LabKey Support: LabKey Server Distribution and Support

Captcha service broken

Tue Feb 11 06:47:43 PST 2020

Hello, Our production instance of LabKey is having an issue with the Captcha service on the registration page. This production instance is on 19.3, and this error does not happen on 19.2. I see the following stacktrace from a 500 error when LabKey calls the captcha service: ``` HTTP Status 500 – Internal Server Error Type Exception Report Message Servlet execution threw an exception Description The server encountered an unexpected condition that prevented it from fulfilling the request. Exception javax.servlet.ServletException: Servlet execution threw an exception org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53) org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1226) org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:215) org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) Root Cause java.lang.NoClassDefFoundError: Could not initialize class java.awt.image.BufferedImage com.google.code.kaptcha.text.impl.DefaultWordRenderer.renderWord(DefaultWordRenderer.java:37) com.google.code.kaptcha.impl.DefaultKaptcha.createImage(DefaultKaptcha.java:43) com.google.code.kaptcha.servlet.KaptchaServlet.doGet(KaptchaServlet.java:84) javax.servlet.http.HttpServlet.service(HttpServlet.java:634) javax.servlet.http.HttpServlet.service(HttpServlet.java:741) org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53) org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1226) org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:215) org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) Note The full stack trace of the root cause is available in the server logs. Apache Tomcat/9.0.27 ```

Displaying additional sample fields in the assay data upload interfaces

Wed Jan 15 08:30:10 PST 2020

Hello, I'm in a Labkey Biologics trial, but I guess my question is general to the platform. In the assay data upload 'interfaces' ('Upload File', 'Copy-and-Paste Data' and 'Enter Data Into Grid') of the assay runs, only Sample Id is used to characterize the samples. Is it possible to expose other Sample fields in these interfaces (even from Data Classes linked via a Lookup)? If you upload assay data via the Manage Samples menu, Sample Id's are nicely pre-populated, but only in the 'Enter Data Into Grid' interface. It would be nice if that could be extended: more fields, and also in the Excel template. For a regular end user, computer generated Id's are very uninformative, which can lead to errors when entering/uploading data. So I was wondering whether it is possible to provide more context in the assay data upload process. Best, Dominique

Sharing/joining datasets between folders

Tue Nov 05 11:53:06 PST 2019

Hello, I would like to join tables from data sets across sub-folders within a project. The below link describes a folder filter option when selecting the Grid option on a data set to customize a grid with a table from another folder, but I'm not seeing that option when I open any of my grids. Is that feature only available in certain folder types or for select data sets? https://www.labkey.org/Documentation/wiki-page.view?name=filterByFolder Is the Shared Project folder the best way to share a data set across sub-folders? Thank you! Karen

Dataset with 2 or more Additional Key Column

Mon Oct 21 07:22:25 PDT 2019

### Multiple Additional Key Columns in a Dataset Is it possible to create a dataset in a study with 2 or more *Additional Key Columns*. As I understand in the _Edit Definitions_ mode one can choose only 1 column as a *Key Column*. If it is not possible with datasets are there any solutions to this issue?

Recompute Timepoints did not work

Fri Oct 11 13:09:05 PDT 2019

Hello, I have negative timepoints on my study and 1 day duration and these are not ideal for our study settings. Therefore, I changed the start Date of the overall project and also change the Default Timepoint Duration to 365. However when I click Update and then RECOMPUTE TIMEPOINTS, the timepoints didn't change to follow the new timepoint settings. I didn't receive any error message so I didn't know what went wrong. I hope you can shed some light on this problem. Regards, Wahyu

Help with Study Reload

Fri Oct 11 07:54:57 PDT 2019

Hello, I'm new to LabKey and attempting to reload a study but I'm not sure on the steps in between the export and import of the reload. I exported the existing study to the pipeline and I have three excels that are reloads of the existing datasets that I need to import. How do I map them to the study? Do they need to be saved somewhere specific so they are captured in the reload process and in a certain file type? I have reviewed the Export, Import, and Reload Study documentation pages but still cannot quite connect the steps. Thank you!

Export data without lookup, remove all columns from grid view option

Tue Oct 08 08:10:08 PDT 2019

Hello, I was advised to submit support tickets by developers for the following items at the LabKey user conference, but I am unable to do this as I am a community user. I will post them here instead and hope they reach the right people. ### Option to export data without lookups Currently, when data using lookups in a LabKey grid view is exported to xlsx/tsv, the data is exported with the lookup value, and there is no option to recover the non-lookup value. It would be nice if this were made available as an option, as the script exports (R/Python/etc) export the raw data without lookup ### Option to create a grid view starting with no columns Currently, you have to base a new grid view on a dataset in the study schema, and if you are only interested in creating a report on a few columns (ie age/sex from demographics, measure 1 from instrument A), then it is a pain to have to remove all columns manually from whichever dataset you choose to base the view on. It would be nice if there was an option to either: - Make a grid view not based on a particular dataset - Remove all columns from the 'selected fields' area after choosing 'customize grid' Thank you for your help.

Configuration Error Detected at LabKey Server Startup

Tue Sep 24 05:57:14 PDT 2019

I use a database of a study which I have always been able to log in to enter data all this time. But today it is showing an error message saying 'Configuration Error Detected at LabKey Server Startup' when I try to open the link to the database. I have attached the screen shot of how it looks when I try to open the database link.

Exporting Data without Lookup?

