LabKey Support: LabKey Server Distribution and Support

Export user "name" vs "id" in Created By and Modified By column

Mon Apr 22 09:40:42 PDT 2024

Hi LabKey, I have a list that contains columns "Created By" and "Modified By", and I am trying to figure out how to access more of the data stored in those columns via your python API. - On the website, those columns contain a user's Display Name as a clickable link, which goes to a little summary page of the user. - When I use the "Export" button online to export the sheet to an excel workbook, the Created By and Modified By columns contain just the display names of users (no link or other data). I'm attaching a screenshot of the export button I'm referring to. - When I use the code below to access the data via your python API, those columns are labelled "CreatedBy" and "ModifiedBy", and contain user ids. ``` my_results = api.query.select_rows( schema_name='lists', query_name='HVTN SDMC Lab/Assay Data Status Tracker', view_name='Full Export' ) ``` Is there a way to use access the Display Names associated with those user ids via the python API? Thanks so much! Beatrix

database schema migration

Fri Apr 12 06:59:32 PDT 2024

Hello LabKey support team, I was running LabKey community edition version 21.11.4 and associated DB in postgres 14. Now I would like to migrate the instance to Version Number: 23.11.11 community edition. I did the dump of the database and loaded it to the new database without issues but when I started the server, LabKey ended up with a couple of internal errors. Most of them are related to the foreign key mismatches. Is there a way to upgrade the schemas from previous versions? If you would like to have the complete error message I am happy to provide that as well. Regards, Vipin

Security updates released for LabKey Server

Wed Apr 10 10:38:36 PDT 2024

We are reaching out to inform LabKey Server users about a critical security update that was released on Monday, April 8. This update addresses several issues, including a vulnerability affecting LabKey Servers operating in Development mode. Development mode provides enhanced logging and troubleshooting features to help identify and solve developer coding issues. While a Production server should never run in Development mode, some Staging, Test, and Development servers are configured to run in this manner. [Follow these steps](https://www.labkey.org/Documentation/wiki-page.view?name=devmode#run) to check if a server is in Development or Production mode. We recommend upgrading your LabKey Server instances to one of the updated releases (links below). If you have servers running in Development mode, this upgrade should happen immediately: - [23.11.11](https://www.labkey.org/Documentation/wiki-page.view?name=prevReleasesDetails&release=23.11.11) - [24.3.2](https://www.labkey.com/download-community-edition/) Similarly, for local development instances, it is recommended to pull the latest changes from LabKey’s Github repository to incorporate these critical updates.

Teamcity CI/CD Maintenance tomorrow 4/5/2024 at 11am PDT

Thu Apr 04 11:17:41 PDT 2024

LabKey TeamCity CI/CD server will be down for maintenance beginning at approximately 11am PDT. We expect the outage to last for approximately 1 hour.

Table doesn't exist within schema

Fri Mar 29 11:11:24 PDT 2024

Hello, I am trying to pull data from the table "HVTN SDMC Lab/Assay Data Status Tracker" using the labkey python API. The table is located at: https://atlas.scharp.org/cpas/list/HVTN/Tools%20and%20Reports/SCHARP%20LDO/Assay%20Tracker/grid.view?listId=24 I have version 3.0.0 of the labkey package installed, and I have tried various combinations of variables which throw different errors. For example: ``` labkey_server = "atlas.scharp.org" project_name = "HVTN" # Project folder name context_path = "cpas" api = APIWrapper(labkey_server, project_name, context_path, use_ssl=True) schema = "lists" table = "HVTN SDMC Lab/Assay Data Status Tracker" result = api.query.select_rows(schema, table) ``` returns the error ```QueryNotFoundError: "404: The specified query 'HVTN SDMC Lab/Assay Data Status Tracker' does not exist in schema 'lists'"``` (full traceback attached). When viewing the page on my browser (I'm using Chrome), the header says: **Lists / HVTN SDMC Lab/Assay Data Status Tracker** **HVTN SDMC Lab/Assay Data Status Tracker [folder image] Assay Tracker** (see attached screenshot). So I have also tried ``` labkey_server = "atlas.scharp.org" project_name = "Assay Tracker" # Project folder name context_path = "cpas" api = APIWrapper(labkey_server, project_name, context_path, use_ssl=True) schema = "lists" table = "HVTN SDMC Lab/Assay Data Status Tracker" result = api.query.select_rows(schema, table) ``` But then I get ```QueryNotFoundError: '404: No such project: /Assay Tracker'```. Going through https://github.com/LabKey/labkey-api-python I couldn't find any utilities that would list projects or tables within a schema -- is there such a method available? I'm sorry I know this is more of a question about the structure of the database I'm trying to access, but I can't figure out how to figure out that structure and thus the appropriate method arguments. Can you advise? Thank you so much! Beatrix

Teamcity CI/CD Maintenance tomorrow 3/12/2024 at 10:30am PDT

Tue Mar 12 14:02:32 PDT 2024

LabKey TeamCity CI/CD server will be down for maintenance beginning at approximately 10:30am PDT. We expect the outage to last for approximately 2 hours.

Teamcity CI/CD Emergency Maintenance today 3/4/2024 at 9am PDT

Mon Mar 04 08:56:56 PST 2024

LabKey TeamCity CI/CD server will be down for emergency maintenance beginning at 9am PDT. We expect the outage to last for approximately 30 mins. We apologize for the short notice.

Remove "Name" field from derive sample forms

Thu Feb 29 03:05:29 PST 2024

Hi, I'm trying to remove the name field from the deriving samples forms becasue my users will fill any available field and ruin my automated naming. I've worked out how to remove it from input forms through "edit metadata" and advanced setting, but I can't work out how/if I can remover it from here as well. Any ideas? This is LabKey community and we're on version 23.11.5 as of today! Best, Katy

Permissions settings for seeing created by colums in sample tables

Mon Feb 26 05:30:30 PST 2024

Hi, I've set up a series of tables in LabKey community where I am the site admin but other users are project and folder administrator. I am able to see the associated name of the user in the created by column however the other project/folder administrator is only able to see the key of the user (screenshot attached). Are there any permissions that I can give that aren't full system admin giving the ability to see the user names instead of the key? I've tried giving her "See user and group details" permissions site wide but it didn't help. Thanks, Katy

LabKey Teamcity Emergency Maintenance 1/31/2024

Wed Jan 31 08:45:50 PST 2024

Teamcity was down this morning from 7:45 AM to 8:30 AM PDT due to unscheduled critical software updates. We prefer to schedule these types of updates when possible, however given the urgency of the required updates, we elected to perform the maintenance as soon as possible. We apologize for any inconvenience this may have caused.

