LabKey Support: LabKey Server Distribution and Support

'survey label' field from surveys.Surveys table

Thu Jan 09 05:56:53 PST 2020

Hi Is there any possibility to automatically fill the question patientid using the 'survey label'? How to access to the survey label field? {"name" : "patientid", "caption" : "Patient ID:", "required" : true, "xtype": "textfield", } Thanks in advance

Hide submit button

Wed Jan 08 03:07:21 PST 2020

Hello, Is there any possibility to hide the submit button in the survey (survey design code)? Thanks in advance

Issue when using alert within a function

Mon Oct 28 04:21:17 PDT 2019

Hello I have the following questions within a survey design code: {"name" : "inidt", caption" : "Data de início:", "xtype": "datefield"}, {"extConfig":{ "fieldLabel": "Descontinuação?", "xtype":"radiogroup", "name":"discquestion", "columns":1, "items":[ {"boxLabel":"Sim", "name":"disc", "inputValue": 1}, {"boxLabel":"Não", "name":"disc", "inputValue": 0}, {"boxLabel":"Desconhecido", "name":"disc", "inputValue": "NA"}]}}, {"extConfig":{ "name" : "discdt", "fieldLabel" : "Data de descontinuação:", "xtype": "datefield", "hidden": true}, "listeners": { "change": { "question": "discquestion", "fn" : "function(me, cmp, newValue, oldValue){var cmp2 = cmp.getValue(); if (cmp2.disc == 1) {me.setVisible(newValue); console.log(cmp2.disc);} else {me.setVisible(false);}} "}}}, {"extConfig": {"name" : "obs", "caption" : " ", "xtype": "textareafield", "grow" : true, "width": 800, "height": 200}, "listeners": { "change": { "question": ["discdt","inidt"], "fn" : "function(me, cmp, newValue, oldValue){var q1 = cmp.getName(); var q2 = cmp.getName(); if (q1 == 'inidt'){q1val = newValue; console.log(newValue);} else if (q2 == 'discdt'){q2val = newValue; console.log(newValue);}; if (q1val>=q2val){alert('nooooooo')};}; console.log(newValue); "}}} I was trying to make question "discdt" visible only if disc = 1 (this is working). Although I would like to add a validation of the dates: discdt has to be more recent than inidt. This is working if i am creating a new survey. Howerver when I try to access a saved/submitted survey it is just "loading" (this is a problem cause I need to access the surveys after they are filled). Could you please help? Thank you!

File Repository Sorting

Fri Oct 11 11:38:54 PDT 2019

I am trying to setup a repository for MRI DICOM and 3D Mesh files. I am using some pictures from a camping trip as dummy files. I've added a few Properties (all single line text <10 characters) to test out the repository and to represent metadata later on. In the toolbar and grid settings I've checked those properties to be sortable. When working in the file repository I can not sort by the custom properties. When I try and sort by the property is just sorts by the file name instead. My goal is to make a system where a user can sort and filter these files and download the results in bulk. I'll worry about more advanced features later.

Plain text password in configuration.xml

Fri Oct 04 07:58:11 PDT 2019

Hello Support, Our company does not allow us to store plain text passwords in files. Credentials must be always encrypted and then decrypted on the fly. Does LabKey support encrypted credentials ? Thanks Des

Labkey 19.2 - Apache Tomcat 9.0.24

Wed Sep 11 12:51:27 PDT 2019

Hello Support, We recently deployed Labkey 19.2 in a clustered Apache Tomcat 9.0.24 environment. When we make changes (ie. add projects) it only appears on one node and we need to restart the 2nd node for changes to appear on it. Is there some sore of cache setting that needs to be adjusted> Please advise. Thanks, Greg

