Effectopedia

***** Effectopedia 0.9.37 Alpha Update Log ***** - New script version of the DNA Intercalation Mediated Cardiomyopathy pathway was added to the source. The pathway is not published yet. - Bug fix: “Ctrl+del” deletion of the elements caused complete disconnection the selected elements. The new version disconnects the pathway elements only if all the pathways they are associated with are currently visible. In all cases the deleted elements are disassociated from the currently visible pathways - Bug fix: The VisulaOptions menu is now updated with the loaded data and aligning and visual properties of the pathway elements can be adjusted as before. - Internal sorting of the pathway elements was rewritten and no longer uses recursive methods. This should avoid possible stack overflow problems. - New internal function for batch assigning of context dimension for all elements of a certain pathway was added. ***** Effectopedia 0.9.36 Alpha Update Log ***** - Biological perturbations were introduced. This new pathway element provides the means to encode the cases in which higher level of biological organization effect has molecular level consequences and would require backward connection (which is not allowed for clarity). The current implementation allows the pathway editor to work with the new element and support all the existing features. - Bug Fix: The zoom level is reset to default when new information is loaded in the PathwayViewer - XMLFile version was updated to 0.936. New version control check was introduced (executed when file is loaded). Warning messages are generated when file format version is greater than currently supported. ***** Effectopedia 0.9.35 Alpha Update Log ***** - New feature was added to CLET mode allowing the insertion of intermediate effect up or downstream from existing link. The link is automatically reconnected and a second link is inserted to maintain the pathway connectivity. - The true delete method is now partially implemented, allowing the deletion of non-generic objects. The objects are disassociated from the currently visible pathways but still remain accessible trough search and show up in the list of existing elements. - Substance type cycler now starts the cycle with a chemical instead of structural alert. - The order of the elements in Effect in Terms Axis was changed to "unknown,long-term,mid-term,short-term,mixed" - PathwayViewer now renders correctly connected fragments of PathwayElements that are not associated with a pathway. The problems occurred in older version when user switched the view space projection containing fragments not associated with any pathway - The address bar user interface was modified to show tooltip with the current file name, and its layout was changed to allowing better resizing behavior. - Bug fix:When changing one of the pathway space axis the other might not have been initialized. The current version verifies that both dimensions are set before rebuilding the view - Bug fix: Multiple phenomena pronounced when changing the pathway space axis, data sources, creating a new pathway with the selected data source, etc were all fixed by complete re-loading of the DataView in all related classes. - Bug fix: Associated pathways list is once again modifiable with the toolbar menu. The function of redirecting the interface on double click was also maintained. - Bug Fix:When existing element is inserted into the pathway viewer the replaced element and all its arcs are now completely removed from the view - Big fix: When pathway elements were deleted their links to other objects remained untouched. The current version unliks the currently deleted object from other objects. - Bug fix: The showing of full caption now verifies against for empty text and does cause division by zero and no rendering of the element. - Bug fix: When title and ID are selected to be visible in the Effect depiction and the title is empty the ID was ignored and not displayed. Current version shows the ID even in case the title is empty. - Bug fix: Each new pathway element created in CLET mode when cyclic over element type replaces the old element and reassign the existing links to the new object. ***** Effectopedia 0.9.34 Alpha Update Log ***** - Pathway space axis labels are now automatically extened or shrunk in synchrone with the size of the content. - Bug fix: The list of associated pathways can be successfully modified with the list editor toolbar. In the last revision readolny flag was raised preventing the Existing pathway dialog from showing. - Bug fix: Interrupting the workflow of CLET interface mode was reversing the direction of the workflow by default. Now the direction of the new cycle is evaluated based on the the exact user action. This caused generation of two Structural Alerts instead of one Structural Alert and link. ***** Effectopedia 0.9.33 Alpha Update Log ***** - Bug Fix: The new script generated versions of Effectopedia pathways were affected by the disabled search indices which in their turn resulted in creating of duplicate objects. (The internal searches failed during the script execution preventing the system to reuse the existing objects) - Bug Fix: location external or internal ID of the object caused a crash in case of non assigned locationObject - Effectopedia now supports unlinking of objects which currently can be used only internally. - Bug Fix: The list of associated pathways in PathwaysListUI was not read-only. This is required in order for double clicking to work and load the existing pathway editing interface. - Bug Fix: QualityAssuranceUI was crashing when the list of contributors is empty. This was manifested when a new Chemical was edited for the first time. - Some additional internal fixes were made which could become problematic in future usage scenarios. ***** Effectopedia 0.9.32 Alpha Update Log ***** - Several cosmetic improvements have been introduced. Related Effects interface now has different titles for upstream causes and downstream effects. All subcomponents also use consistent terms. - Effect Editor caption is now selected based on the class that is currently loaded for editing. - Existing Chemicals Effects and Pathways dialogs now support sorting of their lists. Currently Title sort is used as a default sorting method. - Bug Fix: RelatedEffects was changing its read-only property based on the object that is loaded in the editor. The Existing list of related effects was made read-only to prevent accidental deletion of associations. ***** Effectopedia 0.9.31 Alpha Update Log ***** - Browsing of HistoricalDS pathways is now possible. Users could not make any changes to historical versions of pathways and their elements. If historical data source is loaded in the viewer all editing buttons become hidden and double click on any of the displayed elements loads pathway elements in read only editors. - Search in HistoricalDS is now possible. - SearchResult objects now contain the DataSource from which they were obtained. This however is not displayed to the user - UINavigator now supports two new mechanisms