Rlabkey - HTTP error code 500 using executeSql function

Fri Jan 12 01:57:17 PST 2024

``` > sessionInfo() R version 4.3.2 (2023-10-31) Platform: aarch64-apple-darwin20 (64-bit) Rlabkey_3.1.0 ``` I got an error message (see below) using the executeSql function in Rlabkey. ``` test<-labkey.executeSql( + baseUrl="http://localhost:8080/labkey", + folderPath = "/DEMO", + colNameOpt = "rname", + schemaName = "lists", + sql="SELECT * from Test") ``` Error in handleError(response, haltOnError) : HTTP request was unsuccessful. Status code = 500, Error message = Error on line 1: Syntax error near 'U0VMRUNUJTIwKiUyMGZyb20lMjBUZXN...' If I use the selectRows function I have the correct result: ``` > labkey.selectRows( + baseUrl="http://localhost:8080/labkey", + folderPath="/DEMO", + schemaName="lists", + queryName="Test") Patient ID GENDER Date 1 1022 Male 2016-08-08 2 1030 Male 2016-11-25 > ``` I have checked all the logs and server configuration and I don't understand why the function executeSql does not work. Thank you for your feedback.

Creating an assay in the LabKey Server using an R script

Thu Jan 04 23:49:25 PST 2024

Hi. I have used Rlabkey to create lists and manipulate data on those lists. However, now I need to create assays. labkey.create.domain() which I have used to create lists, accepts the folowing domain types and assays are not an option: • "IntList": A list with an integer key field • "VarList": A list with a string key field • "StudyDatasetVisit": A dataset in a visit based study • "StudyDatasetDate": A dataset in a date based study • "IssueDefinition": An issue list domain • "SampleSet": Sample set • "DataClass": Data class Can you please guide me through creating an assay using an R script? Thank you.

How to use getParameter

Thu Dec 21 12:30:26 PST 2023

I am trying to use make a custom entry form for a list similar to orderReagents form but use a value passed in the url to pre-poluate the form and i have tried to use LABKEY.ActionURL.getParameter(parameterName:param) but it doesn't seem to pick the param value from the URL . Is there a specific way to build the URL to pass the param value to a wiki page different then for a query ?

error while trying to rebuild an old labkey configuration

Mon Dec 18 02:58:36 PST 2023

Hi. Our previous system administrator had configured Labkey using: Oracle JDK 1.8.0_181-b13, Apache Tomcat 8 and Labkey 18.2, postgresql 9.5. Now I am sked to recreate the whole configuration, preferably with newer versions. I am on Ubuntu 22.04.3 LTS (Jammy) . I am using Labkey 23.7.4-7, Apache Tomcat 9 and OpenJDK17U and postgresql 15.5. I followed the installation instructions and managed to successfully see the start up window for Labkey. at this point I am using an empty "labkey" database. I then proceeded to back up the previous database and files. I backed up "Files" from /usr/local/labkey/files and put it in the same directory in the new configuration. I furthermore, backed up and restored the old database in the empty "labkey" database. However, now I get this error (I have attached screenshots of the whole log): - HTTP Status 500 – Internal Server Error - org.labkey.api.util.ConfigurationException: Error running scripts in module Core - org.postgresql.util.PSQLException: ERROR: cannot drop view core.activeusers because other objects depend on it Detail: view core.contacts depends on view core.activeusers Hint: Use DROP ... CASCADE to drop the dependent objects too. Where: SQL statement "DROP VIEW core.activeusers" can you please help me with that?

Custom views with “Timeline” tab encounter this JS error message ext.Timeline

Fri Dec 15 11:06:48 PST 2023

Hello there, Please review the attached document and assist with the solution. thank you, Zafar Olimov zolimov@immunetolerance.org Software Test Engineer II | Data Collaboration Team Immune Tolerance Network | Benaroya Research Institute @ Virginia Mason 1201 Ninth Avenue | Seattle, WA 98101

Build failed

Fri Dec 08 00:33:36 PST 2023

Hello, I want to try to generate deployable software from source code. I have installed the development environment (https://www.labkey.org/Documentation/wiki-page.view?name=devMachine). It includes: 1.Window Server 2019 Standard 2.jdk_x64_17.0.9_9 3.apache-tomcat-9.0.83 4.postgresql-15.5-1 5.Labkey server-23.12.RC0/platform-23.12.RC0 6.IntelliJ IDEA 2023.2.5 (Community Edition) Version number: IC-232.10227.8, built on November 9, 2023 Runtime version: 17.0.9+7-b1000.46 amd64 Virtual Machine OpenJDK 64-bit server VM: JetBrains s.r.o. My first build took a long time but failed. I followed the error message and build again with stacktrace and still got the error message as attached. Thanks, Bika

ETL status stuck

Wed Nov 29 06:51:56 PST 2023

ETL status is stuck to 'running' and can't reset or truncate reset - it said the job is 'pending' and can't be reset. How do I get the ETL to re-run ?

Error message when clicking "Save" under "Site > Admin Console > Site Settings"

Tue Nov 28 06:06:28 PST 2023

I have just installed the latest Labkey version (LabKey23.11.1-2-community). Everything is running fine so far. The only exception: when I apply changes under Site > Admin Console > Site Settings and click save, I get an error message (see below) Can you give me advice on what is wrong? KR, Oliver Error Message: „Upps Oops! An error has occurred. Name is null Please report this bug to LabKey Support by copying and pasting both your unique reference code and the full stack trace in the View Details section below. Your unique reference code is: Z5C82Q View Details: java.lang.NullPointerException: Name is null java.base/java.lang.Enum.valueOf(Enum.java:271) org.labkey.api.util.UsageReportingLevel.valueOf(UsageReportingLevel.java:53) org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1220) org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1140) org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:96) org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:75) org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:195) org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:510) org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1128) org.labkey.api.view.ViewServlet._service(ViewServlet.java:240) org.labkey.api.view.ViewServlet.service(ViewServlet.java:159) javax.servlet.http.HttpServlet.service(HttpServlet.java:623) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:209) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:43) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1470) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:235) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:120) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:168) org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90) org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:481) org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:130) org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93) org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:670) org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74) org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342) org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:390) org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63) org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:928) org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1794) org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52) org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191) org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659) org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) java.base/java.lang.Thread.run(Thread.java:840)

HTTP Status 404 – Not Found

Thu Nov 02 02:05:06 PDT 2023

