LabKey Support Forum

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SQl WHERE statement trouble
(4 responses) katy wiseman 2022-06-14 09:57

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

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Maintenance Notice - Upgrade of labkey.org for Thursday, June 9th 2022 @ 9pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-06-09 16:46

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.

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Scheduled Maintenance - teamcity.labkey.org Friday 6/3/2022 7 AM PDT
stuartm 2022-06-02 15:46

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.

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How to specify full path to project folder ?
(1 response) ambarish nag 2022-05-31 21:52

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.

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Maintenance Notice - Upgrade of labkey.org for Thursday, May 12th 2022 @ 9pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-05-12 13:50
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.
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Scheduled Maintenance - teamcity.labkey.org Thursday 5/5/2022 4-5PM PDT
stuartm 2022-05-04 10:30

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.

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Artifactory Configuration Change
(1 response) Susan Hert 2022-05-02 13:12

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.

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Current user
(1 response) lubomir pavliska 2022-04-27 13:03

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

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Java Vulnerability - Java upgrade recommended
hannahb 2022-04-22 15:09

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.

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LabKey version 19.3.7
(1 response) Gina M Scott 2022-04-19 11:32

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

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Maintenance Notice - Upgrade of labkey.org for Wednesday, April 13th 2022 @ 9pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-04-13 10:50
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.
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Problems with uploading files
(4 responses) Bika 2022-04-06 22:16

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

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Spring MVC security vulnerability - LabKey upgrade required
hannahb 2022-03-31 18:23

Yesterday, the developers of Spring MVC announced a security vulnerability, 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 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.

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Maintenance Notice - Update of labkey.org for Monday, March 29th 2022 @ 9pm PST
(1 response) Jon (LabKey DevOps) 2022-03-29 19:55
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.
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Maintenance Notice - Minor Update of labkey.org for Friday, March 18th 2022 @ 8pm PST
(1 response) Jon (LabKey DevOps) 2022-03-18 16:03
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.
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Maintenance Notice - Upgrade of labkey.org to LabKey 22.3 for Thursday, March 10th 2022 @ 9pm PST
(1 response) Jon (LabKey DevOps) 2022-03-10 12:12
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.
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Maintenance Notice: artifactory.labkey.com access will be limited for Friday, March 4th 2022 @ 4pm PST
(1 response) Jon (LabKey DevOps) 2022-03-04 10:38
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.
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Help with specimen import error: Cache timeout for SchemaTableInfos for labkey, exceeding 300000ms limit
tstellin 2022-03-01 05:15

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

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Maintenance Notice: artifactory.labkey.com upgrade for Monday, February 28th 2022 @ 7am PST
(1 response) Jon (LabKey DevOps) 2022-02-24 17:03
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.
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Scheduled Maintenance - LabKey TeamCity Server - Monday 2/28/2022 4PM-5PM PST
stuartm 2022-02-24 15:22

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.

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Maintenance Notice: artifactory.labkey.com upgrade for Friday, February 18th 2022 @ 7am PST
(1 response) Jon (LabKey DevOps) 2022-02-17 16:27
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
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Configuring PGAdmin4 to access the labkey database
(1 response) timcooper 2022-02-15 00:58

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!

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Maintenance Notice - Update of labkey.org for Friday, February 11th 2022 @ 5:30pm PST
(1 response) Jon (LabKey DevOps) 2022-02-11 17:02
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.
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Maintenance Notice - Upgrade of labkey.org to LabKey 22.2 for Thursday, February 10th 2022 @ 9pm PST
(1 response) Jon (LabKey DevOps) 2022-02-10 17:01
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.
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Conditional formatting for duplicate values
(1 response) katy wiseman 2022-02-08 09:11

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

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Recommended Linux OS
(2 responses) tvaisar 2022-01-25 12:45

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

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Maintance Notice - Teamcity Server 01/24/2022 4:30PM - 5:00PM PDT
(1 response) stuartm 2022-01-24 16:03

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.

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Query validation fails and API getSchema
(4 responses) christian opitz 2022-01-20 07:56

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.

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Maintenance Notice - Upgrade of labkey.org to LabKey 22.1 for Thursday, January 13th 2022 @ 7pm PST
(1 response) Jon (LabKey DevOps) 2022-01-13 12:32
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.
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Issue with web sockets
(3 responses) bront 2022-01-05 13:24

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

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JSON as Lists column data type
(3 responses) kotlenik 2021-12-27 10:05

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

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Upgrading Old Version of Labkey
(2 responses) dslater 2021-12-17 13:09

With the log4j vulnerability out, we were going to upgrade our version of Labkey but its been a few years since we have. We are currently on version 16.3. It looks like from https://www.labkey.org/Documentation/wiki-page.view?name=upgradeSupportPolicy, I have to do a bunch of intermediate upgrades. I need to get version 19.1 but the previous release page at https://www.labkey.org/Documentation/wiki-page.view?name=prevReleases does not have it. How am I able to get 19.1?

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High priority- Log4J security announcement
(8 responses) hannahb 2021-12-10 13:55

Yesterday, researchers announced a critical vulnerability (CVE-2021-44228) in Log4J, a popular Java logging library that LabKey Server versions 20.11 and later use.

All LabKey Server administrators must take action to protect their installations immediately, especially installations that are open on the public Internet. We are making these changes for all hosted customers today which will involve a short server downtime. You will receive notice of this downtime shortly.

Right now, administrators must add a system property (-Dlog4j2.formatMsgNoLookups=true) so that Java will disable the part of Log4J with the vulnerability. The exact mechanism for setting this property depends on how Tomcat is installed and launched.

For Linux installations, locate the JAVA_OPTS or CATALINA_OPTS environment variables for your Tomcat installation. These settings are typically located under the /etc/init.d/tomcat startup file, the /etc/systemd/system/tomcat.service startup file, the /etc/default/tomcat file, or the CATALINA_HOME/bin/setenv.sh script. Once the JAVA_OPTS or CATALINA_OPTS line is located, add -Dlog4j2.formatMsgNoLookups=true to the end of the line and restart Tomcat.

For Windows installations running Tomcat as a service, typically admins should use the “tomcat9w.exe” utility to adjust the settings. The following doc page shows how to adjust these kinds of settings in a variety of environments.

https://www.labkey.org/Documentation/wiki-page.view?name=configWebappMemory

If you are setting the system property, you can confirm that it was picked up after restarting Tomcat. Go to the Admin Console->System Properties and confirm that the “log4j2.formatMsgNoLookups” property is shown with the value “true”.

https://www.labkey.org/Documentation/wiki-page.view?name=siteManagement#diagnostics

Early next week we will release a patched version of LabKey Server that incorporates Log4J 2.15.0 that eliminates the need for the system property going forward. We will post this version to support portals as soon as it is available.

Please reach out via your support portal with questions and requests for help in making these changes.

For more details on the Log4J vulnerability itself, see https://github.com/advisories/GHSA-jfh8-c2jp-5v3q

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Cannot select 'Use SASL authentication'
(4 responses) mkuscuog 2021-12-10 12:32

Hello,

I am not able to check Use SASL authentication in Configure LDAP Configuration popup on Authentication page. It is always unchecked when I open the configuration popup back after successful Apply.

Is there anything I am missing here? I don't remember having this issue in the old UI (long time back)

Thanks,
Mehmet.

 Screen Shot 2021-12-10 at 12.28.06 PM.png 
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Maintenance Notice - Upgrade of labkey.org to LabKey 21.12 for Thursday, Dec 9th 2021 @ 10pm PST
(1 response) Jon (LabKey DevOps) 2021-12-09 16:57
LabKey.org will be offline this evening at 10pm PST for an upgrade to LabKey 21.12

The site will be offline for approximately one hour.

Please save your work before this time.
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KeyError CSRF
(1 response) rakesh yadav 2021-11-23 12:01

Hello Team,

We are trying to query the LabKey using python API but unfortunately not receiving a response but the status code is 200.

This was the response when we passed 'disable_csrf=True', while passing 'disable_csrf=False' we are getting the error "Key Error = CSRF"

Can you please look into the issue and help me where we are going wrong.

Thanks and Regards

 Screenshot 2021-11-23 at 8.52.07 PM.png  Screenshot 2021-11-23 at 8.56.29 PM.png 
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Maintenance Notice - Upgrade of labkey.org to LabKey 21.11 for Thursday, Nov 11th 2021 @ 9pm PST
Jon (LabKey DevOps) 2021-11-11 13:43
Hello everyone,

LabKey.org will be down this evening (Thursday, Nov 11th) for an upgrade to LabKey 21.11 starting at 9pm PST.

The server will be offline for approximately one hour.

Please save your work before this time.

LabKey Support
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Maintance Notice - Teamcity Server 10/28/2021 5PM - 6PM PDT
stuartm 2021-10-27 09:59

We will be performing maintenance on the LabKey TeamCity server on Thursday 10/28/2021 between 5 PM - 6 PM PDT. 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.

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Maximum length for a "Subject identifier"
johann pellet 2021-10-21 09:05

Hi,

I am trying to import some data in a dataset and I have for one entry this error:
ParticipantID value 'XXX_test13_LongAmp_100-extend_1pg' is too long, maximum length is 32 characters.

