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License: MIT License

Java 30.19% CSS 69.32% SCSS 0.49%

portlet

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barcode-dragon-portlet's Issues

Enable printing of samples of type Q_BIOLOGICAL_ENTITY

Currently, only samples of the types listed here:

barcode-dragon-portlet/src/main/java/life/qbic/portal/portlet/control/BarcodeController.java

Line 94 in fa852f9

private List<SampleType> barcodeSamples =

can be printed with the application. For clinical studies, it is required to also print labels from the top level, which is the biological entity.

This is a request that came up by @AntoniaSchuster

Could not aquire user groups from user NPE

This happens after successfully logging in. Even with an admin account this NPE seems to occur.

11.06.2018 11:09:09 [ERROR] [BarcodeDragonUI] - Could not acquire user groups from user.
java.lang.NullPointerException: null
	at life.qbic.portal.portlet.BarcodeDragonUI.initView(BarcodeDragonUI.java:140) [classes/:?]
	at life.qbic.portal.portlet.BarcodeDragonUI.createBarcodeDragonLayout(BarcodeDragonUI.java:114) [classes/:?]
	at life.qbic.portal.portlet.BarcodeDragonUI.getPortletContent(BarcodeDragonUI.java:54) [classes/:?]
	at life.qbic.portal.portlet.QBiCPortletUI.init(QBiCPortletUI.java:72) [portal-utils-lib-1.0.0-SNAPSHOT.jar:?]
	at com.vaadin.ui.UI.doInit(UI.java:693) [vaadin-server-7.7.8.jar:7.7.8]
	at com.vaadin.server.communication.UIInitHandler.getBrowserDetailsUI(UIInitHandler.java:216) [vaadin-server-7.7.8.jar:7.7.8]
	at com.vaadin.server.communication.UIInitHandler.synchronizedHandleRequest(UIInitHandler.java:74) [vaadin-server-7.7.8.jar:7.7.8]
	at com.vaadin.server.SynchronizedRequestHandler.handleRequest(SynchronizedRequestHandler.java:41) [vaadin-server-7.7.8.jar:7.7.8]
	at com.vaadin.server.VaadinService.handleRequest(VaadinService.java:1422) [vaadin-server-7.7.8.jar:7.7.8]
	at com.vaadin.server.VaadinServlet.service(VaadinServlet.java:380) [vaadin-server-7.7.8.jar:7.7.8]
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) [javax.servlet-api-3.1.0.jar:3.1.0]
	at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:857) [jetty-servlet-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:535) [jetty-servlet-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:146) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) [jetty-security-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:257) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:255) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:203) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473) [jetty-servlet-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:201) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:144) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:219) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:126) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.Server.handle(Server.java:531) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:352) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:260) [jetty-server-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:281) [jetty-io-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:102) [jetty-io-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:118) [jetty-io-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:333) [jetty-util-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:310) [jetty-util-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:168) [jetty-util-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:126) [jetty-util-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:366) [jetty-util-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:760) [jetty-util-9.4.10.v20180503.jar:9.4.10.v20180503]
	at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:678) [jetty-util-9.4.10.v20180503.jar:9.4.10.v20180503]
	at java.lang.Thread.run(Thread.java:748) [?:1.8.0_172]

Faster printing

The lpr command is able to print many files much faster using wildcards. the barcode portlet already creates a timestamped folder of each batch of barcodes that are created. the command should be changed to something like lpr [...] timestamp+"/*"

Hide info items that are not available for sample types

Users can select which infos are to be displayed in sheet or on tube barcodes. It would be cool if some of these options would be hidden, if no samples having the respective type are selected. For example, if only DNA samples are selected, no "tissue" information should be available.

Imaging samples may lead to nullpointer exception when creating barcode preview

Tabsheet should be disabled while creating barcodes

Switching from sheet to tube creation or the other way around while one of the two processes is running leads to strange behavior of the progress bar/label. should not be used anyway, so to fix this tab sheet:

barcode-dragon-portlet/src/main/java/life/qbic/portal/portlet/view/BarcodeView.java

Line 129 in 0ef7fcd

tabs = new TabSheet();

should be disabled in this method:
creationPressed()

and enabled in this method:
creationDone()

check if entries are NULL, make sure all sections of the json are correctly set even if data is missing

barcode-dragon-portlet/src/main/java/life/qbic/portal/portlet/io/BarcodeCreator.java

Line 446 in 735d1ba

inv.put("title", investigator.getTitle());

File "/home/tomcat-liferay/liferay_production/barcode-creation/wizard_scripts/samp_sheet.py", line 94, in getPersonTitleAndName
if len(personObject["title"]) > 2:
TypeError: object of type 'NoneType' has no len()

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