Hello, I installed OpenJDK17U-jdk_x64_linux_hotspot_17.0.9_9 and apache-tomcat-9.0.82 and PostgreSQL-15 and LabKey23.3.12-15-community in ubuntu18.04.5. After installation running http ://localhost:8080/ works fine. HTTP Status 404 - Not Found appears when running http://localhost:8080/labkey. After diagnosing myself, I found that /logs does not have labkey.log and labkey-errors.log. Thanks, Bika

How to "refresh" a list

Thu Oct 12 12:56:33 PDT 2023

What is the best way to truncate and re-populate a list using JavaScript. Can that be done without LABKEY.Query.executeSql ?

Beta version for LK 23.11

Tue Oct 03 11:24:22 PDT 2023

Hello, Will there be a beta version of LK 23.11 that will be released prior to 11/16/2023. We are going to bypass LK 23.7 and move right into LK 23.11. Thank you, Emily Lovan

Teamcity CI/CD Emergency Maintenance today 9/19/2023 at Noon PDT

Tue Sep 19 10:10:46 PDT 2023

LabKey TeamCity CI/CD server will be down for emergency maintenance beginning at Noon PDT. We expect the outage to last for approximately 30 mins. We apologize for the short notice.

Out of heap memory after upgrade from v23.3.2 to v23.7.0

Mon Aug 28 18:12:35 PDT 2023

I have a cronjob that makes queries and then performs row deletions on lists using the LabKey API (via the python package). The queries are simple but can return a large number of rows. The deletions are batched to 900 rows per API call. This workflow has been running fine for a while. Last week I upgraded from LabKey v23.3.2 to v23.7.0 and immediately started getting out of memory errors when performing the row deletions. ``` ERROR ExceptionUtil 2023-08-27T01:52:59,521 http-nio-8080-exec-2 : Unhandled exception: Java heap space java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOf(Arrays.java:3537) ~[?:?] at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:228) ~[?:?] at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:582) ~[?:?] at java.lang.StringBuilder.append(StringBuilder.java:179) ~[?:?] at org.labkey.list.model.ListManager$2.exec(ListManager.java:844) ~[list-23.7.0.jar:?] at org.labkey.list.model.ListManager$2.exec(ListManager.java:840) ~[list-23.7.0.jar:?] at org.labkey.api.data.TableSelector.lambda$forEachResults$1(TableSelector.java:278) ~[api-23.7.0.jar:?] at org.labkey.api.data.TableSelector$$Lambda$1265/0x00007fc3d0e3c130.handle(Unknown Source) ~[?:?] at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.handleResultSet(SqlExecutingSelector.java:457) ~[api-23.7.0.jar:?] at org.labkey.api.data.TableSelector.forEachResults(TableSelector.java:273) ~[api-23.7.0.jar:?] at org.labkey.list.model.ListManager.indexEntireList(ListManager.java:839) ~[list-23.7.0.jar:?] at org.labkey.list.model.ListManager.lambda$deleteItemIndex$6(ListManager.java:592) ~[list-23.7.0.jar:?] at org.labkey.list.model.ListManager$$Lambda$1837/0x00007fc3d11bee58.run(Unknown Source) ~[?:?] at org.labkey.api.data.DbScope$CommitTaskOption.run(DbScope.java:2010) ~[api-23.7.0.jar:?] at org.labkey.api.data.DbScope$TransactionImpl.commit(DbScope.java:2327) ~[api-23.7.0.jar:?] at org.labkey.query.controllers.QueryController$BaseSaveRowsAction.executeJson(QueryController.java:4473) ~[query-23.7.0.jar:?] at org.labkey.query.controllers.QueryController$DeleteRowsAction.execute(QueryController.java:4622) ~[query-23.7.0.jar:?] at org.labkey.query.controllers.QueryController$DeleteRowsAction.execute(QueryController.java:4614) ~[query-23.7.0.jar:?] at org.labkey.api.action.BaseApiAction.handlePost(BaseApiAction.java:238) ~[api-23.7.0.jar:?] at org.labkey.api.action.BaseApiAction.handleRequest(BaseApiAction.java:128) ~[api-23.7.0.jar:?] at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:195) ~[api-23.7.0.jar:?] at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:512) ~[api-23.7.0.jar:?] at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1128) ~[api-23.7.0.jar:?] at org.labkey.api.view.ViewServlet._service(ViewServlet.java:240) ~[api-23.7.0.jar:?] at org.labkey.api.view.ViewServlet.service(ViewServlet.java:159) ~[api-23.7.0.jar:?] at javax.servlet.http.HttpServlet.service(HttpServlet.java:623) ~[servlet-api.jar:4.0.FR] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:209) ~[catalina.jar:9.0.79] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) ~[catalina.jar:9.0.79] at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) ~[tomcat-websocket.jar:9.0.79] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) ~[catalina.jar:9.0.79] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) ~[catalina.jar:9.0.79] at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:43) ~[api-23.7.0.jar:?] ``` I am running with 16GB of heap: ``` -Xms16G -Xmx16G -XX:-HeapDumpOnOutOfMemoryError ``` And the overall load on the system is quite low. When investigating I looked at /admin-memTracker.view and was surprised to see ~30 instances of "SearchService:index". But I haven't looked at this page before, so perhaps that is normal. Some other system details: Servlet Container Apache Tomcat/9.0.79 Java Runtime Vendor Eclipse Adoptium Java Runtime Name OpenJDK Runtime Environment Java Runtime Version 17.0.8+7 Database Product Name PostgreSQL Database Product Version 15.3 Is anyone else running into out of memory issues after moving to v23.7.0? Thanks, -Will

Python API - Connection with _netrc failing?

Tue Aug 22 08:41:47 PDT 2023

I'm trying to create a Python script that connects to my LabKey server, however, I'm not getting past authentication when I provide either a username/password or an API key. I've tried moving the _netrc file to the C:/Users/user_account/ path to no avail. I'm not quite sure where I'm going wrong as everything seems to match the documentation. # Python Code ```python # LabKey Settings container_path = "Test_Lab" context_path = "labkey" labkey_server = "mylabkeyserver.ca" api_key = 'apikey|8ba5866e0f50c2b9...' # Debug: print paths and _netrc contents print(f"{'$HOME path:':20s}", os.environ['HOME']) print(f"{'$HOME dir:':20s}", os.listdir(os.environ['HOME'])) print(f"{'_netrc contents:':20s}", open(os.environ['HOME'] + "\\_netrc").read()) # Create the connection to the LabKey API labkey_api = APIWrapper(labkey_server, container_path, context_path, use_ssl = False, api_key = api_key) # Connect and try to get available roles print("\nGetting user") result = labkey_api.security.get_roles() print(result) ``` # Results ``` $HOME path: C:\development\labkey\common $HOME dir: ['_netrc'] _netrc contents: machine mylabkeyserver.ca login apikey password apikey|8ba5866e0f50c2b9... Getting user --------------------------------------------------------------------------- TimeoutError Traceback (most recent call last) ```

LabKey TeamCity Server Maintenance Thursday 8/10/2023 between 7-8 AM PDT

Wed Aug 09 17:38:07 PDT 2023

We will be performing maintenance on the LabKey TeamCity server on Thursday 8/10/2023 between 7-8 AM PDT. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted. We apologize for any inconvenience this may cause.

Capacity of "Lists"?

Thu Jun 22 23:27:00 PDT 2023

Hi, we are developing a solution based on LabKey Community and have different options for how to implement some functionality. Is there a practical limitation to how large a "List", with per-row indexing, can get? Is it feasible to have a "List" with many millions of rows, and to query it in reports?

LabKey TeamCity Emergency Maintenance Monday June 12th 2023

Mon Jun 12 07:56:35 PDT 2023

LabKey TeamCity CI/CD server will be down for emergency maintenance beginning at 8 AM PDT. We expect the outage to last for approximately 30 mins. We apologize for the short notice.

Maintenance Notice - Upgrade of LabKey.org for Thursday, May 11th 2023 @ 9:00pm Pacific Time

Thu May 11 14:15:34 PDT 2023

LabKey.org will be offline this evening at 9:00pm Pacific Time for an upgrade to LabKey 23.5 The site will be offline for approximately one hour. Please save your work before this time.

Assay Data not getting fetched in API

Mon May 08 02:44:31 PDT 2023