Howether, in the Dataset Definition, the type for a ParticipantID is text and the maximum text lenght is set to 4000 characters.
Do we have any lenght restriction for a subject identifier? If yes, could we increase the maximum length?

Thanks.

Regards,
Johann

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Retiring SVN server (svn.mgt.labkey.host) on November 1, 2021
(1 response) jeckels 2021-10-18 10:12

For LabKey Server version 20.11 (about one year ago), we completely migrated all code and configuration from out Subversion server into a variety of GitHub repositories. We retained full history on these files, so that you can see all of the edits made from the beginning of the project.

https://www.labkey.org/Premium/announcements-thread.view?rowId=20912

As we are no longer actively producing builds for older releases, we will be archiving the SVN server, svn.mgt.labkey.host, on or around November 1. While we will retain the ability to spin it up, we do not anticipate needing it again.

If you are using 20.11 or later, you shouldn't be affected at all. If you are using 20.7 or earlier and actively pulling code from Subversion, you'll be unable to do this anymore. Please reach out if you anticipate any problems.

Thanks,
Josh

view message
Maintenance Notice - Upgrade of labkey.org to LabKey 21.10 for Wednesday, Oct 13th 2021 @ 9pm PST
Jon (LabKey DevOps) 2021-10-13 15:10
Hello everyone,

LabKey.org will be down this evening (Wednesday, Oct 13th) for an upgrade to LabKey 21.10 starting at 9pm PST.

The server will be offline for approximately one hour.

Please save your work before this time.

LabKey Support
view message
NAb new study folder missing specimen tab
(4 responses) ehands 2021-10-05 09:38

Hi there,

I am trying to create a new protocol study for HVTN Nab Montefiori lab, and when creating a 'Study' sub-folder in the Montefiori Approved Runs folder, I am no longer seeing the option to select 'Repository Type: Standard Specimen Repository'. As a result, when I go in afterwards to upload specimens to this study folder, there is no Specimen tab available to do this. Please let me know how this can be resolved,

Thanks,
Ellie

 image (16).png 
view message
Update to test binaries in develop
Trey 2021-09-29 17:08

We are making some updates to the LabKey 'testAutomation' repository. They may require some action for folks but, hopefully, shouldn't be too disruptive.

  1. We are removing test.properties from source control and replacing it with test.properties.template. The gradle plugin (or the test harness) will generate test.properties from the template if it is missing when running tests.
    This change is intended to clean up folks' changelists a bit, similar to when we made template files for numerous IntelliJ config files that are frequently edited by IntelliJ.
    Additionally, the template file has been reorganized and annotated to help folks to understand and use the various properties.

  2. We are removing the chromedriver and geckodriver binaries from source control. The versions that are checked in are quite old and it isn't great practice to commit binaries into source control anyway. Going forward, you will need to install them manually.

What do you need to do?

  1. Backup your test.properties file. Once the change is merged and you've synced, run './gradlew :server:testAutomation:initProperties' to generate a new test.properties from the template file. Then copy your properties to the generated file (or restore your backup, but it won't have all the nice new annotations).
  2. Install up-to-date versions of geckodriver/chromedriver. Add/update 'webdriver.gecko.driver'/'webdriver.chrome.driver' properties in 'test.properties' to point at the corresponding binary. (Note: You can also install them somewhere seen by your PATH and forgo the driver properties)

I expect to merge these changes on Friday to let folks prepare and to wait for a needed gradle plugin change.

view message
Maintenance Notice - artifactory.labkey.com upgrade to Artifactory 7.X for Sunday, August 29th 2021 @ 8am PST
(1 response) Jon (LabKey DevOps) 2021-08-26 15:33
There will be an upgrade on artifactory.labkey.com to Artifactory 7.X for the last Sunday of this month (Sunday, August 29th) at 8am PST.

The estimated downtime will be for approximately 4 hours. During this time, the TeamCity build queue will be paused.
view message
Using Aliases for Sample Types
(1 response) ophira 2021-08-15 04:24

Hi,

We created several Sample Types in our Community Edition Labkey Server.
In one of our Sample Types, each row has its own Name which is determined by us during upload, say HA_###.
There is also the Alias field, where we can use to have a more meaningful name, which we can also change without changing the row's Primary Key.

A few questions about this:

  1. can multiple Aliases be assigned to a single row? on first glance it seems that only one Alias can be assigned to a single row. If this is impossible, we can of course concatenate different aliases to a single value ("alias1;alias2")
  2. are there any "special" traits to the Alias field? for example, I noticed that it's not unique, so two rows can have the same alias. I didn't find a lot on this topic in the Documentation, perhaps I missed something.

Thanks,
Ophir

view message
Changing Base Column Labels in a Study
(1 response) Ronny Kursawe 2021-08-12 00:51

We are using Labkey 17.3 and the import of study data with "Study Reload" via "Pipeline". Data are uploaded via WebDav into the pipeline folder.

If I got it correctly, the "datasets_metadata.xml" file allows to specify the names, labels and descriptions of columns. Besides that, there is an option to specify the "subjectColumnName" in the "study.xml" file.

After reloading the study, there is still a section of "Base Columns" (Please find a screenshot enclosed).

Is there an option to change the label and description of such columns? It seems that the settings of the "datasets_metadata.xml" do not work.

 basecolumns.PNG 
view message
edit on list deletes entries rather than updates them
(1 response) Thomas 2021-08-05 01:29

Hi,

I installed the latest labkey version 21.7.0 on windows 10 and have encountered a funny behaviour:
When I edit an entry of a list (pencil symbol) the row disappears from the list rather than being updated
I can add new rows to a list without problems, but edit = delete

Is this a problem with my setup? Has anyone else seen this?

Many thanks

view message
Project migration between servers-Incomplete
(1 response) WayneH 2021-06-30 07:19

Good morning,

we recently ran into an issue migrating a project between servers in our v18.2 community edition. We are preparing to migrate to a licensed current version but are really concerned about the problem we ran into.. On two different occasions one user's migration did not transfer over complete subfolder contents. I myself performed the same using the export/import tools and found that everything transferred over except for the file repository and the assay data (designs, batch/run data and tables). In my case I selected all of the options including files and all subfolder content.
The project is separated into three folders. One main folder and two subfolders within it. The assay data and file repository is in one of those subfolders. The assay data is in the top level folder although the designs/templates are in the subfolder where the file repository is located. I believe this is the structure we have.
Any thoughts on why we're having trouble migrating the project completely?

Thanks

Wayne

view message
Problem to Import FlowJo Workspace
(1 response) johann pellet 2021-06-11 07:59

Hi,

I have a problem with my dataset when I am trying to import a Flowjob Workspace in my Labkey server (LabKey Server 19.3.0).

11 Jun 2021 16:51:18,000 DEBUG: Analysis results contains 275 statistics, 76 graphs
11 Jun 2021 16:51:21,656 ERROR: FlowJo Workspace import failed
org.labkey.api.query.RuntimeValidationException: name: Value is too long for column 'name', a maximum length of 256 is allowed. Supplied value was 259 characters long.
    at org.labkey.api.data.Table.insert(Table.java:708)
    at org.labkey.flow.persist.FlowManager.ensureAttributeName(FlowManager.java:468)
    at org.labkey.flow.persist.FlowManager.ensureAttributeName(FlowManager.java:484)
    at org.labkey.flow.persist.FlowManager.ensureAttributeNameAndAliases(FlowManager.java:549)
    at org.labkey.flow.persist.FlowManager.ensureStatisticNameAndAliases(FlowManager.java:508)
    at org.labkey.flow.persist.AttributeSetHelper.ensureStatisticNames(AttributeSetHelper.java:109)
    at org.labkey.flow.persist.AttributeSetHelper.prepareForSave(AttributeSetHelper.java:89)
    at org.labkey.flow.script.WorkspaceJob.extractAnalysis(WorkspaceJob.java:371)
    at org.labkey.flow.script.WorkspaceJob.createExperimentRun(WorkspaceJob.java:170)
    at org.labkey.flow.script.WorkspaceJob.createExperimentRun(WorkspaceJob.java:148)
    at org.labkey.flow.script.AbstractExternalAnalysisJob.doRun(AbstractExternalAnalysisJob.java:233)
    at org.labkey.flow.script.WorkspaceJob.doRun(WorkspaceJob.java:138)
    at org.labkey.flow.script.FlowJob.run(FlowJob.java:76)
    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: name: Value is too long for column 'name', a maximum length of 256 is allowed. Supplied value was 259 characters long.
    at org.labkey.api.query.RuntimeValidationException.<init>(RuntimeValidationException.java:36)
    ... 19 more
11 Jun 2021 16:51:21,693 INFO : Job completed at 2021-06- 16:51
11 Jun 2021 16:51:21,693 INFO : Elapsed time 40.326s```

The 'name' is too long to be inserted in the database (as I undestand).  Could you please tell me what name refers to this value.

Thank you.

Regards,
Johann
view message
Maintenance Notice - artifactory.labkey.com update for Thursday, June 10th 2021 @ 8am PDT
(1 response) Jon (LabKey DevOps) 2021-06-08 15:53

The artifactory.labkey.com server will be taken offline for maintenance on Thursday, June 10th 2021 @ 8am PDT for approximately 30 minutes max.

During this time, the site will be unavailable and the TeamCity build queue will be paused.