Thu Aug 08 14:04:54 PDT 2019

Hello, I am currently trying to create a study in LabKey. The study data is exported from a number of REDCap projects, which use integer codes for categorical fields. I am uploading the data in this integer-coded form, then using lookup tables (1: 'Male', 2: 'Female' 3: 'Other', etc) to display the text values for these fields in the data grid in an effort to make the data more readable. However, I would like for users to be able to export the data in its original, integer-coded form for use in analysis software. When I explore LabKey's export options, it seems to only be able to export the text lookup, without the ability to go back to the original integer codes. I'm not sure if I'm missing something, but it would be really nice to have that functionality without needing to rely on some external transformation to restore the original codes from REDCap. Thanks for any assistance, Jonathan

ELISA Module Customization: Sample dilutions, using non-linear curve fit for calibration curves

Tue Aug 06 14:12:05 PDT 2019

We are running edition 19.10 of the LabKey Server. We are currently trying to upload a few standard ELISA assays onto our LabKey server and have run into a few problems: 1. There does not appear to be a way to change the calibration curve fit to anything but linear. Is there a setting I am missing or a work-around to fit other kinds of curves (i.e. 4 parameter curve fit) for concentration interpolation? --Is there a way to calculate EC50 in any assay modules and track across time in any other assay modules? _I have attempted to modify a Luminex assay, but I am unable to load our data file_ 2. We have several dilutions per sample on our ELISA plates. I tried to account for this by adding 'other' labels for the well assignments, but I do not see a way to incorporate this into the assay setup. I essentially need a column multiplying the interpolated concentration by the dilution factor. Additionally, I would like to be able to average the 4 wells (2 duplicates*2 dilutions) to get the average concentration and the error associated with the mean. _Is there a way to post-process concentrations in the ELISA module or some kind of work around for it?_ Thank you!

Files in fileset not updating

Fri Jul 12 09:13:04 PDT 2019

I'm running LabKey Server 19.1.1. When I manually add files or directories from the command line to the site-level file root they don't appear on LabKey. What am I missing?

NAB assay QC report in Results Details

Thu Jul 11 07:11:11 PDT 2019

Dear Labkey, We are having some trouble with your NAB assays. When performing a NAB assay on our uniQure NAb server and we want to export "Run Details" in the form of a PDF (Print) the QC data that is excluded does not appear anymore in the PDF. This while in the "Run Details" when data is excluded using the "Review/QC Data" option the excluded wells are marked red. This does not appear in the PDF. Because for the purpose of QA reports we need to show which wells are excluded, is it possible to have these visualized in the PDF?

Error in Site Users - Community Edition 19.1 - Can't view users list

Tue Jul 02 12:59:08 PDT 2019

Version 19.1 We get an error when we click on Site Users - only shows one user and it is not the logged in user and displays this error: An unexpected error occurred Could not convert '-4,-1' to an integer __________________________________________________ Details: org.apache.commons.beanutils.ConversionException: Could not convert '-4,-1' to an integer at org.labkey.api.data.ConvertHelper$_IntegerConverter.convert(ConvertHelper.java:606) at org.apache.commons.beanutils.ConvertUtilsBean.convert(ConvertUtilsBean.java:428) at org.apache.commons.beanutils.ConvertUtils.convert(ConvertUtils.java:217) at org.labkey.api.data.MultiValuedRenderContext.get(MultiValuedRenderContext.java:116) at org.labkey.api.data.DataColumn.getValue(DataColumn.java:243) at org.labkey.api.data.DataColumn.renderGridCellContents(DataColumn.java:324) at org.labkey.api.data.DisplayColumnDecorator.renderGridCellContents(DisplayColumnDecorator.java:51) at org.labkey.api.data.MultiValuedDisplayColumn.renderGridCellContents(MultiValuedDisplayColumn.java:139) at org.labkey.api.data.DisplayColumn.renderGridDataCell(DisplayColumn.java:980) at org.labkey.api.data.DataRegion.renderTableRow(DataRegion.java:1642) at org.labkey.api.data.DataRegion.renderTableContents(DataRegion.java:1601) at org.labkey.api.data.DataRegion.renderTableContent(DataRegion.java:1173) at org.labkey.api.data.DataRegion.renderCenterContent(DataRegion.java:1214) at org.labkey.api.data.DataRegion._renderDataTableNew(DataRegion.java:1188) at org.labkey.api.data.DataRegion._renderTableNew(DataRegion.java:1077) at org.labkey.api.data.DataRegion.renderTable(DataRegion.java:980) at org.labkey.api.data.DataRegion.render(DataRegion.java:2518) at org.labkey.api.view.GridView._renderDataRegion(GridView.java:64) at org.labkey.api.view.DataView.renderView(DataView.java:211) at org.labkey.api.view.DataView.renderView(DataView.java:58) at org.labkey.api.view.WebPartView.renderView(WebPartView.java:476) at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:371) at org.labkey.api.view.HttpView.render(HttpView.java:132) at org.labkey.api.view.HttpView.render(HttpView.java:117) at org.labkey.api.view.HttpView.include(HttpView.java:512) at org.labkey.api.view.HttpView.include(HttpView.java:489) at org.labkey.api.query.QueryView.renderDataRegion(QueryView.java:2231) at org.labkey.api.query.QueryView.renderView(QueryView.java:1977) at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:371) at org.labkey.api.view.HttpView.render(HttpView.java:132) at org.labkey.api.view.HttpView.render(HttpView.java:117) at org.labkey.api.view.HttpView.include(HttpView.java:512) at org.labkey.api.view.HttpView.include(HttpView.java:489) at org.labkey.api.view.HttpView.include(HttpView.java:477) at org.labkey.api.view.VBox.renderView(VBox.java:74) at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:371) at org.labkey.api.view.HttpView.render(HttpView.java:132) at org.labkey.api.view.HttpView.render(HttpView.java:117) at org.labkey.api.view.HttpView.include(HttpView.java:512) at org.labkey.api.view.HttpView.include(HttpView.java:489) at org.labkey.jsp.compiled.org.labkey.core.view.template.bootstrap.body_jsp._jspService(body_jsp.java:259) at org.labkey.api.view.JspView.renderView(JspView.java:170) at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:371) at org.labkey.api.view.HttpView.render(HttpView.java:132) at org.labkey.api.view.HttpView.render(HttpView.java:117) at org.labkey.api.view.HttpView.include(HttpView.java:512) at org.labkey.api.view.HttpView.include(HttpView.java:489) at org.labkey.jsp.compiled.org.labkey.core.view.template.bootstrap.pageTemplate_jsp._jspService(pageTemplate_jsp.java:214) at org.labkey.api.view.JspView.renderView(JspView.java:170) at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:371) at org.labkey.api.view.HttpView.render(HttpView.java:132) at org.labkey.api.view.HttpView.render(HttpView.java:117) at org.labkey.api.action.SpringActionController.renderInTemplate(SpringActionController.java:615) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:495) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1265) at org.labkey.api.view.ViewServlet._service(ViewServlet.java:204) at org.labkey.api.view.ViewServlet.service(ViewServlet.java:131) at javax.servlet.http.HttpServlet.service(HttpServlet.java:741) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1220) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:215) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:200) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:490) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:139) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:668) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343) at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:408) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:834) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1415) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.base/java.lang.Thread.run(Thread.java:835) Caused by: java.lang.NumberFormatException: Character , is neither a decimal digit number, decimal point, nor "e" notation exponential mark. at java.base/java.math.BigDecimal.(BigDecimal.java:518) at java.base/java.math.BigDecimal.(BigDecimal.java:401) at java.base/java.math.BigDecimal.(BigDecimal.java:834) at org.labkey.api.data.ConvertHelper$_IntegerConverter.convert(ConvertHelper.java:595) ... 91 more request attributes LABKEY.OriginalURL = http://labkey.nrel.gov/labkey/user-showUsers.view?returnUrl=%2Flabkey%2Fadmin-showAdmin.view%3F LABKEY.StartTime = 1562084593824 LABKEY.action = showUsers org.springframework.web.servlet.DispatcherServlet.CONTEXT = Root WebApplicationContext: startup date [Sat Jun 15 01:43:22 MDT 2019]; parent: Root WebApplicationContext LABKEY.controller = user LABKEY.Counter = 0 X-LABKEY-CSRF = acfbfcfe610545c7d52c6743d6e51b1f LABKEY.container = LABKEY.RequestURL = /labkey/user-showUsers.view?returnUrl=%2Flabkey%2Fadmin-showAdmin.view%3F LABKEY.OriginalURLHelper = /labkey/user-showUsers.view?returnUrl=%2Flabkey%2Fadmin-showAdmin.view%3F core schema database configuration Server URL jdbc:jtds:sqlserver://ignsql-listener.nrel.gov:1433/Labkey Product Name Microsoft SQL Server Product Version 13.00.5292 Driver Name jTDS Type 4 JDBC Driver for MS SQL Server and Sybase Driver Version 1.3.1