Hi Team, I have created an assay project folder structure screen shot attached.I am trying too invoke http:///labkey/Custom Project 2/subfolder/assay-assayList.api GET API and I get following error { "exception": "Method Not Allowed: GET", "success": false } Is there any issue with the API URL which I have formed ?Please let me know.

Sample Managerment

Mon May 08 01:20:47 PDT 2023

Hello, I am working on labkey community version. I am looking for labkey Sample lifecycle implementation as the documentations/videos but I don't see the relevant menus in my system.Can you please suggest what could be going wrong? Is this feature only available with Professional edition.Please let me know

Maintenance Notice - Update of LabKey.org for Wednesday, April 19th 2023 @ 7:30pm Pacific Time

Wed Apr 19 11:25:25 PDT 2023

LabKey.org will be offline this evening at 7:30pm Pacific Time for a minor maintenance update. The site will be offline for no more than 15 minutes. Please save your work before this time.

Maintenance Notice - Upgrade of LabKey.org for Monday, April 17th 2023 @ 8:00pm Pacific Time

Mon Apr 17 15:48:35 PDT 2023

LabKey.org will be offline this evening at 8:00pm Pacific Time for a maintenance upgrade. The site will be offline for no more than 30 minutes. Please save your work before this time.

Insert pdf as a printout in wiki

Fri Apr 14 15:29:54 PDT 2023

How do you insert a pdf or image into the wiki page? I've tried the following with no luck: This doesn't work at all, this image file is just added as an attachment: This also doesn't work, and throws an error about an illegal element:

Error when editing style "There was a problem while saving: Illegal element"

Fri Apr 14 15:19:10 PDT 2023

I have been trying to add some style elements to my wiki web parts and the text itself works fine, but I try to throw in any style element and it throws an error saying "There was a problem while saving: Illegal element". I checked the html code on another site and the HTML code works fine elsewhere, so I dont' know why I'm getting the error. Example code below:

Maintenance Notice - Upgrade of LabKey.org for Thursday, April 13th 2023 @ 9:30pm Pacific Time

Thu Apr 13 14:58:05 PDT 2023

LabKey.org will be offline this evening at 9:30pm Pacific Time for an upgrade to LabKey 23.4 The site will be offline for approximately one hour. Please save your work before this time.

Getting duplicate key error after upgrade

Wed Apr 05 10:44:31 PDT 2023

Hello, I am new to Labkey so if I get something wrong or you need more info just let me know. I have upgraded our dev environment to the latest version (23.3.2-5) and now I am getting this error: ERROR: duplicate key value violates unique constraint "uq_modulename". Can anyone tell me what I have done to my server and if there is a way to fix it? Any info is greatly appreciated. Thanks

ViewName selection on survey lookup option

Wed Apr 05 07:09:56 PDT 2023

I have multiple survey fields where i need to select a lookup value from a list. Since the value sets a slightly different i am using viewName as in (https://www.labkey.org/Documentation/wiki-page.view?name=questionMetadata#viewName) but while this works for the first field - all subsequent fields have the same viewName applied even if the other fields have different viewName defined on the lookup. Can different survey fields on the same survey use different viewName for subselecting values from the same lookup list ?

LabKey Upgrade Recommended: Security Update

Thu Mar 30 11:23:24 PDT 2023

LabKey is releasing hotfixes that address an important security vulnerability. It affects all LabKey products and was detected by our engineering team. The following maintenance releases include the security update: * 23.3.2 * 22.11.9 * 22.7.9 * 22.3.11 * 21.11.11 It is imperative that system administrators upgrade their LabKey Server instances immediately to remain secure. An updated and secured version of LabKey Server has been made available. We apologize for the inconvenience and thank you for patching your installations. Please note that this update also includes other valuable but non-critical security improvements. At this time, we are not releasing additional details as we do not want to make this vulnerability public for exploitation. We have no indications that anyone outside of LabKey is aware of the detected vulnerability. We take security related issues very seriously, please reach out via the [support forum](https://www.labkey.org/home/Support/LabKey%20Support%20Forum/project-begin.view) if you have questions.

Maintenance Notice - Upgrade of LabKey.org for Thursday, March 9th 2023 @ 9:30pm Pacific Time

Thu Mar 09 18:47:34 PST 2023

LabKey.org will be offline this evening at 9:30pm Pacific Time for an upgrade to LabKey 23.3 The site will be offline for approximately one hour. Please save your work before this time.

How to login to community edition set up

Wed Mar 08 21:28:13 PST 2023

I have set up local LabKey community edition. How to l get access to login first time?

Sample naming pattern - yearlySampleCount

Tue Feb 21 08:20:18 PST 2023

Hi, I'm trying to use the yearlySampleCount in my sample naming pattern but even in a new folder with nothing else in it it's not starting at 1. I entered ${yearlySampleCount} as my name expression and my first test sample was given a name of 17886. The next one was give 17887. I made a new project folder and made a new sample type with ${yearlySampleCount} as the naming expression and my first sample was given 17888. It looks like the scope is maybe extending across folders, but the documentation says it's only "All Sample Types / Data Classes in the current folder". Is this how it's meant to be working or am I doing something very wrong? Thanks, Katy

Maintenance Notice - Upgrade of LabKey.org for Wednesday, February 15th 2023 @ 8:30pm Pacific Time

Wed Feb 15 10:50:59 PST 2023

LabKey.org will be offline this evening at 8:30pm Pacific Time for a minor upgrade of LabKey 23.2 The site will be offline for no more than 30 minutes. Please save your work before this time.

Maintenance Notice - Upgrade of LabKey.org for Friday, February 10th 2023 @ 8:30pm Pacific Time

Fri Feb 10 12:59:24 PST 2023

LabKey.org will be offline this evening at 8:30pm Pacific Time for an upgrade to LabKey 23.2 The site will be offline for approximately one hour. Please save your work before this time.

Validation for Participant IDs

Fri Feb 10 09:27:59 PST 2023

Hello, Is it possible to create a [regex validator](https://www.labkey.org/Documentation/wiki-page.view?name=fieldEditor#regex) for Participant IDs? If not, is there any other way to enforce constraints on Participant IDs at the time users enter data (e.g., require the IDs to be 10-digit numbers)? Thank you! Leah

Maintenance Notice - LabKey TeamCity Build Server on Friday, February 3rd 2023

Wed Feb 01 13:20:08 PST 2023

We will be performing maintenance on the LabKey TeamCity server on **Friday 2/3/2023 starting at 8 AM PST**. During this maintenance the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. We are migrating to a multi-node, high availability configuration to improve performance and reliability. The server will be offline periodically throughout the migration. We hope to have the maintenance complete and validated by 3PM. We apologize for any inconvenience this may cause.

Maintenance Notice - Upgrade of LabKey.org for Wednesday, January 11th 2023 @ 8:30pm Pacific Time

Wed Jan 11 15:39:06 PST 2023

LabKey.org will be offline this evening at 8:30pm Pacific Time for an upgrade to LabKey 23.1 The site will be offline for approximately one hour. Please save your work before this time.

Chart / Graphical display of Cohorts that change during a study

Wed Dec 14 04:29:34 PST 2022