We apologize for any inconvenience this may cause.

view message
Maintenance Notice: Artifactory outage for Friday, June 4th 2021 @ 8am PST
(1 response) Jon (LabKey DevOps) 2021-06-03 14:42

The artifactory.labkey.com server will be taking offline for maintenance on Friday, June 4th 2021 @ 8am PST for approximately 30 minutes max.

During this time, the site will be unavailable and the TeamCity build queue will be paused.

We apologize for any inconvenience this may cause.

view message
Labkey Community Edition Consulting
(1 response) ophira 2021-06-02 01:25

Hello,

We started using Labkey Community Edition. For now, we are trying to avoid the costs of Premium editions, at least until we are certain that this solution is right for our organization.

However, we would love to consult with more experienced people regarding some design and implementation topics.
For this purpose, we are looking for someone who offers consulting services.

Are there organizations/individuals outside of Labkey who offer such a service?

Thanks,
Ophir

view message
Maintenance Notice: Migration of artifactory.labkey.com for Sunday, May 30th @ 12pm PST
(1 response) Jon (LabKey DevOps) 2021-05-27 15:18

We will be working to migrating the current artifactory.labkey.com instance to a new server starting on Sunday, May 30th @ 12pm PST

During this time, all TeamCity jobs will be paused and Artifactory will be unavailable during the migration.

The estimated downtime is approximately seven hours.

We apologize for any inconvenience this may cause.

view message
Creating a single survey that posts data to multiple lists
(1 response) caroline norris 2021-05-20 04:03

Is is possible to use the Survey feature to create a single survey that posts data to more than one list on submission?

There is no information on how to do this in the Survey documentation, so just wondering if it's possible to do so without any custom development on our part?

view message
R Reports - R markdown- knitr pandoc - The input must be a UTF-8 encoded text.
(2 responses) hilariagrieve 2021-05-19 08:19

Hi,
I have installed The last version of labkey Server in a new Server and I reload the study folder with some troubleshoots but finally I did it.
But, I have problems with R reports. I remember that I have the same problem with the old server and I solve It but I don't know how.
I was researching and tried a lot of things but I didn't make it.
The problem is with r markdown, knitr and the error is that the imput must be a UTF-8 encondec text, and The file script.Rmd is not encoded in UTF-8.
I tried to set the File : Save with Encoding UTF-8 in R studio like https://support.rstudio.com/hc/en-us/articles/200532197-Character-Encoding.

Here is the log file:

Error executing command
javax.script.ScriptException: javax.script.ScriptException: An error occurred when running the script 'script.R', exit code: 1).

processing file: script.Rmd

|
| | 0%
|
|.......... | 14%
ordinary text without R code

|
|.................... | 29%
label: labkey (with options)
List of 1
$ echo: logi FALSE

|
|.............................. | 43%
ordinary text without R code

|
|........................................ | 57%
label: setup (with options)
List of 7
$ echo : logi FALSE
$ cache : logi TRUE
$ results : chr "hide"
$ warning : logi FALSE
$ comment : logi FALSE
$ message : logi FALSE
$ comments: chr ""

Loading required package: httr
Loading required package: jsonlite
Executing: pandoc -t html -o "script.html" "script.Rmd"
[WARNING] Could not deduce format from file extension .Rmd
Defaulting to markdown
UTF-8 decoding error in script.Rmd at byte offset 995 (e9).
The input must be a UTF-8 encoded text.
Quitting from lines 24-32 (script.Rmd)
Error in (function (input, format, ext, exec, cfg) : conversion failed
Calls: render ... eval -> eval -> <Anonymous> -> mapply -> <Anonymous>
Adem�s: Warning messages:
1: In readLines(con, warn = FALSE) :
entrada inv�lida encontrada en la conexi�n de entrada 'script.Rmd'
2: In xfun::read_utf8(input) :
The file script.Rmd is not encoded in UTF-8. These lines contain invalid UTF-8 characters: 15, 46, 53, 59, 61, 72, ...
3: In read_utf8(input[1]) :
The file script.Rmd is not encoded in UTF-8. These lines contain invalid UTF-8 characters: 15, 46, 53, 59, 61, 72, ...

Ejecuci�n interrumpida

view message
Trouble Starting LabKey Server Community Edition
(4 responses) etr 2021-05-07 15:27

Hello,
I am trying to install the Labkey server but I am experiencing some difficulties.
Please keep in mind I am not a usual user of either windows or tomcat for that matter.
Running on Windows Server 2012 R2, openjdk 16, tomcat 9.0

Catalina- log says something like this:

07-May-2021 22:05:40.736 SEVERE [Catalina-utility-2] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying deployment descriptor [C:\labkey\apps\tomcat\conf\Catalina\localhost\labkey.xml]
        java.lang.IllegalStateException: Error starting child
                at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:720)
                at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:690)
                at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:706)
                at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:689)
                at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1881)
                at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
                at java.util.concurrent.FutureTask.run(Unknown Source)
                at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
                at java.util.concurrent.AbstractExecutorService.submit(Unknown Source)
                at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:582)
                at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:472)
                at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1660)
                at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:315)
                at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
                at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1151)
                at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1353)
                at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1357)
                at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1335)
                at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
                at java.util.concurrent.FutureTask.runAndReset(Unknown Source)
                at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
                at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
                at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
                at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
                at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
                at java.lang.Thread.run(Unknown Source)
        Caused by: org.apache.catalina.LifecycleException: Error starting the loader
                at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:432)
                at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
                at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5028)
                at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
                at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:717)
                ... 25 more
        Caused by: java.lang.UnsupportedClassVersionError: org/labkey/bootstrap/LabKeyBootstrapClassLoader has been compiled by a more recent version of the Java Runtime (class file version 58.0), this version of the Java Runtime only recognizes class file versions up to 52.0
                at java.lang.ClassLoader.defineClass1(Native Method)
                at java.lang.ClassLoader.defineClass(Unknown Source)
                at java.security.SecureClassLoader.defineClass(Unknown Source)
                at java.net.URLClassLoader.defineClass(Unknown Source)
                at java.net.URLClassLoader.access$100(Unknown Source)
                at java.net.URLClassLoader$1.run(Unknown Source)
                at java.net.URLClassLoader$1.run(Unknown Source)
                at java.security.AccessController.doPrivileged(Native Method)
                at java.net.URLClassLoader.findClass(Unknown Source)
                at java.lang.ClassLoader.loadClass(Unknown Source)
                at java.lang.ClassLoader.loadClass(Unknown Source)
                at java.lang.Class.forName0(Native Method)
                at java.lang.Class.forName(Unknown Source)
                at org.apache.catalina.loader.WebappLoader.createClassLoader(WebappLoader.java:536)
                at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:408)
                ... 29 more
07-May-2021 22:05:40.738 INFO [Catalina-utility-2] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of deployment descriptor [C:\labkey\apps\tomcat\conf\Catalina\localhost\labkey.xml] has finished in [10] ms

If anyone can provide some info please.

Thanks,
ET

view message
Maintenance Notice: Migration of artifactory.labkey.com for Thursday, April 29th @ 8am PST
(1 response) Jon (LabKey DevOps) 2021-04-27 11:13

We will be working to migrating the current artifactory.labkey.com instance to a new server starting on Thursday, April 29th at 8am PST.

During this time, all TeamCity jobs will be paused and Artifactory will be unavailable during the migration.

The estimated downtime is approximately two hours.

We apologize for any inconvenience this may cause.

view message
Updates to IntelliJ config files in develop
Susan Hert 2021-04-26 11:43

I have just merged PR #66 in the LabKey/server repository to bring in some changes to the IntelliJ configuration files and to add a couple of tasks for setting up IntelliJ to use the LabKey default configurations.  These changes should mean you have to adjust fewer IntelliJ configurations manually when starting with a new enlistment and have fewer files in your "Never Commit These" change list.  The changes work best with IntelliJ Version 2021.1 or later.  Older (but not ancient) versions work as well but require more manual adjustment.

To avoid conflicts between the configuration files that this change deleted and the ones that get modified by Intellij for your local installation, please do the following before pulling down these changes:

  • Shut down IntelliJ
  • Make a copy of your .idea directory (just in case)
  • Stash the current changes in the .idea directory using git stash push -- .idea/ from the root of your LabKey enlistment
  • git pull
  • ./gradlew ijConfigure
  • Open your existing project in IntelliJ

Then:

  • Open your project in IntelliJ
  • Do a Refresh in the Gradle window.
  • If you are not using IntelliJ version 2021.1 or later
    • Edit the LabKey Dev configuration to fix the module classpath so it uses labkey-server.server.modules.platform.api.main
    • Edit the LabKey Production configuration to fix the module classpath so it uses labkey-server.server.modules.platform.api.main

If you are developing with TypeScript:

  • Go to Preferences -> Appearance & Behavior -> Path Variables and set a value for NODE_PATH that will point to the node binary used by the build (e.g., C:\Development\labkeyHome\build.node\node-v12.16.0\bin\node, or, for Mac or Linux, use the symlink created by the build that is version-independent: /Users/develop/labkeyHome/.node/node/bin/node).
  • Go to Preferences -> Languages & Frameworks -> Typescript and verify the Node interpreter settings. The interpreter should be pointing to the node version that you set as the NODE_PATH variable. If not, or if you need to change this at some point, you can do that here.

