rc+6]

Fixed or optimized

  • [Installation] The dockerized version of rdf4j-workbench provided with OpenSILEX has been upgraded to version 3.7.7 -> e6bbbaf3
  • [Server CLI] It is now impossible to create duplicate users by CLI -> d8e10669
  • [Ontology] Fixed the deletion of custom properties, which would not delete the restriction and cause an error on the next launch -> 44aa61aa
  • [Web Client] Removed moment.js dependency -> 0a42b846
  • [Web Client] Selector fields now use the whole line to display item names -> 46957e0f
  • [Web Client] Selectors that allow to select multiple items no longer reset their selection after performing a second search -> 46957e0f
  • [Web Client] The base type is now selectable on multiple forms (scientific objects, events, devices) -> 44aa61aa
  • [Web Client] Fixed several issues with the modal selector -> 564539a7
  • [Geospatial] Creation, visualization, modification and deletion of areas now functions properly -> f8416c7c
  • [Geospatial] Services for managing temporal areas were simplified and manage the associated events. It is no longer needed to call the event service manually. -> f8416c7c
  • [Data Visualization] Graphs now take the optimal amount of screen space -> 66428cf5
  • [Data Visualization] If there is no data to plot, a message is shown and an empty graph is still displayed -> 66428cf5
  • [Variable] It is no longer possible to delete a variable component if it is associated to a variable -> fbc69422
  • [Variable] The update of SKOS properties of a variable now works properly -> fbc69422
  • [Variable] Fixed a wrong link in the variable modal list -> fbc69422
  • [Organization] The organization / facility / site access check system has been reworked to function properly -> 540f2adc
  • [Germplasm] Germplasm names no longer need to be unique -> a92e43e3
  • [Germplasm] More than 20 germplasms can now be exported at the same time -> 4c1e68c2
  • [Event] CSV template columns are now correctly generated when the event type is oeev:Move -> 6c7a8043
  • [Vocabulary] Default class is now displayed -> 44aa61aa
  • [Data] Data creation with an incomplete provUsed is no longer possible -> 786b4a9a
  • [Scientific Object] CSV import has been fixed and optimized -> fc5b3041

Added or changed

  • [Authentication] SAML protocol can now be used for authentication to supported federations (e.g. RENATER) -> 701f988c
  • [File Storage] Amazon S3 can now be used for file storage -> 5386906b
  • [Geospatial] Devices are now displayed on the map -> 93b2c8b7
  • [Data Visualization] Images associated with data can now be visualized from a data graph -> a48a59a6
  • [Data Visualization] Filter forms are now reduced after launching the visualization action -> 46957e0f
  • [Experiment / Variable] Germplasm-related fields are no longer displayed if the germplasm menu is excluded on the instance -> 3652ae43
  • [Experiment] Added "record author" field on the experiment description -> 3652ae43
  • [Facility] Associated experiments and devices can now be viewed in the facility details -> 91758cb9

[1.0.0-rc+5.2]

Fixed or optimized

[Scientific Object] Fix CSV export on column size -> 9c88f33 [Documentation] Update migration information for OpenSILEX 1.0.0+rc-2 version -> 9c88f33 [Modularity] Fix Extended module build -> 9c88f33 [TypeScript] Remove http import -> a27cf7e [Documentation] Update Changelog -> a27cf7e

[1.0.0-rc+5.1]

Fixed or optimized

Fix OpenSILEX commands initialization and append test scripts -> cd19dd5

[1.0.0-rc+5]

Warning : upgrading to this new version may require manual operations. Please see the versioning notes.

Warning: since version 1.0.0-rc+2, if you have created scientific objects with the same name in different experiments (with automatic URI generation), their URI would end up being the same. That may cause problems if you intended to create distinct scientific objects, such as some scientific objects being associated with the wrong data.

This bug has been fixed in this version. If you suspect that may have happened to you, please contact us (opensilex-help@groupes.renater.fr).

Added or changed

  • Web client : Major aesthetics and ergonomics improvement -> 9f4eaf90

  • Web client : Visualisation of pictures associated to data -> 45166d2b

  • Web client : Visualisation of experiment data from scientific object and variables c924d260 -> aecfd721

  • Web client : New tab with associated document into variable details page -> ab7b6bb0

  • Web client : Variables selection and contextual actions into variable search page -> da82201c

  • Web client: Add loader on scientific object tree view loading -> cf864292

  • API/Web client : A software (Device) can be linked to a variable -> 8d8cfb43

  • API : Prevent deletion of OS in case of associated experiment, children, data or datafile -> e17caea7

  • API : When storing position for a move, we now use a String representation of x,y,z fields instead of a previous Integer representation -> 9b3a4a27.

