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HIV Study Tutorial
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error message while uploading Flow Cytometry data

Getting an error message while uploading a package of .fcs files and flowjo workspace file. ' an error occured trying to load: java.lang.nullpointerexception (java.lang.nullpointerexception'. From the logs, the stack trace is: java.lang.NullPointerException     at org.labkey.pipeline.api.PipeRootImpl.findRootPath(PipeRootImpl.java:144)     at org.labkey.pipeline.api.PipeRootImpl.relativePath(PipeRootImpl.java:195)...

Step 2: Study Reports

In this step we will look at the variety of reports available in the online example. We will look at both built-in reports (automatically available in all study folders) and custom reports (created by the study researchers or data analysts). As you progress with the walkthrough, notice two things: First, all of these reports are 'live', that is, they represent the current state of the underlying...

Query Metadata: Examples

This topic provides examples of metadataSql used to change the display and behavior of fields in tables and queries. Auditing Level Conditional Formatting Include Row Selection Checkboxes Hide a Field from Users Show/Hide Columns on Insert and/or Update Use a Format String for Display Use a Text Expression for Display Set a Display Width for a Column Display Columns in Specific Order...

"Assay UI.pptx" attached to message "Suggestions for Extensible Assays"

Interacting with Assay Data 1 Basic Ways to Interact: Experiment: cuts across all assay types Assay: by batch, run or sample 2 Assay View: Most of this already exists in labkey Should give user a grid of data from one assay by either batch, run or sample (like grid here: /assay/home/assayRuns.view) I believe much of this already is possible in text-assays, but we should be able to define the...

Ontology Lookup

Premium Feature — Available in the Enterprise Edition of LabKey Server. Learn more or contact LabKey. Ontology Lookup Data Type Lookup Rules Usage Example Concept Picker for Insert/Update with Type-ahead Initialize Expected Vocabulary Ontology Lookup Data Type Once an ontology has been loaded and the module enabled in your folder, the fieldEditor will include an Ontology Lookup data...

"180723_InsertRows Error Log.txt" attached to message "LImit to insertrows query"

WARN MapDataIterator 2018-07-23 10:55:18,110 http-bio-8443-exec-20 : Map already has column named 'ParticipantId' WARN MapDataIterator 2018-07-23 10:55:56,174 http-bio-8443-exec-6 : Map already has column named 'ParticipantId' WARN MapDataIterator 2018-07-23 10:56:39,133 http-bio-8443-exec-19 : Map already has column named 'ParticipantId' WARN MapDataIterator...

dataset5004.tsv

ParticipantId date QCStateLabel Weight_kg Temp_C SystolicBloodPressure DiastolicBloodPressure Pulse Respirations Signature Pregnancy Language ARV ARVtype height_cm 101344 2008-04-27 00:00:00.0 68 37.0 117 83 61 173.0 101344 2008-05-25 00:00:00.0 69 36.8 145 103 71 175.0 101344 2008-06-22 00:00:00.0 71 38.2 166 101 68 175.0 101344 2008-08-17 00:00:00.0 73 36.5 125 95 74 ...

job stuck waiting status

Hi,    a user submit a job but it is stuck in waiting status in the activemq log after it finish the first FAASTA check. 01 Dec 2017 11:40:26,278 INFO : X! Tandem search for all 01 Dec 2017 11:40:26,281 INFO : ======================================= 01 Dec 2017 11:40:26,283 INFO : abac.mzXML 01 Dec 2017 11:40:26,285 INFO : casfdsa.mzXML 01 Dec 2017 11:40:26,287 INFO : cafdsa.mzXML 01 Dec...

Errors upgrading to 11.2

Different people in our group tried test upgrades to 11.2. One, using the windows upgrader, got an error: flow-11.10-11.20.sql : ERROR null value in column "keywordid" violates not-null constraint. Another, doing a manual upgrade on MacOS got: ERROR ExceptionUtil 2011-09-15 14:24:16,072 http-8080-Processor25 : Unhandled exception: 500: Unexpected server error org.labkey.api.data.SqlScriptRunner$SqlScriptException:...