Manual upgrade errors from LabKey18.2-60915.94 to LabKey19.1.1-63156.2

Mon May 20 05:45:56 PDT 2019

Dear LabKey team, Thank you for the providing the LabKey server. We are using the community edition LabKey server version number LabKey18.2-60915.94. It was running smoothly with the sample registrations and other relevant tasks for our use. Recently we upgraded the instance from LabKey18.2-60915.94 to LabKey19.1.1-63156.2. With the upgrade, we didn't find any errors. We have performed the manual upgrade with the provided script `manual-upgrade.sh` from the distribution. When we start the instance now with the version LabKey19.1.1-63156.2, I have been experiencing following problems which were not there in my old version of LabKey18.2-60915.94. Features missing in the new release/or may be this is not rendered properly to my upgrade: - There are no parent child relationship representation with the sample which I selected. This was working nicely before. - New Sample registration fails with the error message RowId or LSID required to get the Sample set materials (ERROR ReadOnlyApiAction 2019-05-20 14:45:11,146 ttps-jsse-nio-443-exec-3 : ApiAction exception: org.labkey.api.query.QueryUpdateServiceException: Either RowId or LSID is required to get Sample Set Material.) I m attaching two screen shots from my instance and I am not sure whether this is something to do with the database schema. I don't know how to do this and let me know if you have seen this before. I am happy to provide the stdout message from my upgrade script run as well. I am not seeing much information from the log message as well. Thank you very much in advance, Vipin

LabKey 19.1.1 updates

Thu Apr 11 09:28:00 PDT 2019

Hello, We recently released LabKey Server 19.1.1, our first patch release for 19.1.x. This patch release fixes a problem with sample export/import and addresses other important issues. We strongly recommend upgrading all LabKey deployments to 19.1.1 or higher as soon as possible. Premium Edition subscribers will find their 19.1.1 distribution on their server builds page. Community Edition users should visit the download page on www.labkey.com: http://www.labkey.com/forms/register-to-download-labkey-server For more details on LabKey 19.1.x, see the release notes: https://www.labkey.org/Documentation/wiki-page.view?name=releaseNotes191 Regards, LabKey Support

Upgrade to 19.1 and Java upgrade on Linux

Mon Mar 25 15:12:34 PDT 2019

Hi, I am trying to upgrade our Labkey Server to 19.1 and have to upgrade Java in the process (from Java 8). Per this page, https://www.labkey.com/the-java-shake-up-what-it-means-to-labkey-and-you/, downloaded OpenJDK12 with HotSpot VM from https://adoptopenjdk.net/. Installed and added the PATHs as references in the Labkey Server manual installation instructions. However, although it appears that the correct java is running (java --version shows version 12), I cannot get the Labkey Server started. From Tomcat log (catalina.out) it appears that it cannot create java virtual machine. Error: Could not create the Java Virtual Machine. Also on Tomcat shutdown.sh the same message appears. Tomas UW

"No data to show"/zero rows in dataset when I navigate to its grid from the Dataset web part, but I can select rows from the same dataset

Tue Mar 05 14:08:02 PST 2019

In my study I have multiple datasets that are reloaded regularly from a study archive. After one such reload last week, the datasets in my study appear to be empty when I navigate to their grids from the Datasets webpart. E.g. I have a dataset called Enrollment. If I create a Datasets web part, and then select the Enrollment dataset, I see an empty grid with no data to show. However I know the data successfully loaded, because if I query 'select * from Enrollment' I see all the expected rows. What might be causing this? As far as I can see, the URL parameter passed to the query when accessing Enrollment from the Datasets webpart is correct (URL is ../labkey/NDDdb/study-dataset.view?datasetId=5001, and 5001 is the correct datasetId for the Enrollment dataset).