I have set up a visit based study with initially 3 Cohorts of participants. During the study 2 more separate Cohorts are generated from within one of the existing Cohorts to make 5 final cohorts. (i.e. some participants start in one cohort and then shift into two others, as their treatments change). Setting this up with automatic cohort assignment with a dataset and visits seems straightforwards. However, when I try to view the data within any dataset graphically with time on the X axis and with participants grouped according to their cohort at any given time, it seems not to recognise that the cohorts change. Is this actually possible to view graphically please (with correct cohort assignment at different times)? I am using Labkey server 21.7. Thank you. Richard

Scheduled Maintenance - LabKey TeamCity Build Server - Wednesday 12/14/2022 between 4-5 PM PST

Tue Dec 13 15:07:40 PST 2022

We will be performing maintenance on the LabKey TeamCity server on Wednesday 12/14/2022 between 4-5 PM PST. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted. We apologize for any inconvenience this may cause.

Maintenance Notice - Upgrade of labkey.org for Monday, December 12th 2022 @ 9:00pm Pacific Time

Mon Dec 12 14:21:55 PST 2022

LabKey.org will be offline this evening at 9:00pm Pacific Time for an upgrade to LabKey 22.12 The site will be offline for approximately one hour. Please save your work before this time.

Maintenance Notice - Upgrade of labkey.org for Thursday, November 10th 2022 @ 8:30pm Pacific Time

Thu Nov 10 13:09:35 PST 2022

LabKey.org will be offline this evening at 8:30pm Pacific Time for an upgrade to LabKey 22.11 The site will be offline for approximately one hour. Please save your work before this time.

Maintence Notice - Teamcity Build Server - Monday 11/7/2022 7-8A M PST

Mon Nov 07 06:41:51 PST 2022

We will be performing maintenance on the LabKey TeamCity server on Monday 11/07/2022 between 7-8 AM PST. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted. We apologize for any inconvenience this may cause.

LabKey Update Recommended: Apache Batik Disclosed Vulnerabilities

Thu Nov 03 10:54:44 PDT 2022

Hello, This is a recommendation to upgrade your LabKey Servers immediately - if you are a LabKey Cloud Customer, we will perform the upgrade and notify you of the short server downtime. For anyone managing their own LabKey Server, or for more details, read on. Recently, the developers of Apache Batik announced two security vulnerabilities, https://nvd.nist.gov/vuln/detail/CVE-2022-41704 and https://nvd.nist.gov/vuln/detail/CVE-2022-42890 Batik is a library that LabKey Server uses to convert SVGs into PNGs and PDFs. We have assessed the vulnerability and determined that some versions of LabKey Server are impacted. LabKey previously added a related mitigation, which is included in versions 22.7.3, 22.9.0, and 22.10.0 (and beyond). The mitigation addresses the vulnerability, even without the patch to Batik itself. LabKey will include the latest version of Batik, 1.16, in the upcoming 22.7.8 and 22.11.0 releases. LabKey has also prepared version 22.3.10 to address 22.3.x deployments. We recommend all LabKey users on versions older than 22.7.3 upgrade to one of the secured versions immediately. By the end of the day today, the LabKey team will push new secured builds to your support portal. We will also make these changes for all LabKey Cloud customers not already on secured versions which will involve a short server downtime. You will receive notice of this downtime. Additionally, OpenSSL has disclosed two recent vulnerabilities in their 3.0.x versions. https://www.openssl.org/blog/blog/2022/11/01/email-address-overflows/ LabKey Server itself is NOT IMPACTED by this. However, other common software, including many recent Linux distributions, relies on OpenSSL so please be aware and patch as appropriate. Please reach out if you have any questions or concerns for us.

Maintenance Notice - Upgrade of labkey.org for Wednesday, October 12th 2022 @ 8:30pm Pacific Time

Wed Oct 12 14:18:46 PDT 2022

LabKey.org will be offline this evening at 8:30pm Pacific Time for an upgrade to LabKey 22.10 The site will be offline for approximately one hour. Please save your work before this time.

Limit on number of sample derivatives created at a time in Sample Manager

Tue Oct 11 10:06:36 PDT 2022

Is it possible to increase the number of sample derivatives a user can create at one time? It seems we are limited to just 20 samples right now (see attached image). Thanks

Maintence Notice - Teamcity Build Server - Wednesday 4 -5 PM PDT

Tue Oct 04 11:09:13 PDT 2022

We will be performing maintenance on the LabKey TeamCity build server on Wednesday 10/05/2022 between 4-5 PM PDT. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted. We apologize for any inconvenience this may cause.

Maintenance Notice - Update of labkey.org for Wednesday, September 28th 2022 @ 6:30pm Pacific Time

Wed Sep 28 11:52:27 PDT 2022

LabKey.org will be offline this evening at 6:30pm Pacific Time for an update The site will be offline for approximately 30 minutes. Please save your work before this time.

withCounter skipping over numbers

Thu Sep 22 15:54:34 PDT 2022

Hi, We have a case where a user generated derivatives of a sample which has a "withCounter" modifier in the sample ID. It is a simple modifier: LIB_${${MaterialInputs:first}_:withCounter(1,'00')} In general, we only make one derivative for a sample, so the tail end of the sample ID would be _01. However, a user generated a second set of derivative samples and they had _101 instead of _02 at the end. The user assures me they didn't create and delete 99 derivatives.... I have not been able to reproduce this in our test environment, each derivative correctly counts up one digit at a time. I also do not see any extra samples in the lineage trail. What could cause this behavior? Thanks Eric

Maintenance Notice - Update of labkey.org for Tuesday, September 20th 2022 @ 5pm Pacific Time

Tue Sep 20 15:19:16 PDT 2022

LabKey.org will be offline this evening at 5pm Pacific Time for an update The site will be offline for approximately 15 minutes. Please save your work before this time.

Maintenance Notice - Upgrade of labkey.org for Tuesday, September 13th 2022 @ 9pm Pacific Time

Tue Sep 13 17:10:18 PDT 2022

LabKey.org will be offline this evening at 9pm Pacific Time for an upgrade The site will be offline for approximately 30 minutes. Please save your work before this time.

Maintenance Notice - Upgrade of labkey.org for Friday, September 9th 2022 @ 8pm Pacific Time

Fri Sep 09 12:22:03 PDT 2022

LabKey.org will be offline this evening at 8pm Pacific Time for an upgrade to LabKey 22.9 The site will be offline for approximately one hour. Please save your work before this time.

Make a Visit an integer

Tue Sep 06 16:18:02 PDT 2022

When setting up a new study if I pick visit, the users have the ability to enter decimal values for the visit. Ex (1.1000,1.2000, etc.) How do I change that so the visit can only be an integer (1,2,3, etc).

Download prolems community edition

Thu Aug 18 01:40:11 PDT 2022

When I try to download the community edition of LabKey I get the following error message (independent of the web browser I use): "The form was unable to submit. Please contact the site administrator." The same problem appears btw when I try to send the contact form. So, maybe there is a general issue with your website. Can someone help to solve the issue?

Installation error of labkey on mac

Sun Aug 14 14:19:53 PDT 2022

Hi I am trying to install labkey on mac but I get the below error when launching it. Would you please advise? Thanks HTTP Status 404 – Not Found Type Status Report Message The requested resource [/labkey] is not available Description The origin server did not find a current representation for the target resource or is not willing to disclose that one exists.

Freezer Rack Configurations

Fri Aug 12 09:13:43 PDT 2022