  • API : Add the "Operating procedure" as a new type of technical document -> e39e3c6b

  • API : Remove opensilex-mobile module from default OpenSILEX modules -> 252e4565

Fixed or optimized

  • Web client : Link for "reset password" in the login page now always redirect to the correct page -> f33941bc

  • Web client : Fixed a problem with a "germplasm" field when editing a scientific object -> df025f7d

  • Web client : optimize loading of variables and variables group tab. Optimize loading of variables and variable groups in forms -> b00c53ba

  • Web client : [Data visualization] Optimizations on date formatting into data visualisation -> 687bfcb3

  • Web client : several fixes for the map visualisation -> 9b3a4a27

  • Web client : [Geospatial] Display calibration position & enhance multi select -> 73811bcb

  • Web client : Fix variable name display on tabular data list -> fd3ea6be

  • API : Variables associated with a variable of type "date" are now stored and exported correctly -> 624e99dd

  • API : Better error handling in case of Invalid character when evaluating a SPARQL REGEX -> 326be84c

  • API : Fix URI generation when providing a URI on scientific object creation and CSV import -> e17caea7 , a77a3629

  • API : Remove no duplicate name constraint when importing OS into global graph -> 45bcf04a

  • API : Optimize search and loading for entities, characteristics, methods, units, variables and variable groups -> b00c53ba

  • API : Fix deletion and existence checking for gridfs file-system connection -> e1034199

[1.0.0-rc+4.1] - 2022-07-13

Fixed

  • Fix opensilex install command
  • Install will now create a repository with graphdb triplestore

[1.0.0-rc+4] - 2022-06-13

Warning : upgrading to this new version requires to update the ontologies. Please run the following command to make sure they are up-to-date :

# From the directory which contains your OpenSILEX executable .jar file
java -jar opensilex.jar --CONFIG_FILE=<config_file> sparql reset-ontologies

Added or changed

  • Add Device type and specifics properties management driven by ontologies: import template generation and driven forms.
  • The variable selector has been enhanced; variables are now selected through a modal form where they can be filtered by name, entity, characteristic, etc.
  • Variables can now be filtered by datatype and time interval.
  • When a groups of variables are created or Updated, there are a redirection on detail part of the group.
  • Associated experiments are now listed in the project description.

Fixed

  • Events can now be correctly filtered by end date (even if multiple events have the same end date).
  • Germplasm search and export have been optimized.
  • Fixed some variable bugs: filters, display of species, datatype and time interval translation.
  • Data exportation bug about column offset.
  • Fix germplasm export: optimize search and export in order to avoid timeout interruption.
  • Improve specific properties management of scientific objects.
  • Fix bug on ResetOntologies for not completed classes, properties ou restrictions.

[1.0.0-rc+3] - 2022-05-05

Be careful, updating to this new version need some manual operations to be done. See versioning notes. New installations don't need further action.

Added or changed

  • Display of menu entries can now be configured via user profiles
  • Species of an experiment are now automatically deduced by the germplasms of scientific objects
  • The geocoding service for address autocompletion can now be specified in the configuration file
  • Factor levels can now be exported from the factor detail page
  • In the facilities list, facilities can now be filtered by name
  • In an experiment or in the global context, data can now be filtered by target uris
  • Documents can now reference an external resource by URL instead of uploading a file
  • Species can now be updated like any other germplasm
  • Documents can now be stored using the GridFS Mongo Connector (see versioning notes)
  • Events and annotations can now be added on a device
  • Facilities are now part of their own menu entry
  • A new document type "Archive" was added to represent a compressed set of files, where each can be described as a document (but they cannot be downloaded)

Fixed

  • Updated factor categories to be more understandable
  • Fixed some inaccurate controls based on user profile and credentials
  • Some columns in the event CSV template that were present twice are now shown only once
  • The scientific object filter for experiment data now correctly shows the scientific objects of the experiment
  • Fixed empty line after adding factor level via CSV
  • The address field in facility form now works correctly if the facility has specific properties
  • Data visualization from a device now shows variables correctly
  • Uniqueness check on data import now takes the device into account
  • Fixed a problem on new installations where it was impossible to log in
  • Factor levels can now be correctly exported from a set of scientific objects
  • Optimized loading of the map, fixed the problem where it would sometimes freeze
  • Data can now correctly be filtered by a big number of targets (API : POST /core/data/by_targets)
  • Provenances can also be filtered by a big number of targets (API : POST /core/data/provenances/by_targets)
  • Filtering documents by keyword now correctly works
  • Importing germplasms with specific properties via CSV now works properly; no line are skipped
  • Improved data visualization and fixed some display problems
  • Fixed the creation of scientific objects with an associated facility (with the property "isHosted")
  • Optimized data import, changed data URI generation on import
  • Fixed error shown when opening an experiment hosted by at least one facility
  • Fixed "reset" button on project list filters
  • Fixed cookie management that could cause multiple problems; including "Request header too long" errors on requests
  • Variables can now correctly be sorted in the table view
  • Some visual and ergonomic changes

[1.0.0-rc+2] - 2022-01-23

Be carful, updating to this new version need to execute some actions. See Versioning notes. New installations don't need updating action.