Log- or ongoing-style data

Thu Feb 28 16:45:14 PST 2019

Hi, I am trying to build out a study the has been going on for some time. So I am uploading data. The study has a Participant ID - Visit Number structure for most data. However, some data were collected without a Visit Number but only have a Participant ID and a date. In addition, there are multiple entries for each Participant ID (and also Participant ID-date). An example is a "concomitant medication log" in which the Paticipant ID, Start Date, Stop Date, and Med Name are recorded in each row (a "log-book") regardless of study visits. Another example is a "vital status follow up log" in which each phone call or contact with a participant is recorded for years after the last formal study visits. So each row is Participant ID, Date of Call, Vital Status. Is there a way I can integrate these data into a study with a Participant ID-Visit Number structure? I have been trying with a General Assay but having no success, as it is demanding a Visit Number when I copy over the data from the assay to the study. Is there a way around this? Or do I need to assign dummy Visit Numbers or use some other work around? Thanks, Scott

Tutorial - Excel import not working when Timezone CEST

Thu Feb 28 01:42:37 PST 2019

Hi LabKey team, I am going through the tutorials and noticed that the import of the Excel dataset is not working in my local instance of Labkey (which I find really amazing by the way, congratulations). I live in France (CEST timezone). The error message is attached. As I was debugging I noticed that CEST was not correctly handled in DateUtil.java resolveDatePartEnum(s) (line 297) returns null as CEST is not in the TimeZone list (line 252): ``` z("UTC"),gmt("UTC"),ut("UTC"),utc("UTC"), // North America est(-5*60),edt(-4*60),cst(-6*60),cdt(-5*60),mst(-7*60),mdt(-6*60),pst(-8*60),pdt(-7*60), // Europe cet("CET"), wet("WET") ; ``` Now if you did add it, TimeZone.java translates it automatically to "CET" which causes another issue in DateUtil.java (line 292): ``` return (null != entry && StringUtils.startsWithIgnoreCase(entry.getKey(), s)) ? entry.getValue() : null; ``` this returns null and another process starts to try and recognise CEST thanks to TimeZone.getTimeZone(s). Unfortunately TimeZone.getTimeZone(s) does not recognise CEST and translates it to GST. resolveDatePartEnum(String s) will return null which will raise an exception. That issue was raised by Christine Rousseau: https://www.labkey.org/e545879c-dd5d-1032-a3b5-e5ac4624956c/announcements-thread.view?entityId=414cafa3-6e2f-1035-b86e-fe851e083e48&_docid=thread%3A414cafa3-6e2f-1035-b86e-fe851e083e48 I am not sure whether it has been fixed but I thought I would let you know about my investigations before it gets lost. I hope that helps. Cheers, Nico

Scrolling Issue on 18.2

Fri Nov 30 10:10:52 PST 2018

Dear LabKey team, One of our users pointed out after upgrading to 18.2 the following issue: "when we are scrolling through a repository with many files, the repository will start flashing and stop scrolling for a bit. I tried to take a screen shot but that resets the screen." Is this a possible bug? Please advise. Thanks in advance.

Problem with Aliases

Tue Nov 27 07:01:12 PST 2018

Hi LabKey team, I have created the following tables in a study: 1) Alias mapping table 2) Demographics table 3) General dataset with participant IDs These are the steps I took: 1) Turned on the alias settings within the "Manage Study" page. 2) imported my general dataset with lab IDs Results: 1) General dataset with lab IDs successful were transformed to the alias IDs as expected. However, as per our change management procedures I tested how to remove aliases and found the following: Results (2): 1) I went to manage study view and removed aliases from the study 2) The general dataset did not revert back to the labID, and in fact kept the alias This is a major concern for us as we had know way to revert back to LabIds, and we are concerned that the database was overwritten with the alias ID. Furthermore, I even tried to manually change back the ID to no avail - It seems as though the study would not refresh. Please advise. Thanks, - Sara

Problem with copying Expression Matrix assay run data to a study

Tue Nov 20 18:52:39 PST 2018

Hi LabKey Server support: Thank you for your help in advance. I have an "Expression Matrix" assay, and I have successfully imported the "sample information" file, "feature annotation" file and "gene expression matrix" file into the assay. The assay run result is a table of 4 columns: "Value", "Probe Id", "Sample Id" and "Run". I want to copy this table to a Study. When doing so, LabKey asks me to provide "Participant ID" and "Visit ID" for each row. My problem is: I have tens of thousands of rows and there is no way I can manually enter these values for all rows. There must be a way to get these two fields automatically mapped, but I have tried all I could and read LabKey documents I could find and I cannot find a way of doing so. The LabKey tutorials on this subject apply to many other assay types but not to "Expression Matrix" assay type. I tried to add a "ParticipantVisitResolver" field in the assay's design (the batch property) and LabKey doesn't accept it. I customized the grid view of the run data (the table I want to copy to the study) by adding the "Participant ID" and "Visit ID" columns to it (they are linked to the sample id in the sample set so I can add them to the table), but LabKey doesn't recognize them and still asks me to provide values for those two fields. Please give me a clue on how to automatically map these two fields. Your help is greatly appreciated! Regards Joann

Indexing of large lists

Mon Nov 19 20:44:18 PST 2018

I have an installation of LK Community Edition running on Win server 2012. I am uploading some very large lists (up to 1.7 million lines). Part of my goal in uploading these lists is that I can search them all at the same time for their contents using the LK “search” function. The problem is, not all the lists seem to be getting indexed, what I assume takes place, to allow for rapid searching. When I first loaded the lists, searching returned no results. Leaving them over the weekend, most of the smaller lists now return matches with the same search terms that failed previously. Hence my theory about the lists getting indexed in some way. These smaller lists only contain ~200,000-400,000 lines. So far, after about a week, the larger lists still do not return any matches, even when I know they contain the search term. I can filter each list individually using the search term directly in that column of the list, it works fine and is quite fast. Are there any limits on list size and what will work with the generic LK search function? Is there something I can do to get this working on my system with the larger lists? Thanks for any suggestions, Peter

Issue Tracker Assigned User List Issue

Mon Nov 19 13:28:30 PST 2018

Dear LabKey Admin, During User acceptance testing we noticed that once we add a project group of users to the editor role within a folder, the issue tracker is not updated. Our issue tracker is currently set up to populate the assigned users list from "All Project Users", yet when we add a new project group these users are not reflected in the list. Please advise. Cheers, Sara

I have downloaded the labkey server but still cannot create a project. What else do I need to do?