For instructions on setting up a development environment from scratch, see this page.

If you have any problems that seem related to these changes, please let us know.

Susan

view message
How to create and append to a dataset using R labkey API?
(1 response) kristen dang 2021-04-23 10:42

Hello,
I am having several errors when trying to use the R labkey API to create and load a dataset. I am able to load this same file as a dataset using the GUI, but cannot seem to do it with the R API.

When creating the design, I get an error about reserved fields. In the GUI I resolve this by matching specific upload file column names with reserved field names. I don't know how to do this in R:

fields <- labkey.domain.inferFields(baseUrl=labkey.getBaseUrl(), folderPath=fp, df=inDF)
 dd <- labkey.domain.createDesign(name=batch$batch, fields=fields)
 k = which(dd$fields$name %in% c("ParticipantId", "visitCode", "sampleName"))
 dd$fields$isPrimaryKey[k] = TRUE

    eaLabkeyList = labkey.domain.create(baseUrl=labkey.getBaseUrl(), folderPath=fp, domainKind="StudyDatasetVisit", domainDesign=dd, options=list(categoryName="SequencingTest",demographics=FALSE,useTimeKeyField=FALSE,keyPropertyName="sampleName"))

Error:

HTTP request was unsuccessful. Status code = 500, Error message = java.lang.IllegalArgumentException: Property: ParticipantId is reserved or exists in the current domain.

Once I create this file in the web UI, I'm not able to append other data to it by upload since the column names don't match. Is there some documentation for how to take care of the key name matching so I can do this in R?

Thanks for any help.

view message
How to use createAndLoad for Lists or Datasets using R?
(1 response) kristen dang 2021-04-23 10:32

Hello,
In the R labkey package, I tried to use to use the labkey.domain.createAndLoad to create and load a list, but was unable to understand the error message. I'd like to be able to use this command for List and Dataset creation. Can you please suggest how I should address the issue with "strictFieldValidation?" I included my command and the response below.

labkey.domain.createAndLoad(baseUrl = labkey.getBaseUrl(),folderPath=fp,name="sequencing_vendor_QC_metrics", df=combined, domainKind="VarList")

Error in handleError(response, haltOnError) : 
HTTP request was unsuccessful. Status code = 500, Error message = Unrecognized field "strictFieldValidation" (class org.labkey.list.model.ListDomainKindProperties), not marked as ignorable (22 known properties: "entireListTitleTemplate", "discussionSetting", "keyName", "name", "entireListIndexSetting", "titleColumn", "eachItemBodyTemplate", "fileAttachmentIndex", "allowDelete", "listId", "eachItemBodySetting", "lastIndexed", "description", "allowExport", "eachItemTitleTemplate", "domainId", "entireListIndex", "allowUpload", "keyType", "entireListBodySetting", "entireListBodyTemplate", "eachItemIndex"])

view message
How to make a link in a List to a file in the Files tab using R API?
(1 response) kristen dang 2021-04-22 17:54

Hello,
I have several Lists that include a column listing relevant files which are also loaded in the Files tab. I would like to add a link to the List that points to the file in the Files tab. There is an extensive page on how to do this with the GUI, but I am not sure how to do it with the R labkey package. Can this be done with R?

view message
Maintenance Notice: Migration of artifactory.labkey.com for Monday, April 26th @ 8am PST
(1 response) Jon (LabKey DevOps) 2021-04-22 13:20
We will be working to migrating the current artifactory.labkey.com instance to a new server starting on Monday, April 26th at 8am PST.

During this time, all TeamCity jobs will be paused and Artifactory will be unavailable during the migration.

The estimated downtime is approximately two hours.

We apologize for any inconvenience this may cause.
view message
RLabkey: Permissions when inserting/updating rows
(1 response) christian opitz 2021-04-13 00:55

I am trying to update/insert rows using the provided R library. Trying with .netrc, explicitly setting admin user/password via labkey.setDefaults() or only using the API key generated as admin results in:

Error in handleError(response, haltOnError) :
HTTP request was unsuccessful. Status code = 403, Error message = User does not have permission to perform this operation.

Everything (API key, credentials) are tight to the administrator. I can however retrieve the data using getRows() or selectRows().

The target of the operation is a targetedmslist table that was imported via Skyline.

Any help is appreciated.

Thank you.

view message
Maintenance Notice: Migration of artifactory.labkey.com for Monday, April 5th @ 11am PST
(1 response) Jon (LabKey DevOps) 2021-04-02 14:54
We will be working to migrating the current artifactory.labkey.com instance to a new server starting on Monday, April 5th at 11am PST.

During this time, all TeamCity jobs will be paused and Artifactory will be unavailable during the migration.

The estimated downtime is approximately one hour.

We apologize for any inconvenience this may cause.
view message
Problem while using the "Import and Export a XAR File" tutorial
(4 responses) ophira 2021-03-22 09:50

Hello,

I am trying to understand the Experiment module using the documentation by following these instructions:
https://www.labkey.org/Documentation/wiki-page.view?name=xarSamples

I got stuck here:

  • Download either XarTutorial.zip or XarTutorial.tar.gz and extract to your computer.
  • Select the Pipeline tab, and click Setup.
  • Click Set a pipeline override.
  • Enter the path to the directory where you extracted the files.
  • Click Save.

On step “Select the Pipeline tab, and click Setup.”, I didn’t find any “Setup” and “Set a pipeline override” anywhere.
Should this feature work in the Trial version? In the CE version?

My trial server:
https://oa1.trial.labkey.host/home/project-begin.view?

Tried the above on the "Example Project" as well as a newly created project named "proj4experiment".

Thanks,
Ophir

view message
Custom Postgres Method in Labkey Query
(2 responses) sleisle 2021-03-17 16:08

Hello Labkey,

I'm attempting to use a custom postgres method to join two tables in a file-based module query, but when running the query, it errors out stating "Method not found". I saw a similar forum post from 2013 that talked about this being unsupported, but seeing how old the post was I figured I should check if it has been updated. Is there any way to call a custom method, or is it unsupported?

Thanks!

view message
Editor permission without deleting permission.
(4 responses) Chichero 2021-03-15 11:22

Dear LabKey team,

Is there a way to allow a user to insert and update data in a dataset and a sample set without allowing for deleting this data?

Could you propose a workaround if it is not possible?

Thank you,
Natalia

view message
Upgrade Labkey
(1 response) hilariagrieve 2021-03-04 03:13

Hi, I have installed the 17.2 version of Labkey Server Community Edition. I designed and implemented a LIMS for the Forensic Genetics Laboratory. I want to upgrade to 20.11 version but I read that is not recomended to upgrade from 17.2 to 20.3 directly. Can you send me the old versions to upgrade step by step the versions of labkey? I tried to installed a new instance of labkey and import the study folder but the assay data is not imported correctly. Thanks you very much. Hilaria Grieve

view message
Module Upgrade : Error: Unable to initialize search index.
(1 response) hilariagrieve 2021-03-03 06:17

ALL SITE ERRORS returns me this log file. Can you help me?

ERROR LuceneSearchServiceImpl 2021-03-03 09:24:27,258 Module Upgrade : Error: Unable to initialize search index. Search will be disabled and new documents will not be indexed for searching until this is corrected and the server is restarted.
java.nio.file.NoSuchFileException: C:\Program Files\Apache Software Foundation\Tomcat 8.5\temp\labkey_full_text_index_4zf_Lucene50_0.tip
at sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:79)
at sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:97)
at sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:102)
at sun.nio.fs.WindowsFileSystemProvider.newFileChannel(WindowsFileSystemProvider.java:115)
at java.nio.channels.FileChannel.open(FileChannel.java:287)
at java.nio.channels.FileChannel.open(FileChannel.java:335)
at org.apache.lucene.store.MMapDirectory.openInput(MMapDirectory.java:238)
at org.apache.lucene.codecs.blocktree.BlockTreeTermsReader.<init>(BlockTreeTermsReader.java:176)
at org.apache.lucene.codecs.lucene50.Lucene50PostingsFormat.fieldsProducer(Lucene50PostingsFormat.java:445)
at org.apache.lucene.codecs.perfield.PerFieldPostingsFormat$FieldsReader.<init>(PerFieldPostingsFormat.java:292)
at org.apache.lucene.codecs.perfield.PerFieldPostingsFormat.fieldsProducer(PerFieldPostingsFormat.java:372)
at org.apache.lucene.index.SegmentCoreReaders.<init>(SegmentCoreReaders.java:109)
at org.apache.lucene.index.SegmentReader.<init>(SegmentReader.java:74)
at org.apache.lucene.index.ReadersAndUpdates.getReader(ReadersAndUpdates.java:145)
at org.apache.lucene.index.ReadersAndUpdates.getReadOnlyClone(ReadersAndUpdates.java:197)
at org.apache.lucene.index.StandardDirectoryReader.open(StandardDirectoryReader.java:103)
at org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:473)
at org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:103)
at org.apache.lucene.search.SearcherManager.<init>(SearcherManager.java:108)
at org.apache.lucene.search.SearcherManager.<init>(SearcherManager.java:76)
at org.labkey.search.model.WritableIndexManagerImpl.<init>(WritableIndexManagerImpl.java:106)
at org.labkey.search.model.WritableIndexManagerImpl.get(WritableIndexManagerImpl.java:86)
at org.labkey.search.model.LuceneSearchServiceImpl.initializeIndex(LuceneSearchServiceImpl.java:232)
at org.labkey.search.model.LuceneSearchServiceImpl.start(LuceneSearchServiceImpl.java:327)
at org.labkey.search.SearchModule.startBackgroundThreads(SearchModule.java:190)
at org.labkey.api.module.ModuleLoader.attemptStartBackgroundThreads(ModuleLoader.java:1309)
at org.labkey.api.module.ModuleLoader.initiateModuleStartup(ModuleLoader.java:1286)
at org.labkey.api.module.ModuleLoader.afterUpgrade(ModuleLoader.java:1451)
at org.labkey.api.module.ModuleLoader.lambda$startNonCoreUpgradeAndStartup$3(ModuleLoader.java:1433)
at java.lang.Thread.run(Thread.java:748)
ERROR StudyReload 2021-03-03 09:24:27,508 QuartzScheduler_Worker-1 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:29:27,418 QuartzScheduler_Worker-2 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:34:27,422 QuartzScheduler_Worker-3 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:39:27,426 QuartzScheduler_Worker-5 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:44:27,415 QuartzScheduler_Worker-6 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:49:27,419 QuartzScheduler_Worker-7 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:54:27,423 QuartzScheduler_Worker-9 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:59:27,427 uartzScheduler_Worker-10 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:04:27,416 QuartzScheduler_Worker-1 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:09:27,420 QuartzScheduler_Worker-3 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:14:27,424 QuartzScheduler_Worker-4 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:19:27,428 QuartzScheduler_Worker-5 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:24:27,417 QuartzScheduler_Worker-7 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:29:27,421 QuartzScheduler_Worker-8 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:34:27,425 QuartzScheduler_Worker-9 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:39:27,429 QuartzScheduler_Worker-1 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:44:27,418 QuartzScheduler_Worker-2 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)