for setting up the ReadOnly flag for the editor before loading. One is event based and the other is the encoded in the url readonly flag. ***** Effectopedia 0.9.3 Alpha Update Log ***** - CommandToolbarUI was moved to the top of the application in order to emphasize that all commands are executed for the the currently selected datasource. - New address bar with location and navigation was designed and implemented. The location combobox shows the list of available data sources. During program loading the location combobox is initialized with connection to the centralized database string and upon successful download it does display the current revision number. - Bug Fix: Coordinates of Sex axis were not correcly read from old files still using the Gender name for the same axis. Small patch was added to make the new version backward compatible ***** Effectopedia 0.9.295 Alpha Update Log ***** - Bug fix: The interface of newly added description sections was not linked to the newly created objects causing loss of changes made in the current session. Another side effect of this miss linkage is the absence of scrollbars when the content is bigger of the visible viewport. Both problems were solved by linking the interface and newly created description section object. - Gender axis was renamed to Sex axis along with all internal variables associated with it. - New "copy" and "paste" capabilities were introduced to Reference interface. They allow coping the full list of references and adding the a new line separated references from clipboard into the list. ***** Effectopedia 0.9.29 Alpha Update Log ***** - Bug fix: Associated pathways list had a readonly property set to true by default ignoring the object's and interface settings making the addition of new pathways impossible. Now the property is set according to the element read-only flag. - All title fields in the element editors have hints that contain the content of the entire field. - Bug fix: When the content of a description section is updated with text larger than the component size no scroll bars appear (unless the whole editor is reloaded). The description section editor was updated to respond to changes of its content. ***** Effectopedia 0.9.285 Alpha Update Log ***** - Effectopedia jar (windows wrapped executable version) now accept file name as command line parameter to open in the list of available data sources. - Script version for about 300 new MIEs, endpoints and adverse outcomes was completed and the result was stored in a new revision (4) of Effectopedia database. - Big fix: Cloning of DataValues representing searchable properties was cloning the SearchableItem including the referred object which is now correctly redirected to the new clone parent object. ***** Effectopedia 0.9.28 Alpha Update Log ***** - The appearance of the effects and chemicals in the pathway viewer can be customized. The visual content of effect and chemical was broken into sections which could be individually enabled and disabled. Several new displayable fields were added – Quality Assurance, Pathway Associations and Groups and Keywords. The new options are available in the View tab in the formatting section of the buttons. - New search results navigator was introduced at the bottom of the search results page. It provides links for navigation between result pages (if more than one) and also reports the total number of matches. - Gender list now includes hermaphrodite. ContexDimensions were updated accordingly - Big fix: Scale is now reset to the default level on loading a new pathway in the editor. - Big fix: The effect editor user interface now scrolls to the top on loading. ***** Effectopedia 0.9.27 Alpha Update Log ***** - Effectopedia no longer uses FTP protocol for communication with the server and instead uses HTTP for all of its transactions. - New list capability was added to the search tab showing all elements form a certain type in the search results - Multiple changes to both server side processing and generation of notifications were made. The new capabilities are still undergoing testing and not active in the current release. - Big list of MIEs, Adverse Outcomes and Endpoints was prepared as a script for adding into the Effectopedia database. Further refinement will be performed on the list before the list is published. ***** Effectopedia 0.9.25 Alpha Update Log ***** - New FeedbackToolbar was added to all editor headers enabling users to create general comments about the edited objects. - Discussion associated with a given topic is now correctly loaded in the editor. New topic element was added to the DiscussionPosting XML import/export that preserves the parent object (which is the topic for the postings) - Related topics panel is now functional. It lists all related topics from the associated list of pathways. By clicking on a certain row from the table of topics the topic is loaded along with its postings. - The discussion interface now has two modes: one for creating and editing discussion topics and the other for discussion postings. If the topic is newly created or the same user is logged in and no postings exist the editor is topic edit mode otherwise in posting edit mode. - QualityAssurance interface now displays the list of reviewers along with the list of contributors. - Bug fix. Discussion postings now calculates the needed amount of space for visualizing the postings' content ***** Effectopedia 0.9.24 Alpha Update Log ***** - The notification system now generates the notifications based on revision history. All actions since last revision are added as notifications to the SYSTEM user. Currently no user specific notifications are created. So far the notifications system has been tested only with new discussion topics. - Revisions array form EditHistory is now updated just before the file is saved to XML stream - Bug fix. The References class has not been added to list of REGISTERED TracableClasses resulting in the smaller number of copied default objects in the EditHistory when using addDefault method - Bug fix. Complete edit history is now preserved. Some actions were omitted in the older versions ***** Effectopedia 0.9.235 Alpha Update Log ***** - Pathway editors now display "- read only" in their captions when a flagged object is loaded. - The readonly inheritance was modified for the nested EffectopediaObjects. The read only status is determined as a disjunction between the "Load" function parameter (often reflecting parent readonly flag) and self readonly flag. - Script version of Lhasa pathway examples was updated. - Bug fix. The new locking mechanism was not protecting references from editing. - Bug fix. The discussion topics are now successfully located after publishing and starting a new session. ***** Effectopedia 0.9.23 Alpha Update Log ***** - Mechanism for locking the editing of whole pathways or separate elements/subelements was introduced. This is achieved with the new "readonly" XML attribute in pathway elements' description. Elements with such attribute will load in the editors in read only mode and cannot be modified.