Issues with running LabKey Python API

Tue Sep 10 09:52:30 PDT 2019

Hi, I am trying to write the .netrc for my MacOSX laptop. I have started a LabKey trial site called ‘ANag_LabKey_Trial’ accessible at https://nrel-anag.trial.labkey.host It is not clear to me what I should write in the line: machine When I use the following lines in the .netrc file: machine nrel-anag.trial.labkey.host login ambarish.nag@nrel.gov password ******** I get the following error when I try to run the example case in https://github.com/LabKey/labkey-api-python Can you please help me fix these errors ? Thanks, Ambarish. >>> result = select_rows(server_context, schema, table) Traceback (most recent call last): File "/anaconda3/lib/python3.6/site-packages/urllib3/connection.py", line 159, in _new_conn (self._dns_host, self.port), self.timeout, **extra_kw) File "/anaconda3/lib/python3.6/site-packages/urllib3/util/connection.py", line 80, in create_connection raise err File "/anaconda3/lib/python3.6/site-packages/urllib3/util/connection.py", line 70, in create_connection sock.connect(sa) ConnectionRefusedError: [Errno 61] Connection refused During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/anaconda3/lib/python3.6/site-packages/urllib3/connectionpool.py", line 600, in urlopen chunked=chunked) File "/anaconda3/lib/python3.6/site-packages/urllib3/connectionpool.py", line 354, in _make_request conn.request(method, url, **httplib_request_kw) File "/anaconda3/lib/python3.6/http/client.py", line 1239, in request self._send_request(method, url, body, headers, encode_chunked) File "/anaconda3/lib/python3.6/http/client.py", line 1285, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/anaconda3/lib/python3.6/http/client.py", line 1234, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/anaconda3/lib/python3.6/http/client.py", line 1026, in _send_output self.send(msg) File "/anaconda3/lib/python3.6/http/client.py", line 964, in send self.connect() File "/anaconda3/lib/python3.6/site-packages/urllib3/connection.py", line 181, in connect conn = self._new_conn() File "/anaconda3/lib/python3.6/site-packages/urllib3/connection.py", line 168, in _new_conn self, "Failed to establish a new connection: %s" % e) urllib3.exceptions.NewConnectionError: : Failed to establish a new connection: [Errno 61] Connection refused During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/anaconda3/lib/python3.6/site-packages/requests/adapters.py", line 449, in send timeout=timeout File "/anaconda3/lib/python3.6/site-packages/urllib3/connectionpool.py", line 638, in urlopen _stacktrace=sys.exc_info()[2]) File "/anaconda3/lib/python3.6/site-packages/urllib3/util/retry.py", line 398, in increment raise MaxRetryError(_pool, url, error or ResponseError(cause)) urllib3.exceptions.MaxRetryError: HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /labkey/ModuleAssayTest/login-whoami.api (Caused by NewConnectionError(': Failed to establish a new connection: [Errno 61] Connection refused',)) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/anaconda3/lib/python3.6/site-packages/labkey/utils.py", line 93, in make_request response = handle_response(self._session.get(csrf_url)) File "/anaconda3/lib/python3.6/site-packages/requests/sessions.py", line 546, in get return self.request('GET', url, **kwargs) File "/anaconda3/lib/python3.6/site-packages/requests/sessions.py", line 533, in request resp = self.send(prep, **send_kwargs) File "/anaconda3/lib/python3.6/site-packages/requests/sessions.py", line 646, in send r = adapter.send(request, **kwargs) File "/anaconda3/lib/python3.6/site-packages/requests/adapters.py", line 516, in send raise ConnectionError(e, request=request) requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /labkey/ModuleAssayTest/login-whoami.api (Caused by NewConnectionError(': Failed to establish a new connection: [Errno 61] Connection refused',)) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "", line 1, in File "/anaconda3/lib/python3.6/site-packages/labkey/query.py", line 286, in select_rows return server_context.make_request(url, payload, timeout=timeout) File "/anaconda3/lib/python3.6/site-packages/labkey/utils.py", line 98, in make_request handle_request_exception(e, server_context=self) File "/anaconda3/lib/python3.6/site-packages/labkey/utils.py", line 157, in handle_request_exception raise ServerContextError(server_context, e) labkey.exceptions.ServerContextError: 'Failed to connect to server. Ensure the server_context domain, context_path, and SSL are configured corr