view message
Removing server/modules/build.gradle file
(1 response) Susan Hert 2021-02-05 11:44

In order to do away with some flawed logic related to applying the LabKey gradle plugins, I am planning to remove the server/modules/build.gradle file early next week in our develop branches, in time for LabKey Server version 21.3.0. If you are maintaining your own local modules, you may need to add or update your build.gradle files in order to apply the plugin that had been being applied from this file. See this page for more details.

After this file is removed, and we update to the 1.25.0 version of the LabKey Gradle plugins, if the Gradle plugin detects a module that has a module.properties file but does not have a module task, a warning like the following will be shown at the end of running the deployApp command:

The following projects have a 'module.properties' file but no 'module' task. These modules will not be included in the deployed server. You should apply either the 'org.labkey.build.fileModule' or 'org.labkey.build.module' plugin in each project's 'build.gradle' file.
        :server:modules:myModule
        :server:modules:otherModule

You can fix this by applying the appropriate plugin as suggested or by defining your own module task that creates the .module file needed for inclusion in your LabKey Server instance.

Also, if you previously had a build.gradle file that references configurations, tasks, etc. defined in the Gradle plugins, you may encounter errors during the configuration phase when running a Gradle task like the following.

FAILURE: Build failed with an exception.

* Where:
Build file '/path/to/Development/labkey/root/server/modules/myModule/build.gradle' line: 6

* What went wrong:
A problem occurred evaluating project ':server:modules:myModule'.
> Could not find method implementation() for arguments com.sun.mail:jakarta.mail:1.6.5 on object of type org.gradle.api.internal.artifacts.dsl.dependencies.DefaultDependencyHandler.

This is fixed in the same way, by applying the plugin that had been being applied in server/modules/build.gradle.

If you have questions or encounter problems, please let us know.

Susan

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Rlabkey webdav access failing with 401 unauthorized
(3 responses) Marcel de Leeuw 2021-01-31 06:31

Hello,

We are unsuccessful acessing files on the labkey server through Rlabkey. Selectrows in a folder succeeds, bu then acessing files through webdav in the same folder for the same user (API key) fails with error code 401 (unauthorized). Aslo, webdav through the browser works fine. What needs to be configured for webdav through Rlabkey?

baseurl <- "http://bifx.mrmhealth.com:8080/labkey"
folderpath <- "/MRM Health/M002/Pre-clinical/E-00065 Rat"
setwd("~/labkey/M002/Pre-clinical")

library(Rlabkey)

labkey.mgx <- labkey.selectRows(
  baseUrl = baseurl,
  folderPath=folderpath, 
  schemaName="assay.General.Whole metagenome", 
  queryName="Runs", 
  viewName="", 
  colNameOpt="rname")
datafile <- gsub(".+@files/(.+)", "\\1", labkey.mgx$realtiveabundances)

labkey.webdav.get(
  baseUrl=baseurl,
  folderPath=folderpath,
  remoteFilePath=datafile,
  localFilePath="rat.mgx.tsv",
  overwrite=T)

Error in handleError(response, haltOnError) :
HTTP request was unsuccessful. Status code = 401, Error message = /_webdav/MRM Health/M002/Pre-clinical/E-00065 Rat/@files/assaydata/ca-mrm-bacteria-filtered-ra_2020_12_04_20_04.tsv

Thanks and regards

view message
Troubleshotting Reloading Study in a new server with a new version of Labkey Server
(2 responses) hilariagrieve 2021-01-26 08:03

Hi!
I have problems reloading the Study in a new version of Labkey Server in another Server.
I have instaled in one server Labkey v17 with a Study Proyect data.
Now we have e new server, and I installed the new version of labkey v20.7. I tried to creat the same Study Proyect exporting the Study Proyect from the old server and importing this export in the new server.
Everything was fine untill the pipeline got an error.

This is the log file:
26 ene. 2021 11:55:33,943 INFO : Starting to run task 'org.labkey.study.importer.StudyImportInitialTask' at location 'webserver'
26 ene. 2021 11:55:36,082 INFO : Reloading study from LIMS SGFER_2021-01-26_10-44-53.folder.zip
26 ene. 2021 11:55:36,222 INFO : Loading top-level study properties (label, start/end date, description, etc.)
26 ene. 2021 11:55:40,028 INFO : Done importing top-level study properties (label, start/end date, description, etc.)
26 ene. 2021 11:55:49,286 INFO : Loading QC states
26 ene. 2021 11:55:50,341 INFO : Done importing QC states
26 ene. 2021 11:55:50,349 INFO : Loading treatment data tables
26 ene. 2021 11:55:51,090 INFO : Done importing treatment data tables
26 ene. 2021 11:55:51,138 INFO : Loading assay schedule tables
26 ene. 2021 11:55:51,620 INFO : Done importing assay schedule tables
26 ene. 2021 11:55:51,780 INFO : Loading datasets manifest from datasets_manifest.xml
26 ene. 2021 11:55:51,900 INFO : Loading dataset schema from datasets_metadata.xml
26 ene. 2021 11:55:56,663 INFO : Successfully completed task 'org.labkey.study.importer.StudyImportInitialTask'
26 ene. 2021 11:55:56,910 INFO : Starting to run task 'org.labkey.study.pipeline.StudyImportDatasetTask' at location 'webserver'
26 ene. 2021 11:55:57,055 INFO : Start batch Lims SGFER.dataset
26 ene. 2021 11:55:57,079 INFO : Causas: Starting delete
26 ene. 2021 11:55:57,098 INFO : Causas: Deleted 5075 rows
26 ene. 2021 11:55:57,130 INFO : Causas: Starting import from dataset5001,tsv
26 ene. 2021 11:56:14,049 DEBUG: commit complete
26 ene. 2021 11:56:14,084 INFO : Causas: Successfully imported 5091 rows from dataset5001,tsv
26 ene. 2021 11:56:14,126 INFO : Secuenciacion ABI: Starting delete
26 ene. 2021 11:56:14,128 INFO : Secuenciacion ABI: Deleted 0 rows
26 ene. 2021 11:56:14,147 INFO : Secuenciacion ABI: Starting import from dataset5003,tsv
26 ene. 2021 11:56:15,202 ERROR: dataset5003,tsv -- Two columns mapped to target column: CausasId
26 ene. 2021 11:56:15,339 INFO : Extracción de ADN: Starting delete
26 ene. 2021 11:56:15,341 INFO : Extracción de ADN: Deleted 0 rows
26 ene. 2021 11:56:15,344 INFO : Extracción de ADN: Starting import from dataset5004,tsv
26 ene. 2021 11:56:15,716 ERROR: dataset5004,tsv -- Two columns mapped to target column: CausasId
26 ene. 2021 11:56:15,737 INFO : Cuantificación Fluorimétrica: Starting delete
26 ene. 2021 11:56:15,739 INFO : Cuantificación Fluorimétrica: Deleted 0 rows
26 ene. 2021 11:56:15,741 INFO : Cuantificación Fluorimétrica: Starting import from dataset5005,tsv
26 ene. 2021 11:56:15,899 ERROR: dataset5005,tsv -- Two columns mapped to target column: CausasId
26 ene. 2021 11:56:15,921 INFO : Cuantificación Real Time: Starting delete
26 ene. 2021 11:56:15,923 INFO : Cuantificación Real Time: Deleted 0 rows
26 ene. 2021 11:56:15,926 INFO : Cuantificación Real Time: Starting import from dataset5006,tsv
26 ene. 2021 11:56:16,017 ERROR: dataset5006,tsv -- Two columns mapped to target column: CausasId
26 ene. 2021 11:56:16,039 INFO : Amplificación por PCR: Starting delete
26 ene. 2021 11:56:16,041 INFO : Amplificación por PCR: Deleted 0 rows
26 ene. 2021 11:56:16,044 INFO : Amplificación por PCR: Starting import from dataset5007,tsv
26 ene. 2021 11:56:16,538 ERROR: dataset5007,tsv -- Two columns mapped to target column: CausasId
26 ene. 2021 11:56:16,545 INFO : Finish batch Lims SGFER.dataset
26 ene. 2021 11:56:16,549 INFO : Updating participant visits
26 ene. 2021 11:56:16,566 INFO : Updating participants
26 ene. 2021 11:56:16,749 INFO : Updating participant visit table
26 ene. 2021 11:56:16,750 INFO : Updating visit table
26 ene. 2021 11:56:16,752 INFO : Updating cohorts
26 ene. 2021 11:56:16,754 INFO : Clearing participant visit caches
26 ene. 2021 11:56:16,757 INFO : Finished updating participants
26 ene. 2021 11:56:16,807 INFO : Successfully completed task 'org.labkey.study.pipeline.StudyImportDatasetTask'