Hi, Is it possible to configure rack partitions? For example; Shelf01-->Rack01-->Partition01-->Plates Partition02-->Plates Partition03-->Plates etc.. I do not see any partition configure racks as a storage unit. The reason I ask is that we have various racks with different numbers of partitions, and in our case, we store up to 25 plates per partition. If I just configure rack01-->plates, there could be more than 100 plates, which isn't very clean to look at in the freezer view. Also, our partitions are divided by projects and researchers, so that would be lost in the freezer configuration. Thanks

A "pipeline-filewatcher" type job with pipeline task "Imports specimen using data file" reuses existing job record

Fri Aug 12 05:25:10 PDT 2022

A month or so ago we updated our labkey jobs to use the new "pipeline-filewatcher" type job with pipeline task "Imports specimen using data file". Since doing this, we have observed a strange behavior: instead of creating a new Job record for a new "Imports specimen using data file" task, LabKey re-uses the most recent previously-existing job record. See attachment. The attachment shows that the job was created on 2022-06-27 and last updated on 2022-08-12. When the task starts, it seems to re-use the old Job record. Every day, this record (with primary key rowId=98469) is re-used and modified to reflect that day's import. The job details page https://atlas.scharp.org/cpas/pipeline-status/HVTN/Tools%20and%20Reports/Specimen%20Management/details.view?rowId=98469 lists **all** previous runs in the log output (which I think will eventually make the page difficult to load). Is this behavior expected? In the past, a new Job record (with a "created on" set to the timestamp the task started) would be created. We also see this behavior on our staging system (running v22.3.9).

Maintenance Notice - Upgrade of labkey.org for Wednesday, August 10th 2022 @ 8pm Pacific Time

Wed Aug 10 12:21:34 PDT 2022

LabKey.org will be offline this evening at 8pm Pacific Time for an upgrade to LabKey 22.8 The site will be offline for approximately one hour. Please save your work before this time.

Artifactory Migration -- Completed

Tue Jul 19 16:46:53 PDT 2022

On Friday, July 22, we will be moving our Artifactory server and, as a consequence, the domain will be updated from artifactory.labkey.com to labkey.jfrog.io. We are working to update to the new URL in all gradle and npm files that reference the old URL in develop as well as our release branches for 21.11, 22.3, and 22.7. If you are not building your own standalone modules that reference the old URL, you won’t need to do anything other than pull down the latest code for the release you are building from. If you are building your own module or otherwise have references to artifactory.labkey.com, you will need to update these to labkey.jfrog.io. A simple find and replace of artifactory.labkey.com:443 and artifactory.labkey.com with labkey.jfrog.io should be all you need to do. Our recommended update steps are below. As a precaution, we recommend clearing the npm cache and the all node_modules directories prior to building. Please run these commands from the root directory of your enlistment: ``` bash npm cache clear --force #(Optional command -- only recommended if you are doing active React development) gradlew cleanNodeModules gradlew deployApp ``` The domain artifactory.labkey.com will remain for unauthenticated reading until 8/12. Please submit a ticket to your support portal or contact your Account Manager if you have any questions.

Maintenance Notice - Upgrade of labkey.org for Friday, July 15th 2022 @ 10pm Pacific Time

Fri Jul 15 10:57:37 PDT 2022

LabKey.org will be offline this evening at 10pm Pacific Time for an upgrade to LabKey 22.7 The site will be offline for approximately one hour. Please save your work before this time.

Tomcat service is getting by itself after almost 24 hours

Fri Jul 15 01:53:10 PDT 2022

**Tomcat service one our prod server is getting killed by itself and hence labkey is giving 502 error after almost 24 hours everyday from last 3 days. Labkey is running on EC2 instance on our server. I have checked logs but couldn't find anything which causes the service to stop.**

SQl WHERE statement trouble

Tue Jun 14 09:57:02 PDT 2022

Hi, I'm trying to use a vey simple WHERE statement in my SQL query but I keep getting an error saying could not resolve column. You documentation seems to suggest what I'm trying to do is possible so I'm a bit lost. I'm trying to do: SELECT * FROM miseq_results WHERE well = "A01" and I get this error: Query 'lists_temp_5991' has errors Edit Query Error on line 5: Could not resolve column: A01 edit lists_temp_5991 and your documentation says that it should be possible to use where to filter on a value, rather than column=column: Filter the results for certain values. Example: SELECT * FROM "Physical Exam" WHERE YEAR(Date) = 2010 Could someone help me with where I'm going wrong please? Katy

Maintenance Notice - Upgrade of labkey.org for Thursday, June 9th 2022 @ 9pm Pacific Time

Thu Jun 09 16:46:30 PDT 2022

LabKey.org will be offline this evening at 9pm Pacific Time for an upgrade to LabKey 22.6 along with additional maintenance tasks. The site will be offline for approximately two hours. Please save your work before this time.

Scheduled Maintenance - teamcity.labkey.org Friday 6/3/2022 7 AM PDT

Thu Jun 02 15:46:59 PDT 2022

We will be performing maintenance on the LabKey TeamCity server on Friday 06/03/2022 between 7 - 8 AM PDT. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted. We apologize for any inconvenience this may cause.

How to specify full path to project folder ?

Tue May 31 21:52:12 PDT 2022

Hi, I am looking at the code example for creating a list domain in https://github.com/LabKey/labkey-api-python/blob/develop/samples/domain_example.py If I want to add a subfolder to the project folder name, e.g. project_name ="Study/Study1" then the code crashes with the error: labkey.exceptions.ServerContextError: '"403: You don\'t have permission to create a new domain"' How can this problem be fixed ? Thanks in advance.

Maintenance Notice - Upgrade of labkey.org for Thursday, May 12th 2022 @ 9pm Pacific Time

Thu May 12 13:50:42 PDT 2022

LabKey.org will be offline this evening at 9pm Pacific Time for an upgrade to LabKey 22.5 The site will be offline for approximately one hour. Please save your work before this time.

Scheduled Maintenance - teamcity.labkey.org Thursday 5/5/2022 4-5PM PDT

Wed May 04 10:30:56 PDT 2022

We will be performing maintenance on the LabKey TeamCity server on Thursday 05/05/2022 between 4 PM - 5 PM PST. This maintenance only affects developers. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted. We apologize for any inconvenience this may cause.

Artifactory Configuration Change

Mon May 02 13:12:22 PDT 2022

On Thursday, May 5 at 8:00 Pacific time, we will be updating our Artifactory configuration such that our libs-release, plugins-release, and libs-snapshot repositories will no longer proxy for certain third-party maven repositories, including MavenCentral and https://plugins.gradle.org. You will likely not have to make any changes as a result of this reconfiguration since we have updated our ```build.gradle``` files in the develop branch as well as all currently supported release versions to declare the required external repositories separately. However, if you maintain your own ```build.gradle``` file that includes a ```repositories {}``` configuration, you may need to add ``` mavenCentral() ``` at the top of that configuration block or add a separate ``` maven { url: “https://some.repository.url” } ``` declaration in order to properly resolve external artifacts. If you have questions or problems as a result of this, please let us know.

Current user

Wed Apr 27 13:03:57 PDT 2022

Hello. How can I get the name of current user (current logged) in R Report? I need it for identification rows in excel file exported from R report. I tried it via res=GET("http://vav.fno.cz/login-whoAmI.api") prettify(rawToChar(res$content)) but no working, empty content. Thanks Lubomir