Fri Nov 02 08:40:44 PDT 2018

Delete large list

Mon Oct 29 15:04:23 PDT 2018

I have a list on my system that says it has 999,999 records. When I try to delete it using the list manager or the folder manager, the application becomes unresponsive. I that another way to manually delete the records?

Chose administrators of moderator review page? and other Qs

Thu Oct 25 16:32:39 PDT 2018

Hi, We are creating a job's board on the Skyline website and have a few questions: I have set up a test board with the permissions for the messages as follows: "readers" set to "guests" "Message board contributors" set to "all site users". I have set the "default settings for Messages " to "no email" (we don't need to spam our whole list every time we get a posting). So to read the listings, you don't have to have an account. But to post you do. So that's the settings: Questions: * was is the benefit of assigning "Author" instead of "Message Board Contributor". * Secondly, I have the job board set up with "moderator review" -- where do I assign accounts to be "moderators" -- it seems to say that "administrators" will be invited to approve the posting. I just want a few people that will "moderate" not every admin we have set up on the Skyline site. * when I look at the postings, there's an option to "respond" -- as this is a job board -- I'd rather not give the option to reply to the posting, just email or call the employer directly. Is there a way to turn off the "respond" feature. * is there a way to also turn off the "delete post" option for authors? I'd rather just have people edit it as "filled" Thanks! -- Nat

Automate linking of participant ids to flow cytometry analysis

Tue Oct 23 16:07:33 PDT 2018

We are importing a number of flow cytometry analyses into LabKey. We need to link the analyses to the participants. We can import the flow data into the study. But then we have to manually associate each participant with the flow analysis. I've attached screenshots. Is is possible to automate this? We are running version 18.2 on a Windows 10 server. Thanks, Bill

Create embedded chart for 18.2

Tue Oct 23 15:58:14 PDT 2018

We recently upgraded to version 18.2. Now we can't figure how to create individual participant charts as described here: https://www.labkey.org/Documentation/wiki-page.view?name=participantViews#chart The "add chart" button/link has disappeared. We are running LabKey on Windows 10 server and using Postgres as the backend. Any help appreciated! Thanks, Bill

integrating datasets beyond variable lookup ..

Tue Oct 16 14:05:10 PDT 2018

A question from a freshman (version 15 community edition user): My data are registered in separate datasets according to visit/sequence. Is there an easy way to feed these separate datasets into one main dataset (which includes all visits) real-time ?

'Copy' files from one Files directory to another?

Tue Oct 16 12:19:21 PDT 2018

Hi, Quick question: is it possible to 'copy' files from one @files directory within LabKey to another. The toolbar certainly allows for 'moving' files but how about copying? Seems like just modifying the "move" function to add a checkbox allowing "copying" would be an easy fix? Thanks ! -- Nat

Error: Failed to locate comet/tandem.

Thu Oct 11 09:06:18 PDT 2018

Hi LabKey team, I was trying to use the MS2 module in our internal LabKey server, and was not able to run comet or tandem. The error message I got is posted below. = = = = = 2018 23:38:44,413 ERROR: Failed to locate tandem. Use the site pipeline tools settings to specify where it can be found. (Currently 'D:\Program Files\LabKey Server\bin') Caused by: java.io.FileNotFoundException: Failed to locate tandem. Use the site pipeline tools settings to specify where it can be found. (Currently 'D:\Program Files\LabKey Server\bin') = = = = = The folder D:\Program Files\LabKey Server\bin' does exist on our server computer, but there is no tandem or comet executable file under folder "D:\Program Files\LabKey Server\bin". I attached the screenshot image of that folder. That all the files we can see now. I wonder if our setting is correct. Could you help us to set up the MS2 module? Thank you Best, Han-Yin

Prompt to re-login but account not recognized?

Thu Oct 11 07:29:32 PDT 2018

I've been trying to login to the Zika Open-Research Portal (https://zika.labkey.com/project/home/begin.view?) and even though I have a LabKey account it's not letting me log in? I'm clearly logged in today but it won't let me log in there. It doesn't even seem to acknowledge that I have an account since I click on "forgot password" but never receive a password reset e-mail for it. I'm not sure what happened since I was able to log in before.

help setting up file uploads/downloads to an external service

Mon Sep 17 23:50:03 PDT 2018

Hi I'm hoping to get some advice on the best way to upload and download files to an external server via Labkey. **Here's the situation...** We are planning to upload large image datasets to labkey along with other trial data etc so that they can be shared amongst users. We've been allocated a cloud based server with a small amount of storage on it that we can run LabKey from. We've also been allocated a large amount of storage space on a separate system (it's for storage only) that at present cannot be mounted as a drive to our VM server. We can however copy files between the 2 using pshell (a python based program that contains simple commands for file management). I pretty new to LabKey and I haven't set up a file server before but the options I'm considering are **(a)** set up a different file service that uses pshell beind the scenes to access the storage space and place a url link to the files in this service within rows of labkey. **(b)** use trigger scripts within Labkey to trigger a pshell script to copy or retrieve files as needed. **How I think (b) might work** uploads: Use the normal labkey file upload system to upload the files onto the labkey server. A trigger script would be used to run a pshell script to move the files to the remote location. If it is not possible to attatch a trigger script to the file upload section then one could be attached to the “create” and “update” calls when an appropriate entry is created or edited in a table associating the files with patient data. The table would have a file link as per the “Linking Data Records with External Files” tutorial. A field indicating whether the file was locally stored or not (“local storage”) would be present and when the file transfer was complete the script could update this field to indicate that the file was no longer stored locally. Downloads: The table mentioned above would also have a field indicating that the file should be retrieved. This would default to false. When a user wanted to download the file they would need to edit the row and change this field to true. Upon update a trigger script would then fetch the file and change the “local storage” field to true indicating that the user could now use the link to download the file. One issue is how to know when to remove the file from local storage again. This could perhaps occurr after a specific interval or daily. At any rate it seems like it will be problematic. **My actual questions...** - Can anyone suggest a good (hopefully easy to set up and use) file-server that could run pshell under the hood to access files? - Is my plan for getting labkey to use pshell reasonable? Is there a better and/or simpler method of doing this? Ideally I would like the process to be as user frinedly as possible and I feel the plan I've outlined above is not ideal in that respect. thanks