I attached a dataset file example that got that error, and this have 2 columns names that mapped to target column CausasId, "CaudasId" and "ParticipantId".

Please, can you help me to resolve this problem?
Everything is reloaded in the new study but the datasets data.
Thank you very much!
Hilaria

view message
GUI not fully loading
mitch blocher 2021-01-25 13:37

Ive noticed that occasionally The GUI will not display certain information such as scripts, Pop up boxed etc. I have ensured popups and JavaScript were enabled in my chrome browser, and cookies and Cache were deleted. All labkey servers worked fine except for one. The solution I found was to reset all settings in my chrome browser, however the specific culprit causing the issue was not found.

view message
Scheduled Maintenance: artifactory.labkey.com Friday January 22, 2021 @ 7 AM PDT
(1 response) Jon (LabKey DevOps) 2021-01-20 13:01
We will be performing scheduled maintenance on LabKey's artifactory server ( https://artifactory.labkey.com/ ) on Friday January 22, 2021 @ 7 AM PDT.

The expected downtime should be approximately 60-90 minutes.

This will affect build artifacts during this maintenance period.

While Artifactory is unavailable, you should use the --offline flag for gradle when building.

We are performing this maintenance to install the latest security patches for Artifactory and its underlying operating system.
view message
migration from standard server to docker and authentication
(1 response) ramez saour 2021-01-18 04:06

I have migrated labkey and tomcat7 config from standard host to docker image tomcat8 and same config as labkey, however, since moved to docker I cant authenticate to labkey portal. is there way to use local account (admin) or configure ldap connection inside docker?

I have also
<Resource name="ldap/ConfigFactory" auth="Container"
type="org.labkey.premium.ldap.LdapConnectionConfigFactory"
factory="org.labkey.premium.ldap.LdapConnectionConfigFactory"
host="10.5.0.9"
port="389"
principal="CN=zSvcADBindRDLK,OU=ServiceAccounts,OU=GEL,DC=corp,DC=gel,DC=ac"
credentials="***********"
/>

view message
XML counter columns
(1 response) katy wiseman 2021-01-14 01:43

Hi,

I'm trying to get an XML counter column to work as described here at the bottom of the page:
https://www.labkey.org/Documentation/Archive/20.7/wiki-page.view?name=sampleIDs

However it's not working. I've created the sample type as it's shown in the example and pasted the XML code into the XML metadata but it's not generating an automatic 'SampleInLot' number for each new 'Lot' in the table.

This is the XML metadata suggested:

<tables xmlns="http://labkey.org/data/xml">
<table tableName="MySampType" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.experiment.api.CountOfUniqueValueTableCustomizer">
<properties>
<property name="counterName">
SampleCounter
</property>
<property name="counterType">
org.labkey.api.data.UniqueValueCounterDefinition
</property>
<!-- one or more pairedColumns used to derive the unique value -->
<property name="pairedColumn">
lot
</property>
<!-- one or more attachedColumns where the incrementing counter value is placed -->
<property name="attachedColumn">
sampleInLot
</property>
</properties>
</javaCustomizer>
</table>
</tables>

Does anyone have any thoughts about how to get this to work? Or any other alternatives?

Thanks,

Katy

view message
Security Vulnerability Notice for LabKey users on PostgreSQL - PgMiner botnet
Jon (LabKey DevOps) 2020-12-15 18:09

Due to the PgMiner botnet exploit/vulnerability (https://www.zdnet.com/article/pgminer-botnet-attacks-weakly-secured-postgresql-databases), we recommend any LabKey user that has a self-hosted environment to read the article and take the following precautions:

  • If you still have the default postgres user that came with your PostgreSQL installation, please do the following:
  1. Create a replacement superuser on your database.
  2. After creating the replacement user, delete the default postgres user.
  • Confirm that your PostgreSQL database can only be accessed by your LabKey server on your specific designated port. By default, PostgreSQL uses port 5432. Consider either changing to a different port or update your security settings (i.e. Firewall, pg_hba.conf file) so only your LabKey instance can access your PostgreSQL server.

For more information on securing your PostgreSQL server, please checkout the following resource:

https://www.enterprisedb.com/blog/how-to-secure-postgresql-security-hardening-best-practices-checklist-tips-encryption-authentication-vulnerabilities

view message
Error: Search is disabled because the search index is misconfigured. Contact the system administrator of this server.
(1 response) hilariagrieve 2020-12-04 05:05

Hi!
I have this problem, how Can I fixit? thanks!

org.apache.lucene.store.LockObtainFailedException: Lock held by this virtual machine: C:\Program Files\Apache Software Foundation\Tomcat 8.5\temp\labkey_full_text_index\write.lock
at org.apache.lucene.store.NativeFSLockFactory.obtainFSLock(NativeFSLockFactory.java:127)
at org.apache.lucene.store.FSLockFactory.obtainLock(FSLockFactory.java:41)
at org.apache.lucene.store.BaseDirectory.obtainLock(BaseDirectory.java:45)
at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:804)
at org.labkey.search.model.WritableIndexManagerImpl.get(WritableIndexManagerImpl.java:78)
at org.labkey.search.model.LuceneSearchServiceImpl.initializeIndex(LuceneSearchServiceImpl.java:232)
at org.labkey.search.model.LuceneSearchServiceImpl.resetIndex(LuceneSearchServiceImpl.java:343)
at org.labkey.search.SearchController$AdminAction.handlePost(SearchController.java:319)
at org.labkey.search.SearchController$AdminAction.handlePost(SearchController.java:221)
at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:101)
at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:80)
at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:177)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:416)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1226)
at org.labkey.api.view.ViewServlet._service(ViewServlet.java:205)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:132)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
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:52)
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.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.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1147)
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:217)
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:198)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:478)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:624)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:799)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:868)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1455)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)

view message
Apologies for inadvertent notification email "RE: Table view permissions"
chetc (LabKey Support) 2020-12-03 10:17

On 12/2, you were inadvertently sent a message from LabKey Support with the subject "RE: Table view permissions." The default email setting for our support forum was set too broadly; we have corrected the problem. We sincerely apologize for the inconvenience.

view message
LabKey React npm package available - @labkey/components
cnathe 2020-11-17 06:30

Hello All,
For any LabKey module developers out there who are working on creating LabKey pages or applications using React, we would like to let you know that the first public version of the @labkey/components npm package has been released and is available for use within your modules. This package contains some React based components, models, actions, and utility functions that will help with data access and display of LabKey schemas/tables in your React application.

You can get further information about the available components, how to install the package locally, and see some example usages from the Public API doc page.

Thanks,
Cory Nathe

view message
Table view permissions
(3 responses) sjvanro 2020-11-12 11:41

When impersonating a reader for my tables, I'm able to see data within the table. However, users within a group under reader permissions are not able to see data in the tables. How do I resolve this?

view message
wiki bug
(1 response) Stefan Nicolet 2020-11-10 03:59

A long JSON message (attached) arrises when people edit (add, remove, modify) elements of a list that has been integrated into a wiki page the following way:

<h4>People in the network</h4><br>
<div id="list_div"></div>
<script>
var wp = new LABKEY.WebPart({ renderTo: 'list_div', partName: 'List - Single', partConfig: { listName: 'medict_network'}, frame: 'none'});
wp.render();
</script>

This bug does not happen if the edition is done on the list itself.

 displayed_message.txt 
view message
Some code issues found by Static Code Analyzer that may need reviewing
(1 response) stevec 2020-11-09 10:17

I ran a static Code Analyzer on the Labkey code and found the following issues that may need reviewing:

========================================================================================

  1. The String equals method is called with argument org.labkey.api.util.Path, not a String. The equals method will always return false.

2 examples, please note the getPath() method returns a org.labkey.api.util.Path, not a String.