Java Vulnerability - Java upgrade recommended

Fri Apr 22 15:09:37 PDT 2022

We were recently made aware of a potential Java vulnerability affecting ECDSA (Elliptic Curve Digital Signature Algorithm) signatures. For more details, see https://nvd.nist.gov/vuln/detail/CVE-2022-21449 This vulnerability affects deployments that use ECDSA, however, we strongly recommend that every deployment immediately upgrade to the latest Java release, 17.0.3+7. As always, please reach out if you have any questions or concerns for us.

LabKey version 19.3.7

Tue Apr 19 11:32:18 PDT 2022

We are facing the log4j issue and cyber is asking us to upgrade Tomcat - Can someone tell me if Tomcat 9.0.31 will work without issues for LabKey verison 19.3.7. thank you Gina

Maintenance Notice - Upgrade of labkey.org for Wednesday, April 13th 2022 @ 9pm Pacific Time

Wed Apr 13 10:50:12 PDT 2022

LabKey.org will be offline this evening at 9pm Pacific Time for an upgrade to LabKey 22.4 The site will be offline for approximately one hour. Please save your work before this time.

Problems with uploading files

Wed Apr 06 22:16:59 PDT 2022

Dear Labkey I have installed a Labkey Server v19.1 or v21.3. When I upload a file in the files interface. I get the following error：“Couldn't create file on server. This may be a server configuration problem. Contact the site administrator.” Please help me to solve this problem. Deployment Environment for Labkey v19.1: Windows Server 2008 R2 SP1 PostgreSQL Version 9.52 Java Runtime Version12.0.2.10 Apache Tomcat Version 9.0.37 Deployment Environment for Labkey v21.3: Windows Server 2012 R2 PostgreSQL Version 13.1 Java Runtime Version 15.0.1.9 Apache Tomcat Version 9.0.40 Best Regards Bika

Spring MVC security vulnerability - LabKey upgrade required

Thu Mar 31 18:23:50 PDT 2022

Yesterday, the developers of Spring MVC announced a security vulnerability, [CVE-2022-22965](https://tanzu.vmware.com/security/cve-2022-22965). Spring is a popular open source library used by LabKey Server. We have assessed the vulnerability. While LabKey Server is fortunately not subject to the most commonly reported exploit variant, a customized attack against LabKey Server might succeed. In the interest of providing hotfixes as quickly as possible, LabKey has applied the Spring development team’s [recommended remediation](https://spring.io/blog/2022/03/31/spring-framework-rce-early-announcement) for software that cannot immediately adopt the latest Spring MVC releases (5.3.18 or 5.2.20). We will upgrade to Spring 5.3.x in a future release, but have tested that the current hotfix eliminates the security concern. By the end of the day today, the LabKey team will push new hotfixed builds to all Premium Edition Clients' support portal. We will also make these changes for all LabKey Cloud customers today which will involve a short server downtime. Community Edition clients should download the latest binaries and perform an upgrade. In order to minimize the impact of this vulnerability, all administrators must upgrade their installations immediately. As always, please reach out if you have any questions or concerns for us.

Maintenance Notice - Update of labkey.org for Monday, March 29th 2022 @ 9pm PST

Tue Mar 29 19:55:08 PDT 2022

An upgrade of labkey.org will occur this evening at 9pm PST. The site is expected to be down for no more than 30 minutes. Please save your work before this time. We apologize for any inconvenience this may cause.

Maintenance Notice - Minor Update of labkey.org for Friday, March 18th 2022 @ 8pm PST

Fri Mar 18 16:03:22 PDT 2022

A minor update to labkey.org will occur this evening on Friday, March 18th 2022 @ 8pm PST. The server should be offline for no more than 30 minutes. Please save your work before this time.

Maintenance Notice - Upgrade of labkey.org to LabKey 22.3 for Thursday, March 10th 2022 @ 9pm PST

Thu Mar 10 12:12:26 PST 2022

LabKey.org will be offline this evening at 9pm PST for an upgrade to LabKey 22.3 The site will be offline for approximately one hour. Please save your work before this time.

Maintenance Notice: artifactory.labkey.com access will be limited for Friday, March 4th 2022 @ 4pm PST

Fri Mar 04 10:38:56 PST 2022

Special work is required for the artifactory.labkey.com server this early evening at 4pm PST. During this time, the TeamCity queue will be paused and the artifactory.labkey.com server will be intermittently available. The expected outage window will last no later than 5pm PST. We apologize for an inconvenience this may cause.

Help with specimen import error: Cache timeout for SchemaTableInfos for labkey, exceeding 300000ms limit

Tue Mar 01 05:15:16 PST 2022

On 2022-02-28 and 2022-02-22, our labkey server failed to import specimen data with an error we haven't seen before (stacktrace below). Are there any details on this error someone can provide? Is there a known way to address it? ... 28 Feb 2022 23:22:47,298 INFO : Updating vial rows 8040001 through 8050000. 28 Feb 2022 23:22:49,078 INFO : Updating processing locations on the specimen table... 28 Feb 2022 23:23:28,338 INFO : Complete. 28 Feb 2022 23:23:28,342 INFO : Updating first processed by initials on the specimen table... 28 Feb 2022 23:24:07,391 INFO : Complete. 28 Feb 2022 23:24:07,393 INFO : Updating vial availability... 28 Feb 2022 23:24:07,402 INFO : Marking vials unavailable based on Custom Query: study.UnavailableAccordingToLdms 28 Feb 2022 23:29:30,743 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/primary_types.tsv 28 Feb 2022 23:29:30,760 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/specimens.tsv 28 Feb 2022 23:29:30,764 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/column_translations.tsv 28 Feb 2022 23:29:30,769 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/additives.tsv 28 Feb 2022 23:29:30,772 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/labware_sample_types.tsv 28 Feb 2022 23:29:30,776 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/derivatives.tsv 28 Feb 2022 23:29:30,780 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/labs.tsv 28 Feb 2022 23:29:30,787 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615 28 Feb 2022 23:29:30,835 INFO : Failed to complete task 'org.labkey.api.specimen.pipeline.StudyImportSpecimenTask' 28 Feb 2022 23:29:30,836 ERROR: Cache timeout for SchemaTableInfos for labkey, exceeding 300000ms limit org.labkey.api.pipeline.PipelineJobException: Cache timeout for SchemaTableInfos for labkey, exceeding 300000ms limit at org.labkey.api.specimen.pipeline.AbstractSpecimenTask.doImport(AbstractSpecimenTask.java:162) at org.labkey.api.specimen.pipeline.AbstractSpecimenTask.run(AbstractSpecimenTask.java:67) at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:818) at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1055) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:304) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630) at java.base/java.lang.Thread.run(Thread.java:831) Caused by: java.lang.RuntimeException: Cache timeout for SchemaTableInfos for labkey, exceeding 300000ms limit at org.labkey.api.cache.BlockingCache.get(BlockingCache.java:130) at org.labkey.api.cache.BlockingCache.get(BlockingCache.java:91) at org.labkey.api.data.SchemaTableInfoCache.get(SchemaTableInfoCache.java:49) at org.labkey.api.data.DbScope.getTable(DbScope.java:1148) at org.labkey.api.data.DbSchema.getTable(DbSchema.java:426) at org.labkey.experiment.api.property.StorageProvisionerImpl.getSchemaTableInfo(StorageProvisionerImpl.java:604) at org.labkey.experiment.api.property.StorageProvisionerImpl.createTableInfoImpl(StorageProvisionerImpl.java:580) at org.labkey.api.exp.api.StorageProvisioner.createTableInfo(StorageProvisioner.java:71) at org.labkey.api.specimen.model.SpecimenTablesProvider.createTableInfo(SpecimenTablesProvider.java:201) at