Added

  • Concept of "Site" with an address : use W3C vcard specification.
  • Filter on variables with filter in entity, entity of interest, characteristic, method, unit, group of variables
  • Search in germplasm's attributs in Webapp
  • Service in Ontology API to rename an URI.
  • New filter on variable in Search Device service, for provenance's agent.
  • Append FOAF.rdf ontology
  • OpenSILEX migration modules with command.
  • Command org.opensilex.migration.GraphAndCollectionMigration for SPARQL graph and MongoDB collection renaming after URI generation update

Added in pre-production

  • Visualisation og device value by variable. See. Variable / visualisation
  • Species become optional in an experiment

Fixed or improvement

  • WARNING: Update model graph from sets/<model_name> to set/<model_name>. Update URI generation by using "id" instead of "set" : this improvement need an action. See Versioning notes if updating.
  • WARNING: Organization and Facilities ontologies. See Versioning notes if updating
  • Control access in the Web interface, in progress
  • Variable and device association on data creation
  • Protect Device from removing when data exists
  • Manage ambiguity of variable / device association at data creation
  • API JSON message for duplicated attributes, or any kind of errors
  • Remove experiment name using into URI generation
  • Scientific Object tree filter, in progress
  • Bugs fixed :
    • germplasm uri redirecting
    • all device type are linked to its root device type
    • others bugs

Some Known Issues

  • Problem of authentification when migrate. It's due to FOAF import. You need to remove <http://xmlns.com/foaf/0.1/Agent> rdfs:label "Agent"
  • When installing other version, PHIS ontology is imported. You need to remove http://www.opensilex.org/vocabulary/oeso-ext context
  • Some installation have problem with geospatial visualisation.

[1.0.0-rc+1] - 2021-11-02

Added

  • Variable:

    • add concept of Entity Of Interest to represent which is characterized by variable.
    • add Export Variables functionalities in CSV.

  • User documentation at homepage.

  • Impove Organization in progress:

    • Association of Groups to Organizations: you can now associate some groups with an organization at the creation or update of it.

Fixed or optimized

  • Provenance : fix no device selector render when selecting oeso:SensingDevice's Agents .
  • Ergonomic mistakes fixed

[1.0.0-rc] - 2021-10-08

Added

  • Data management:

    • Import, export in CSV format
    • A standard provenance for usual provenances or methods
    • Ability to put data on other entities such as sites, areas, factors, etc. except people. So now, you have to use target instead of scientificObject in the API. This is also the case for importing data via the web interface. See Versioning notes when upgrading.
    • Ability to mention raw data of a measure (i.e. for repetition)

  • Variable:

    • Add a species attribute to link a variable to a specific species.
    • Ability to create groups of variables. Add a default group for environmental variables.
    • Prevent incorrect update of variables with data attached
    • Ability to add a document to methods

  • Scientific Object:

    • Unicity of a scientific object name in an experiment.

  • Map:

    • Ability to specify a geospatial event on Map
    • Ability to see objects over time on Map
    • Export Map in PNG, PDF and Shapefile

  • Event:

    • Add a document to an event (image, video, etc.)

  • Added system details in the administration menu : instance version, loaded modules, link to web API documentation, etc.

Fixed or optimized

  • Geospatial filters on the Map
  • Optimized vocabulary menu
  • Optimized data sorting and pagination
  • Improved multiple selection, now you can select 10000 scientific objects
  • Improved export and import
  • Fixed brapi error
  • Various data bug fixes
  • Various translation mistakes

Changed

  • Data Model : "scientificObject": "target"
  • DataFile Model : "scientificObject": "target"

Link to the upgrade scripts: 1.0.0-rc migration

Major bugs identified

  • Problem with filters
  • Specific properties of Event are not manage in Map
  • Specific properties of Event are not apply on Forms.

[1.0.0-beta+2.1] - 2021-07-27

Added

  • Add global provenances management interface allows to create and visualize them

Fixed

  • Issue on device association
  • Miscellaneous data bugs fixed

[1.0.0-beta+2] - 2021-05-07

Added

  • Geospatial vizualisation improvement with control panel and simple filters
  • Global data management : tabular view and datafile view
  • Data vizualisation on device, object in or out of experiments : enriched with events view, manual data annotation and event addition.
  • Add CHANGLOG.md file to track changes

Changed

  • Data API : list to single scientific object association
  • Events improvement : specific properties for class management and optimisation.

[1.0.0-beta+1] - 2021-04-27

Fixed

  • Vocabulary description and Bug correction

[1.0.0-beta] - 2021-04-20

Pre-release of OpenSILEX. New features and improvement. Device, Event, Move, Import and Export Data, etc.

Added

  • Device
  • Event
  • Global Scientific Object management
  • Raw data file management
  • Data Import and Export
  • All these functionalities are in beta version

Fixed

  • Geospatial visualisation improvement
  • Structural Area managment
  • Graphic Visualization of a Scientific Object or Device Data
  • Organization (beta version)
  • Web Services have been homogenised: semantic, fields order, paths, etc.

[1.0.0-alpha] - 2020-11-30

Tag for phis field testers.

Added

  • Users, Groups
  • Project, Experiment
  • Variable
  • Germplasm
  • Others functionalities