Example 1

org.labkey.api.webdav.AbstractWebdavResource
                                .......
                                .......
                                public boolean canRead(User user, boolean forRead)
                                {
                                if ("/".equals(getPath()))

=====================================================================================
Example 2

                    org.labkey.api.webdav.WebFilesResolverImpl
                                .......
                                .......
                                 public boolean canRead(User user, boolean forRead)
                                 {
                                 if ("/".equals(getPath()))

~========================================================================================

  1. The org.labkey.api.util.Path equals method is called and passes a String, the org.labkey.api.util.Path.equals method will return false when the input Object is not org.labkey.api.util.Path,

File: ./server/modules/platform/core/src/org/labkey/core/webdav/DavController.java

             public void writeProperties(WebdavResource resource, Find type, List<String> propertiesVector)

                        ......
                        ......
                        .......

                  String displayName = resource.getPath().equals("/") ? "/" : resource.getName();

========================================================================================


                       public void writeProperties(WebdavResource resource, Find type, List<String> propertiesVector) throws Exception
                        {
                        json.object();
                        json.key("id").value(resource.getPath());
                        String displayName = resource.getPath().equals("/") ? "/" : resource.getName();


========================================================================================
~

  1. The HashMap.get(Object) call passes in object ColumnInfo which is not the key defined for the HashMap. The HashMap key is a String.

     Map<String, Integer> outputMap = DataIteratorUtil.createColumnAndPropertyMap(it);       // String is the key to this HashMap

        ColumnInfo containerColumn = table.getColumn("container");
 

        Integer indexContainer = outputMap.get(containerColumn);       // containerColumn is not a String

=====================================================================================

~
4. NullPointerExceptions

variable raf will get NullPointerException

class: org.labkey.core.webdav.DavbController$PutAction

WebdavStatus doMethod() throws DavException, IOException, RedirectException {

....
.....
....

           RandomAccessFile raf = null;
            OutputStream os = null;

            try
            {
                if (!exists)
                {
                    temp = getTemporary();
                   if (temp)
                        markTempFile(resource);
                    deleteFileOnFail = true;
                }

                File file = resource.getFile();
                boolean isBrowserDev = getUser().isTrustedBrowserDev();
                if (range != null)
                {
                    if (resource.getContentType().startsWith("text/html") && !isBrowserDev)
                        throw new DavException(WebdavStatus.SC_FORBIDDEN, "Partial writing of html files is not allowed");
                    if (null != AntiVirusService.get())
                        throw new DavException(WebdavStatus.SC_FORBIDDEN, "Partial writing not supported with virus scanner enabled");
                    if (range.start > raf.length() || (range.end - range.start) > Integer.MAX_VALUE)

=====================================================================================

variable context will get NullPointerException

org.labkey.api.reports.report.ScriptReportDescriptor

  public ReportDescriptorDocument getDescriptorDocument(ImportContext context)
    {
        // if we are doing folder export (or module file save), we don't want to double save the script property
        if (null != context)
            return getDescriptorDocument(context.getContainer(), context, true, Set.of(Prop.script.name()));
        else
            return getDescriptorDocument(context.getContainer(), context, true, Collections.emptySet());
    }

=====================================================================================

  1. To honor if statement, remove Semicolon at:

if (BACKGROUND_WELL_GROUP.equals(group.getName()));

class: org.labkey.elispot.ElispotPlateTypeHandler

   {
        Map<String, Map<String, Double>> backgroundMap = new HashMap<>();
        WellGroup backgroundGroup = null;

        for (WellGroup group : plate.getWellGroups(WellGroup.Type.CONTROL))
        {
            if (BACKGROUND_WELL_GROUP.equals(group.getName()));
            {
                backgroundGroup = group;
                break;
            }
        }

view message
automatically defining all dataset fields with a specific number format
(1 response) karenchait841 2020-11-05 01:27

Hi,
In study module when I create a new dataset how can I define all fields with type decimal to have a specific number format? I have a very long list of fields and it impossible to do it manually for all of them. I tried to define the number format of the study folder but it did not solve this issue.
Thanks,
Karen

view message
Setting expression matrix assay
(1 response) karenchait841 2020-11-05 01:19

Hello, I am trying to set up Labkey as our labs database. Some of the projects include expression matrix data but the assay format is not as I expected. If I understand correctly in the Samples Type the columns are the samples so it is not an annotation file for samples, and the Assay List is the expression matrix but in a list format and not a matrix. Is there a different way to do it? For now I uploaded the data to a subfolder defined as study, but the genes annotations can't be integrated with the data.
Thanks for any advice,
Karen

view message
TeamCity Trunk project rename
Trey 2020-10-27 13:41

As announced previously, we have finished migrating our source code from SVN to Git.
To reflect this, we are updating the "Trunk" project name on TeamCity. Henceforth, it will be labeled "Develop" to match our Git branch naming.

Note: In order to maintain backward compatibility with existing bookmarks and scripts, IDs will not be changed at this time.

view message
Source Code migration to Git
ians 2020-10-21 14:41

Hi All,

For 20.11 we have finished migrating our source code to git. Prior releases will remain in SVN and continue to be maintained based upon our Release and Upgrade policy. Changes and updates to to the source code for 20.11 and beyond will only be performed in git. If you are building from SVN trunk source please migrate at your earliest convenience.

Migration instructions:

For this example these instructions the original enlistment is in ./trunk/:

  1. Clone the new repo's develop branch to a sibling directory of your current enlistment
    git clone https://github.com/LabKey/server labkeyServer
  2. Then reenlist or copy over the server/modules directory to the corresponding new location
    cp -r trunk/server/modules labkeyServer/server/
  3. Reenlist or Copy over any additional enlistments (./remoteapi/*, ./server/testAutomation, etc.)
  4. Copy over any other changes -- specifically ./settings.gradle, ./server/configs/pg.properties, ./server/configs/mssql.properties, etc.
    cp trunk/server/configs/pg.properties labkeyServer/server/configs/pg.properties
  5. cd into the new directory
  6. execute ./gradlew cleanNodeModules from the new enlistment's root --- our initial testers ran into some conflicts and errors within these directories
  7. execute ./gradlew pickPg or ./gradlew pickMSSQL
  8. The new enlistment should then build as normal.
  9. (optional) If you are using IntelliJ, you will need to update the various project settings as you would for any new enlistment. Copying over the .idea directory can retain these, but it may also carryover some project specific settings that don't apply in the new location.

Ian

view message
list table quadruples when upgrading labkey from v17 to v19.1
(4 responses) qing chang 2020-10-06 07:19
We have recently upgraded one of our labkey servers from v17 to v20.7. We had to first upgrade to v19.1 before going to 20.7. We use postgresql 9.6 as backend.

We noticed there was a big jump in storage usage after upgraded to 19.1. A closer look revealed that ALL list type tables have quadrupled in storage usage without any changes in contents. One of the table was 10G, it became 40G after upgrade.
-------
 list.c185d2069_modc_test | 10 GB
 list.c185d2069_modc_test | 40 GB
-------

The row count is 50 mil before and after upgrade. The first 10 rows are identical. I have no reason to believe there is any difference in other rows.

Can someone shed some light on this?

Thanks in advance.

Qing Chang
view message
Questions about the study module
(1 response) eva pujadas 2020-09-25 09:06

Dear LabKey supporters,

We are using LabKey Server 19.3.7.

  1. Is it possible to have the PrticipantId filed to be of type integer? By default it is text, and it does not sort properly when the IDs are numbers. See attached screenshot "participant_id_sorting.png").

  2. When inserting a new record from the Participant view of a particular participant ID (see screenshot "insert_demographic_record_1.png"), shouldn't the form field for the participant ID be already populated with the ID? (see screenshot "insert_demographic_record_2.png").
    It seems this to be expected behavior, also because the URL to the insert form contains the participant ID as parameter. E.g. : ....dataset-insert.view?datasetId=5019&quf_ParticipantId=455585

Thank you and regards,
Eva

 insert_demographic_record_2.png  insert_demographic_record_1.png  participant_id_sorting.png 
view message
LabKey database not populated on startup
(3 responses) james gregoric 2020-09-11 10:18

2020-09-11 Update: When we go to the Tomcat Web Application Manager page and click on the labkey link the following error appears:
java.lang.NullPointerException at
org.labkey.api.module.ModuleLoader.upgradeCoreModule(ModuleLoader.java:1332) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:499) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:239)

Looking at our PostGres database we see that the LabKey tables have been created, but all tables are empty. So for some reason the tables are not being populated even though we clearly have write access to the database (since the tables were created by the startup process).