org.labkey.api.specimen.model.SpecimenTablesProvider.createTableInfo(SpecimenTablesProvider.java:125) at org.labkey.api.specimen.SpecimenSchema.getTableInfoSpecimen(SpecimenSchema.java:145) at org.labkey.api.specimen.SpecimenSchema.getTableInfoSpecimen(SpecimenSchema.java:138) at org.labkey.study.query.SpecimenDetailTable.getSpecimenAndVialFromSQL(SpecimenDetailTable.java:404) at org.labkey.study.query.SpecimenDetailTable.getFromSQL(SpecimenDetailTable.java:374) at org.labkey.api.data.AbstractTableInfo.getFromSQL(AbstractTableInfo.java:313) at org.labkey.query.sql.QueryTable._getSql(QueryTable.java:363) at org.labkey.query.sql.QueryTable.getFromSql(QueryTable.java:267) at org.labkey.query.sql.QTable.appendSql(QTable.java:85) at org.labkey.query.sql.QuerySelect._getSql(QuerySelect.java:1524) at org.labkey.query.sql.QuerySelect.getSql(QuerySelect.java:1468) at org.labkey.query.sql.QuerySelect$2.getFromSQL(QuerySelect.java:1296) at org.labkey.query.QueryServiceImpl.getSelectSQL(QueryServiceImpl.java:2624) at org.labkey.query.QueryServiceImpl.getSelectSQL(QueryServiceImpl.java:2440) at org.labkey.api.data.Table.getSelectSQL(Table.java:1055) at org.labkey.api.specimen.importer.RequestabilityManager$CustomQueryRule.getFilterSQL(RequestabilityManager.java:564) at org.labkey.api.specimen.importer.RequestabilityManager$RequestableRule.updateRequestability(RequestabilityManager.java:408) at org.labkey.api.specimen.importer.RequestabilityManager.updateRequestability(RequestabilityManager.java:828) at org.labkey.api.specimen.importer.RequestabilityManager.updateRequestability(RequestabilityManager.java:845) at org.labkey.api.specimen.importer.SpecimenImporter.updateCalculatedSpecimenData(SpecimenImporter.java:1083) at org.labkey.api.specimen.importer.SpecimenImporter.process(SpecimenImporter.java:390) at org.labkey.api.specimen.importer.SpecimenImporter.process(SpecimenImporter.java:306) at org.labkey.api.specimen.pipeline.AbstractSpecimenTask.doImport(AbstractSpecimenTask.java:132) ... 9 more

Maintenance Notice: artifactory.labkey.com upgrade for Monday, February 28th 2022 @ 7am PST

Thu Feb 24 17:03:30 PST 2022

An upgrade of https://artifactory.labkey.com will occur on Monday, Feb 28th 2022 @ 7am PST The estimated downtime will be approximately one hour. The TeamCity queue will be paused during this time. Please plan accordingly.

Scheduled Maintenance - LabKey TeamCity Server - Monday 2/28/2022 4PM-5PM PST

Thu Feb 24 15:22:09 PST 2022

We will be performing maintenance on the LabKey TeamCity server on Monday 02/28/2022 between 4 PM - 5 PM PST. This maintenance only affects developers. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted. We apologize for any inconvenience this may cause.

Maintenance Notice: artifactory.labkey.com upgrade for Friday, February 18th 2022 @ 7am PST

Thu Feb 17 16:27:14 PST 2022

Hello Everyone, An upgrade of https://artifactory.labkey.com will occur for Friday, February 18th @ 7am PST. The estimated outage time is approximately one hour. Please plan accordingly. Regards, Jon

Configuring PGAdmin4 to access the labkey database

Tue Feb 15 00:58:53 PST 2022

I'm attempting to add my local LabKey server to PGAdmin4. The server is running and accessible at: http://localhost:8080/labkey I followed the setup detailed here: https://www.labkey.org/Documentation/wiki-page.view?name=installComponents However, I am receiving an error: Unable to connect to server: connection to server at "localhost" (127.0.0.1), port 8080 failed: expected authentication requrest from server, but received H My PGAdmin settings are as follows: Host name/address: localhost Port: 8080 Maintenance database: labkey Username: labkey (used to setup tomcat - I've also tried the username I initially created when first accessing the labkey server at http://localhost:8080/labkey) Password: the database password associated with 'labkey' What am I doing wrong? Thanks!

Maintenance Notice - Update of labkey.org for Friday, February 11th 2022 @ 5:30pm PST

Fri Feb 11 17:02:13 PST 2022

An update to labkey.org will occur at 5:30pm PST. The site should be down for approximately 30 minutes. Please save your work before this time. We apologize for any inconvenience.

Maintenance Notice - Upgrade of labkey.org to LabKey 22.2 for Thursday, February 10th 2022 @ 9pm PST

Thu Feb 10 17:01:09 PST 2022

LabKey.org will be offline this evening at 9pm PST for an upgrade to LabKey 22.2 The site will be offline for approximately one hour. Please save your work before this time.

Conditional formatting for duplicate values

Tue Feb 08 09:11:43 PST 2022

Hi, I'm trying to set some conditional formatting to show when the same entry is in a column more than once. Is there way to do this with the conditional format criteria for a given field? Thanks, Katy

Recommended Linux OS

Tue Jan 25 12:45:48 PST 2022

Hi Labkey team, with the recent EOL of CentOS 8 (Dec 31,2021), I was wondering what is the recommended Linux operating system for Labkey Server? a) if we were to upgrade current installation b) if we were starting from scratch Thanks a lot, Tomas

Maintance Notice - Teamcity Server 01/24/2022 4:30PM - 5:00PM PDT

Mon Jan 24 16:03:47 PST 2022

We have scheduled a short maintenance window tonight at 4:30 PM PDT to install updates to Teamcity. We will pause the Teamcity queue, apply the updates and restart. We expect the downtime to be less than 30 minutes.

Query validation fails and API getSchema

Thu Jan 20 07:56:58 PST 2022

Following the upgrade to 21.11.4 (thanks to log4j), I am not able to retrieve a table called **RunRepresentativeDataState** for the **targetedms** schema via the Rlabkey package. _getSchema_ throws the following Error: _Status code = 404, Error message = Could not find the query_ Funnily enough the table is contained in the data frame returned by _getQueries_. However, one cannot use _getQueryDetails_ with this particular as expected. Running the query validation within Labkey confirms this error with: _targetedms.RunRepresentativeDataState: Query not found: RunRepresentativeDataState_ Is there any remedy to this? Thank you very much.

Maintenance Notice - Upgrade of labkey.org to LabKey 22.1 for Thursday, January 13th 2022 @ 7pm PST

Thu Jan 13 12:32:56 PST 2022

LabKey.org will be offline this evening at 7pm PST for an upgrade to LabKey 22.1 The site will be offline for approximately one hour. Please save your work before this time.

Issue with web sockets

Wed Jan 05 13:24:20 PST 2022

hi, We are working on setting up 21.11.3-4-nci on Ubuntu 18.04 and are having some problems with web sockets. We're getting 404 errors. Our LabKey installation resides on a separate server behind an Apache reverse proxy. The only allowed connection is TLS over port 8443. Here is our current Apache setup: RewriteEngine on RewriteCond ${HTTP:Upgrade} websocket [NC] RewriteCond ${HTTP:Connection} upgrade [NC] RewriteRule /(.*) wss://172.19.20.190:8443/$1 [P,L] ProxyPass / https://172.19.20.190:8443/ ProxyPassReverse / https://172.19.20.190:8443/ Any help or examples would be greatly appreciated. Thanks, bront

JSON as Lists column data type

Mon Dec 27 10:05:50 PST 2021

Hi guys, I am exploring LabKey Server (dockerized community version 21.10.0, PostgreSQL as database) for some features needed by my client, among others - custom JSON data for each entity recorded in list. I was able to find TEXT column data type as an option to record custom JSON content for record in list, practically as string. Keeping in mind that these are options to use JSON specific functions within PostgresSQL, https://www.labkey.org/Documentation/wiki-page.view?name=labkeysql#postgresJson could you guide me towards material, or give me advice about alternative and more appropriate ways to record and query back JSON in list records - through a more specific column data type, or some other way? Cheers and thanks, Adam