"PhysicalExam.xls" attached to page "R Report Builder"

data ParticipantID Date Height Weight Temperature Systolic Diastolic Pulse Respirations ARV? ARVRegimenType 101 2008-05-17 184.4000 86 36.0 129 76 64 17 101 2008-08-04 184.7000 84 37.0 133 79 67 18 101 2008-09-02 183.4000 83 37.0 133 85 68 15 101 2008-11-23 185.3000 80 36.7 135 85 70 14 101 2009-01-18 184.8000 79 36.8 142 90 75 17 101 2009-02-17 185.2000 79 37.3 129 87 79 13 101 2009-03-16...

"Package_test_script.txt" attached to page "SND: APIs"

<button onClick="populateCategories()">Populate Categories</button> <button onClick="mySavePackage()">Save Package</button> <button onClick="populatePackageEvent()">Create Package Event</button> <button onClick="addPackageToProject()">Add Package to Project</button> <button onClick="myGetPackage()">Get Package</button> <button onClick="myDeletePackage()">Delete Package</button> <button onClick="myLookups()">Populate...

withCounter skipping over numbers

Hi, We have a case where a user generated derivatives of a sample which has a "withCounter" modifier in the sample ID. It is a simple modifier: LIB_${${MaterialInputs:first}_:withCounter(1,'00')} In general, we only make one derivative for a sample, so the tail end of the sample ID would be _01. However, a user generated a second set of derivative samples and they had _101 instead of _02 at the...

"BadSQLGrammarError.txt" attached to message "Bad SQL grammar error when deleting project"

org.springframework.jdbc.BadSqlGrammarException: SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "gw_labkey.x_lk_outbd_specimens" does not exist Position: 13 at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:231) at org.springframework.jdbc.supp...

Module has already been set - error

I am building a continuous integration environment for our labKey development team so that we can better QA and manage our releases. I have been able to successfully compile and push (copy) the web app to the staging server along with a restoring database from production. It seems that the web-server starts up correctly; however, upon first accessing the web-app, I receive the following error...

Help with javascript API's insertRows()

Hi, I'm developing a labkey 12.3 w/Ext4 file module that inserts rows into a table in a user-created schema (in a postgres db). The table contains multiple date columns whose dates are collected via a Ext form with datefield xtype widgets. Every time I try to insert I get this error: ERROR: column "date_used" is of type timestamp without time zone but expression is of type character varying...

Dataset Properties

The properties of a dataset include how it is keyed, categorized, and shown or shared. Dataset Properties Page Action Buttons Edit Dataset Properties Data Row Uniqueness Additional Key Fields Using Time as an Additional Key Advanced Settings Edit Dataset Fields Dataset Properties Page Administrators can view and edit dataset properties either by clicking the name of a dataset...

Reagents.tsv

Key Reagent 1 AD-mix 2 Acetyl chloride 3 Aluminium chloride 4 Armstrong's acid 5 Azobisisobutyronitrile 6 9-Borabicyclononane 7 Benzyl chloroformate 8 Benzyltrimethylammonium fluoride 9 1,8-Bis(dimethylamino)naphthalene 10 (Bis(trifluoroacetoxy)iodo)benzene 11 Bis(trimethylsilyl)acetamide 12 Bis(trimethylsilyl)amine 13 N-Bromosuccinimide 14 Burgess reagent 15 Tert-Butyl hydroperoxide 16 N-Butyllithium...

"labkey-errors.log" attached to message "How to export a folder with linked schemas"

ERROR QueryServiceImpl 2015-08-26 09:59:28,279 http-bio-8080-exec-4 : Error creating linked schema test_linked_schema java.lang.NullPointerException at org.labkey.query.LinkedSchema$LinkedSchemaUserWrapper.<init>(LinkedSchema.java:452) at org.labkey.query.LinkedSchema.getSourceSchema(LinkedSchema.java:158) at org.labkey.query.LinkedSchema.get(LinkedSchema.java:103) at org.labkey.query.QueryServiceImpl.getLinkedSchema(QueryServiceImpl.java:1333)...

Module Upgrade : Error: Unable to initialize search index.

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...

"labkey.log" attached to message "Error while running trigger script"

INFO ScriptService$Console 2020-04-07 17:59:07,547 io-127.0.0.1-8080-exec-4 : ** evaluating: queries/study/BasicsCase.js INFO ScriptService$Console 2020-04-07 17:59:07,584 io-127.0.0.1-8080-exec-4 : Getting entries in BasicsCase, success: 33 rows returned. INFO ScriptService$Console 2020-04-07 17:59:07,584 io-127.0.0.1-8080-exec-4 : Selected rows BasicsCase: INFO ScriptService$Console...