As noted in the error dump, the error occurs at line 1332 in ModuleLoader.java. (See ..\server\modules\platform\api\src\org\labkey\api\module). The code there reads:

1325 // If modules table doesn't exist (bootstrap case), then new up a core context
1326 if (getTableInfoModules().getTableType() == DatabaseTableType.NOT_IN_DB)
1327 coreContext = new ModuleContext(coreModule);
1328 else
1329 coreContext = getModuleContext("Core");
1330
1331 // Does the core module need to be upgraded?
1332 if (!coreContext.needsUpgrade(coreModule.getSchemaVersion()))
1333 return false;

Evidently, the call to ModuleContext() on line 1327 is returning a null value for coreContext. We assume that is because the database is not populated.

view message
Lookups/Links to primary key/normal values in SQL queries
(5 responses) max diesner 2020-08-24 02:36

Hi,

we have no for some time a community edition labkey server running in the lab and it is just awesome. I have recently setup some SQL queries for keeping track of our Lab inventory which is also working quite nicely. However there is a minor thing that keeps bugging me. The resulting query table does not copy automatically the lookup/ Text link for a certain value from the underlying table (list). I checked the documentation and it states that you can easily get this done by applying the lookup through the Metadata properties. Thus, i accordingly changed the column to a lookup from the appropriate underlying column. I also checked the Metadata code and can see that the appropriate <fk></fk> part has been added to the metadata code. Nevertheless the resulting table still does not show the appropriate text links. Do you need to check some option that i am missing or does the LEFT JOIN statement in the SQL code overrides any potential lookups for certain values? I am trying to connenct primary keys for your information. When i am referencing from a table where the value is already a lookup it is copying the textlink right away.

I am looking forward to hear from you!

Cheers Max

view message
Labkey/Panorama server not recognized in Skyline
(3 responses) mlane 2020-08-13 14:42

Hi,

We just set up Community edition Labkey to test Panorama with Skyline. I was able to access it directly through browser, log-in and create project folders and subfolders setup as Panorama.

However, Skyline don't connect to the server and gives error that reads
that our server url is not a Panorama server. I'm wondering if it's a setting for the site, or permission? See attached for error message.

Thanks,

Monica Lane

 Labkey_error_08132020.pdf 
view message
Date error msg: "couldn’t convert date field, should be of type timestamp"
(6 responses) panthea tzourio 2020-08-10 03:46

Hello support, our Labkey server is situated in France with CET time zone (Central Europe Time). We encounter a persistent CEST (Central Europe Summer Time) exception on date fields each time we try to import datasets in a Study type folder (time and participant are mandatory fields). Even the simple and structured excel files David Hansons uses for his demos produce the same error : “couldn’t convert date field, should be of type timestamp” while the field is already of type timestamp. The result is the same on both V18.3 and V20.3 (pre prod) Labkey installs. Please find attached, the Look and feel setting with the default date format to which I added a "z" to force the system date; the CEST error message, an example of an Excel file generating the exception. Only the “Demographics” file doesn't generate the error eventhough the date is in the same format. I assume there’s no such control on date field in demographics files. I deleted in Study the default CEST date format in case this caused the error but the result is the same. This very first step error prevents us to go further on our Labkey investigation tests.
Thanks in advance for your time.

 Look and feel.PNG  Error msg CEST.PNG  LabResults.xls 
view message
Survey Design - Card Layout - Section skip logic
(1 response) rita alves 2020-08-07 07:39

Hello,

In case i am doing a survey design with a card layout. Is it possible to hide section based on an answer to a question in a different section?

Thank you in advance!

view message
R dataframe from external data source to data grid
(1 response) dhutchison 2020-08-06 18:21

Hi,

I have an R script that queries an external data source (through jdbc, not labkey.xml) and would like to display the resulting dataframe as a data grid in labkey. I want the data to be dynamically loaded - that is, the query runs each time the report is viewed. I'm thinking this should be straightforward, but not quite seeing how to do it.

For example:

result<- dbGetQuery(con, sql)
# ${htmlout:csvfile}
write(unlist(result), file="csvfile")

will output the result text in the report tab, but not as a grid.

If I don't "unlist", I get an error:

Error in cat(x, file = file, sep = c(rep.int(sep, ncolumns - 1), "\n"), :
argument 1 (type 'list') cannot be handled by 'cat'"

because write expects an atomic list, I guess.

Any thoughts on how to wrangle the dataframe into a Data Grid?

Thanks

view message
Mascot Server issue
david lee 2020-07-10 11:45

Hi.
A new user of Labkey here. We have just set up our Dev instance.
We are trying to connect to our internal Mascot server to run MS2 pipelines.
On the Admin config page we test connection and everything work... the report says "Test Passed"
I go to a project and try to set up a search... but get this error:
There was a problem retrieving the database list from the server: Failed to interact with the Mascot server.

Any help would be welcome.

Thanks

David Lee

view message
Trigger process after successful specimen import
(4 responses) tstellin 2020-06-29 12:23

Hi,

We'd like to kick off a post-specimen import process that starts when labkey finishes a specimen import pipeline job. Does a feature like this exist in Labkey Server? I've looked through the UI and documentation, and didn't see anything, but wanted to double-check and make sure it doesn't exist.

Thanks!
-Tobin

view message
Generating a folder access report
(1 response) jgane 2020-06-25 12:28

Hi,

I was wondering if there is a way to generate a list of all users that have access to a folder for every folder/subfolder on LabKey? Essentially we want to collect the /folderAccess.view page for every folder into something like a JSON.

We tried using the R API to pull a list of all the folders on LabKey and then querying the core.Users table for each folder, however we ran into an issue where if a user is a part of a project group, they will show up in the core.Users table for every subfolder regardless of whether they actually have access to that subfolder or not. Even if that project group is not added to any folders and has no ability to access anything in that project, the users in that group will still show up in the core.Users table for every subfolder.

In case it helps we are running on version 20.3.

Any suggestions or ideas would be appreciated.

Thanks,
Jon

view message
Enabling CORS and file deletion issues
(7 responses) inaki martinez 2020-06-24 08:35

Dear Labkey community

we are having some issues while enabling CORS in labkey for some external collaborators. Our labkey instances work fine without CORS but as soon as we enable it, some labkey functionality does not work. As far as we could test, only file deletion stops working, but still is a problem.

Our labkey server has the following versions:

  • apache-tomcat: 8.5.53
  • openjdk:13.0.2
  • LabKey19.3.10-65330.20

The CORS configuration is as follows, although I've tried using just the default values without any luck.

     <filter>
        <filter-name>CorsFilter</filter-name>
        <filter-class>org.apache.catalina.filters.CorsFilter</filter-class>

        <init-param>
          <param-name>cors.allowed.origins</param-name>
          <param-value>https://bc2-labkey-dev.bc2.unibas.ch, https://bc2-labkey-dev.bc2.unibas.ch, https://labkey-dev.scicore.unibas.ch, https://labkey-dev.scicore.unibas.ch, https://wiki.biozentrum.unibas.ch, https://labkey.scicore.unibas.ch</param-value>
        </init-param>

        <init-param>
          <param-name>cors.allowed.methods</param-name>
          <param-value>GET,POST,OPTIONS</param-value>
        </init-param>

        <init-param>
           <param-name>cors.allowed.headers</param-name>
           <param-value>Access-Control-Expose-Headers,Access-Control-Allow-Origin,X-Requested-With,Content-type,Authorization</param-value>
        </init-param>

        <init-param>
          <param-name>cors.exposed.headers</param-name>
          <param-value>Access-Control-Expose-Headers,Access-Control-Allow-Origin,X-Requested-With,Content-type,Authorization</param-value>
        </init-param>

        <init-param>
          <param-name>cors.support.credentials</param-name>
          <param-value>true</param-value>
        </init-param>

        <init-param>
          <param-name>cors.preflight.maxage</param-name>
          <param-value>1800</param-value>
        </init-param>
      </filter>

      <filter-mapping>
        <filter-name>CorsFilter</filter-name>
        <url-pattern>/*</url-pattern>
      </filter-mapping>

Even with a simpler CORS setup it does not work:

     <filter>
        <filter-name>CorsFilter</filter-name>
        <filter-class>org.apache.catalina.filters.CorsFilter</filter-class>

        <init-param>
          <param-name>cors.allowed.origins</param-name>
          <param-value>*</param-value>
        </init-param>

      <filter-mapping>
        <filter-name>CorsFilter</filter-name>
        <url-pattern>/*</url-pattern>
      </filter-mapping>

Upon trying to delete a file I have just uploaded in the files tab, I get "Failed to delete" message. Firefox devel tools show:

Request URL:https://bc2-labkey-dev.bc2.unibas.ch/labkey/_webdav/home/%40files/afile_to_delete.txt?method=DELETE&pageId=4267287a-97a1-1038-bf7a-3c9cbf81b968
Request Method:POST
Remote Address:0.0.0.0:443
Status Code:
403
Version:HTTP/1.1
Referrer Policy:origin-when-cross-origin

The logs don't show any error during this request.

Is there anything else we should modify, or add for this to work? I'm currently out of ideas.

Best regards,
Iñaki

view message
How to track deletion of a row in a dataset?
(5 responses) Chichero 2020-06-19 04:07

I have not found any log information that states explicitly that a particular user deleted an entry in a dataset. In our study I looked in Audit Log - Assay/Experiment Events but only found info about who created an entry, Derive sample from sampleid-X and comment with Run deleted.

Could you help me to find a log with precise information about who deleted, who created and who modified an entry in a dataset and/or a sample set?

view message

Welcome to the LabKey Support Forum. This forum is for questions regarding LabKey Server general usage, installation, or development.

Posting Questions

Before you post a new question, please search to see if someone has already asked a similar one.

Next, please review the Community Forum Guidelines.

When you post a question, please include the following information:

  • Your operating system.
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  • A detailed description of your problem or question, including instructions for reproducing your issue.
  • Error information. Please attach log files to your message, rather than pasting in long text. Error pages and log files also include an Error Code. Please include this code in your message.

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