Update documentation for folder-level email template customization

Tue Sep 11 14:52:13 PDT 2018

Hi, Was trying to remember how to get to folder level customization of email templates and searched and found this link: https://www.labkey.org/Documentation/Archive/18.2/wiki-page.view?name=customEmail&_docid=wiki%3A8003189b-69a8-1036-a854-8d7bb845bfdb This is the old way I used to customize an email template. Now I think there are several ways of getting there without having to edit URLs. The way I figured out was to click on the "messages" container for a folder and click on "admin" from the triangle icon to the right. This brings up the "Customize Messages" page and at the bottom, I clicked on the link for "Customize Template for this Folder" which sends me to the "Customize Folder-Level Email" where I can make changes to the folder's email template. Since this is a little cryptic to remember -- especially when one rarely needs to update customizing folder-level templates ... would be nice to have the documentation updated. -- Nat

Non-responsive UI element (Knitr Options) when trying to create a new R report?

Tue Aug 21 14:32:04 PDT 2018

I am trying to learn a bit about creating R reports by following the tutorial here https://www.labkey.org/Documentation/wiki-page.view?name=knitr. But I can't get past the step 'Specify which source to process with knitr. Under knitr Options, select HTML or Markdown', because when I'm on the Source tab, the 'expand node' icon on the Knitr Options bar is not functional. Nothing happens when I click the arrow to expand the node, so I can't view the Knitr config options to complete the rest of the steps. Any ideas why this is happening? I'm on LabKey v18.1, and this is reproducible on every browser I've tried (Safari, Chrome, & Firefox, all on a Mac).

Prompts to re-login when switching between subfolders

Tue Aug 07 06:33:18 PDT 2018

I have a LabKey project containing three subfolders (which may themselves contain subfolders later on). Each of these folders inherits its permissions from the parent folder, in which I'm the administrator. When I start a new session (fresh browser, cache cleared), I need to log in to each of these folders separately (meaning the first time I navigate to each of these subfolders I get another login prompt). Is this due to a misconfiguration of my security settings, and if so how should they be set so that I can log in only once and navigate freely between subfolders?

Audit Log access to Non-Admin

Mon Aug 06 15:33:20 PDT 2018

Per the recommendation here: https://www.labkey.org/Documentation/wiki-page.view?name=audits I've assigned the role "See Audit Log Events" to a particular user on our system, and saved the changes. Going to Admin --> Site --> Site Permissions, I confirmed that the assignment 'stuck'. Now, impersonating that user, I cannot find the audit trail. Am I correct in thinking that it'd be accessed for this user the same way an Administrator would access it, namely, Admin --> Site --> Admin Console --> Admin Console Links --> Audit Log? Or is there another route to the Audit Log that's typically used for users with the "See Audit Log Events" role? Chrome on Mac, LabKey 17.3 Thanks, Patrick

How do we ignore existing rows in a dataset when “importing bulk data” and import only new rows

Wed Aug 01 06:33:25 PDT 2018

Hi support team, How do we ignore existing rows in a dataset when “importing bulk data” and import only new rows? This feature exists when importing data in a sample set. Attached is a screenshot of the feature, and I highlighted the one that are important to us. Is there a way we can include the feature to our datasets? This will be helpful because we can download an excel sheet, add new rows on our computer, and import the excel sheet successfully into labkey portal without getting a blank or an error message saying “some rows already exist in the dataset on Labkey”. Thank you very much.

Displaying all the users information that have access to a sub folder

Wed Aug 01 06:08:39 PDT 2018

Hello, For every subfolder, is there a way we can show the contact information of all the users or people who have access to it? We tried using the contact web part (also called “Project Contacts”) and the information we followed can be found here https://www.labkey.org/Documentation/wiki-page.view?name=contacts. By default, the contact web part show all the users in the project. Our project has multiple subfolders and every user only has access to some folders. Is there a way we can make this web part show only the users in a given subfolder? Thank you very much.

paid vs Community version

Tue Jul 24 12:04:48 PDT 2018

Hi support team... Just had to reach out regarding this question of differences in functionality in paid vs free version (would be a great bit of info to put on the website perhaps). I reached out to Bernie but didn't get a response. I include a copy of the email here but basically it relates to concerns here about not necessarily much making use of the 'paid' modules(for now anyway) and particularly our middleware team wanting us to run the latest version of the tool.. Can you provide some information on this or direct me to a resource discussing this detail..? It will certainly help this discussion that periodically arises. Thanks WH

Missing experiment numbers

Mon Jul 23 13:04:57 PDT 2018

I have an experiment list in my lab notebook and it has randomly skipped numbers when a new experiment was added. I start with experiment 1, experiment 2, then skipped experiment 3-4 when I selected "add new experiment". It's also skipped some in the teens. Are these experiments in limbo land somewhere and I can add them back in? How can I find them and add them back into the line up?

ETL to become premium feature in v18.3

Wed Jul 18 09:42:54 PDT 2018

Hi, Today I received an email notification about the release of LabKey v18.2 and at near the bottom of the message was a note that in v18.3, "ETL module will become a premium feature." Does this mean the existing ETL functionality will be removed from the community edition? Or will there be new ETL functionality added that will be premium only and the community edition will retain the current level of ETL functionality? thanks, -Will

Creating a multipage hopscotch tour

Tue Jun 26 12:45:22 PDT 2018

I am trying to create a multipage tour, using the tour builder. I have successfully created callouts on our Home page however, once the tour moves to the 2nd page I cannot get the callouts to start. How can this be fixed.

Notification Issues

Tue Jun 12 08:24:19 PDT 2018

I am using LabKey to communicate via message boards. Currently we have noticed that we cannot trigger an email notification to project users unless a body of text is added. Sometimes colleagues use only the title to communicate an announcement. Is there a setting to allow for all new announcements/messages to trigger an email? Or is this a system design to only allow the notifications if a body of text is added? Kind Regards, Sara

Bug when clearing a dual-filtered column

Sun Jun 10 09:00:04 PDT 2018

Hi, Here is a reproduction of what looks like a bug to me: 1) http://localhost:8080/labkey/query/home/executeQuery.view?schemaName=core&query.queryName=Users 2) Click on email column header -> Filter... 3) Create dual filter with "Contains" the string "@" and "Is Not Blank" 4) Try to remove the "Is Not Blank" filter by click on the orange ''X' by the filter description in the grid header. Result: Both filters are removed Expected: Only Is Not Blank filter is removed and Contains @ filter is retained. -Will

Changing display/header name for study's subject ID field

Fri Jun 08 16:03:16 PDT 2018

I have a study that was initialized to display subject IDs as "Subject ID" in Manage -> Change Study Properties -> Subject Column Name. Now I've been asked to standardize the way all the identifiers are displayed across our study and change this display to "SubjectID" (remove the space). I've tried both changing the value in Subject Column Name to reflect this as well as individually setting the columnTitle value for all of my datasets in datasets_metadata.xml and re-importing dataset definitions, but all my datasets still display "Subject ID" in their header. Oddly, if I change the Subject Column Name to something else with a space in it, like "my friends", it will display as "myfriends" without a space. But it won't subtract the space if I set the display name to "Subject ID"--inconveniently the one instance where I don't want it to preserve the space. I don't see any constraints on this field's display name in the docs here (https://www.labkey.org/Documentation/wiki-page.view?name=studyFields). Is there a way for me to change this field's header to display the way I want?

500 Error when accessing the fileContentSummary.view for certain folders

Thu Jun 07 17:13:16 PDT 2018

I have written a script which crawls the LabKey Server project list to determine the FileRoot for a given project and if any subfolders might be using a custom file or pipeline root. The script finds this information by accessing fileContentSummary.view for each container. One our server, there are a number of folders where this view returns a HTTP response code of 500 with JSON output of { "exception" : "Malformed input or input contains unmappable characters: /path/to/files/on disk/", "exceptionClass" : "java.nio.file.InvalidPathException", "stackTrace" : [ "sun.nio.fs.UnixPath.encode(UnixPath.java:147)", "sun.nio.fs.UnixPath.(UnixPath.java:71)", "sun.nio.fs.UnixFileSystem.getPath(UnixFileSystem.java:281)", "java.io.File.toPath(File.java:2234)", "org.labkey.filecontent.FileContentServiceImpl.getDefaultRootPath(FileContentServiceImpl.java:255)", "org.labkey.filecontent.FileContentServiceImpl.getFileRootPath(FileContentServiceImpl.java:216)", "org.labkey.filecontent.FileContentServiceImpl.getMappedDirectory(FileContentServiceImpl.java:666)", "org.labkey.filecontent.FileContentServiceImpl.getMappedAttachmentDirectory(FileContentServiceImpl.java:653)", "org.labkey.filecontent.FileContentServiceImpl.getNodes(FileContentServiceImpl.java:1181)", "org.labkey.filecontent.FileContentController$FileContentSummaryAction.getChildren(FileContentController.java:702)", "org.labkey.filecontent.FileContentController$FileTreeNodeAction.execute(FileContentController.java:794)", "org.labkey.filecontent.FileContentController$FileTreeNodeAction.execute(FileContentController.java:786)", "org.labkey.api.action.ApiAction.handlePost(ApiAction.java:180)", "org.labkey.api.action.ApiAction.handleGet(ApiAction.java:133)", "org.labkey.api.action.ApiAction.handleRequest(ApiAction.java:127)", "org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:177)", "org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:415)", "org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1231)", "org.labkey.api.view.ViewServlet._service(ViewServlet.java:205)", "org.labkey.api.view.ViewServlet.service(ViewServlet.java:132)", "javax.servlet.http.HttpServlet.service(HttpServlet.java:742)", "org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)", "org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)", "org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)", "org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)", "org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)", "org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)", "org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)", "org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)", "org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1138)", "org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)", "org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)", "org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:214)", "org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)", "org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)", "org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)", "org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)", "org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)", "org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)", "org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)", "org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:496)", "org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)", "org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)", "org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)", "org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)", "org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)", "org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:803)", "org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)", "org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790)", "org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1459)", "org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)", "java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)", "java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)", "org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)", "java.lang.Thread.run(Thread.java:748)" ] } To access this page I am using a URL similar to https://panoramaweb.org/home/filecontent-fileContentSummary.view??node=CONTAINERID Is this error occurring when the server is reading the file path from the database or is the server attempting to access the filesystem and the information returned from the filesystem is bad or encoded in some bad way. Please note, we have had some filename encoding problems where the server was using UTF-8 encoding when storing the file/directory names in the database, but filesystem was using something different (such as ISO-8859-2). This is most like the cause, but I want to verify it is not something else. Brian

Assay run imports are successful, but no data rows are visible

Wed Jun 06 12:57:10 PDT 2018

I have an assay defined with multiple batches/runs uploaded that were previously uploaded successfully and a trigger script to populate additional columns. Recently I tried to re-import one of my runs after making some edits to my trigger script. The re-import was successful in that no errors are thrown and the new run shows up in my Assay Runs webpart, but when I clicked on the newly created run name (or the View Results button) to view the assay results I didn't see any associated data rows. To troubleshoot, I decided to delete my existing batches/runs/data and import them from scratch to see if this would resolve the issue. But I am seeing the same issue now when importing 'new' data: the run itself imports and is visible in the webpart, clicking on the run returns no rows associated with the new Run integer id. And if I remove the 'Run=[###]' filter while viewing assay results I still see an empty grid displaying 'No data to show'. So far I've verified that this same behavior occurs even after I disable my trigger script. I've also verified that new records are being inserted into the underlying postgres tables (exp.experimentrun, exp.data, and assayresult.c5d91_nanodrop_qc_data_fields) after import, as shown in the query below: Before importing a new run: ``` labkey=# SELECT rowid FROM exp.experimentrun; rowid ------- 1 2 (2 rows) labkey=# SELECT DISTINCT dataid FROM assayresult.c5d91_nanodrop_qc_data_fields; dataid -------- (0 rows) ``` The same two queries after import: ``` labkey=# SELECT rowid FROM exp.experimentrun; rowid ------- 1 2 136 (3 rows) labkey=# SELECT rowid,dataid FROM assayresult.c5d91_nanodrop_qc_data_fields; 3750 | 269 3751 | 269 3752 | 269 3753 | 269 3754 | 269 3755 | 269 3756 | 269 3757 | 269 3758 | 269 3759 | 269 3760 | 269 3761 | 269 3762 | 269 3763 | 269 3764 | 269 3765 | 269 3766 | 269 3767 | 269 3768 | 269 3769 | 269 3770 | 269 3771 | 269 3772 | 269 3773 | 269 3774 | 269 3775 | 269 3776 | 269 (39 rows) ``` Any ideas on how to fix this would be much appreciated. Thanks.

X! Tandem search error with trypsin/chymotrypsin

Mon May 21 03:51:07 PDT 2018

Good evening, It seems the pipeline looks for [FKLMRWY]|{P} for trypsin/chymotrypsin digest but the GUI inputs as strict chymotrypsin in the XML: [RKWYF]|{P} I tried to correct the XML script to match and the GUI came up with an error: The enzyme '[RKWYFML]|{P}' was not found. Is there a quick fix for this? Best regards, Trevor Windows 7 Enterprise SP1 (64 bit) Firefox Quantum 60.0.1 (64 bit) Labkey v18.1-57017.17 Sorry there isn't an error code other than the following (trimmed out the list of accepted enzymes except the one in question). 21 May 2018 22:20:10,500 INFO : ERROR: Unsupported search enzyme. 21 May 2018 22:20:10,501 INFO : Use one of the following cleavage site specifications: 21 May 2018 22:20:10,508 INFO : trypsin/chymotrypsin - [FKLMRWY]|{P} 21 May 2018 22:20:10,504 INFO : Failed to complete task 'org.labkey.ms2.pipeline.tandem.XTandemSearchTask' 21 May 2018 22:20:10,510 ERROR: Failed running C:\Program Files (x86)\LabKey Server\bin\Tandem2XML, exit code 1

The schema for the reagent module did not appear. Why?

Sun May 20 06:54:27 PDT 2018

Hi, After installing the reagent module, I found that the schema is not available in the labkey (see as Reagent-1). The reagent schema can be seen through pgAdmin(see as Reagent-2).I am in urgent need of reply.Thanks!

Panorama QC Plot 'Create Guide Set' Grayed Out

Fri May 18 16:27:33 PDT 2018

Hi All, We installed LabKey server since we would like to use Dr. Michael MacCoss' AutoQC program to help QC our mass specs. We were able to upload data to the server using the AutoQC program. However, we were not able to create guide set using our uploaded data. One key component of the QC process is the Pareto Analysis. And to perform Pareto Analysis one needs to be able to create a 'Guide Set'. On our QC Plot dashboard, however, the "Create Guide Set" is grayed out. I am attaching a screenshot of the grayed out button. When I moused over the grayed out button, it says "Enable/disable Create Guide Set mode". I suspect that I need to "enable Create Guide Set mode" somewhere. I looked around and could not figure out how to enable this "Create Guide Set Mode". Any suggestion will be very much appreciated. Best regards,

Non-responsive UI buttons on bottom of page

Tue May 08 19:43:33 PDT 2018

Posting here since I don't know if there's another more appropriate place for reporting a possible bug: This may be a known issue already, but I have found that on very long forms in LabKey where the Submit or Cancel buttons are pushed to the very bottom of my browser window, these buttons are non-responsive (can't be clicked, no cursor change on mouse-over, etc.). I've seen this happen on multiple LabKey interfaces, but one reproducible example is navigating the Insert New Row page for a dataset where many fields are defined (30+ or so). I am using Safari 11.0.3 and Firefox 59.0.2, and both seem to exhibit this behavior. Fortunately it's not a problem on forms where there are a pair of Submit buttons on both the bottom and top of the page, since the top buttons seems to work consistently as expected.

Required Date column for demographic dataset in a study without timepoints

Mon Apr 30 20:09:39 PDT 2018

Lately I've been curious as to why there is a requirement for a date column in demographic datasets in LabKey, and whether there is any way I might bypass this requirement. A number of the datasets we collect are demographic in nature, so having to arbitrarily add a date is not ideal. Is there a safe workaround for this, either by modifying the table in Postgres directly (which I'm guessing voids my warranty and is a very bad idea) or by making edits to some underlying XML for our demographic datasets? Relatedly, in non-demographic datasets we collect where records ARE tied to a specific date, is there a way for me to redefine one of my dataset's existing datetime fields to serve as part of the table's multi-column key (instead of the generic 'Date' column that comes standard with every Dataset) ? For instance, let's say I have a dataset where each row is uniquely identified by both a SubjectID and a datetime field we call 'ChartReviewDate'. Rather than have to populate the 'Date' column with the value from 'ChartReviewDate', is there a way for me to rename 'Date' to something more informative/modify the header so a more descriptive name appears in the grid view?

Weird Editing Permissions error

Tue Apr 24 12:25:31 PDT 2018

I had granted editing permissions to a colleague (mwfoster@duke.edu (mwfoster)) to work on our Duke University Course page: https://skyline.ms/project/home/software/Skyline/events/2018%20Duke%20Course/begin.view? When making an edit and trying to save he gets a very odd error that says: “error saving wiki” in the basic editor or “rel attribute must be set to noopener noreferrer with target=”_blank”. Error on element .” in the advanced editor. The only way we could work around this was removing all the "target=”_blank”" tags from the page ... I got the same error when I impersonated him but did not when I tried to edit as myself. Attached is the thread we had about this ... Nat