Suspected problems with Server.xml config

Mon Aug 12 06:22:43 PDT 2019

Hi, A newbie here. I'm working with my IT colleagues to set up LabKey Server. We have run through the manual install process with the online documentation. All seemed to go ok (except for the certificate security - but that's less important at the moment). We are using LINUX App Server and Postgres SQL server. We know tomcat is runningok as we can connect to the path: https://localServer:8443 But we get an "HTTP Status 404 – Not Found" when we try to access https://localServer:8443/labkey/ Any ideas on what we should be looking at - the IT guys want someone to lookover the Server.xml file. Is that something I can get help with here? Dave

Using a local R scripting engine

Thu Jul 25 11:49:35 PDT 2019

I am using the trial version of labkey. I was hoping to set up some R Reports, but the Labkey trail R engine does not have the packages installed that I need. I tried to change the R scripting engine to my local R.exe, but it doesn't seem to be letting me do that. Is installing new packages/using a local R scripting engine possible with the labkey free trial? If not, what version of labkey would allow me to do this?

Re-install Labkey

Fri Jul 19 06:05:50 PDT 2019

The PC where Labkey was installed will need to be replaced. Is it possible to migrate everything to a new machine? In case that is possible, how can we transfer everything from a machine to another one?

Edit a Wiki

Fri Jul 19 06:04:10 PDT 2019

Hello, Is it possible to lock the edition of a Wiki to a user who have "editor" permissions? Thank you!

Survey: Submitted to Pending

Mon Jun 03 01:34:27 PDT 2019

Hello, Is there any option for an Administrator user to change the survey status from "Submitted" to "Pending"? Thanks!

xls columns not imported

Wed Apr 24 10:34:23 PDT 2019

Hello, I've set up a cloud trial server and project and am trying to import a simple .xls file into the Laboratory Data but only half of my columns are being imported. I believe that I've set the data type correctly. Some Strings come through, others don't and it's the same with Numbers (Double). I've tried twice with the same result. Thanks, CM

Blank page when accessing Explore Sample Project

Fri Mar 29 09:45:22 PDT 2019

I'm getting a blank page when I click on the "Explore Sample Project" button at the Home page in the LabKey Biologics module.

Remote Login API

Thu Mar 28 12:27:24 PDT 2019

Hi am trying to test the Remote Login API as described in the documentation here: https://www.labkey.org/Documentation/wiki-page.view?name=remoteLoginAPI&_docid=wiki%3A32d706ed-ed56-1034-b734-fe851e088836 I have tried it on my hosted trial version and on a local VirtualBox VM. No matter what I put int for the returnUrl I get "Error: a valid returnUrl was not specified." Is there a configuration setting I must use? Thanks, Craig

"Send notification emails to all new users" does not work

Wed Mar 20 12:49:51 PDT 2019

Hello, We installed LabKey v 18.3 and set ldap login. When I add a new user, the "Send notification emails to all new users" does not work. I tested "Test Email Configuration" and it was able to send an email. It appears no packet sent out when used "Send notification emails to all new users" to invite a new user. Thanks for anyone if would help, wangxn

Two columns mapped error

Mon Dec 17 09:35:55 PST 2018

Hi, When I try to upload datasets I get an error message "Two columns mapped to target column: ptid_full". I am not sure why this is. "ptid_full" is the subject ID as defined in the Study Properties. There is a second column in the Excel sheet named "ptid" as you can see in the screen shot. Deleting this column in Excel fixes the problem, but I don't understand why LabKey is trying to map two columns instead of only the "ptid_full" column. Thanks, Scott Additional finding-- renaming the column "ptid" to "ptidnum" in Excel (instead of deleting) also allows upload.

Participants not cleanly deleted?

Sat Dec 01 17:23:32 PST 2018

Hi, In learning with the trial I have uploaded some data then wanted to delete it. However when I delete it the participants remain. See attached screenshot which says "clean data tracks data in 0 datasets over 1 visit. Data is present for 214 Participants. " This is after uploading a dataset, using the file to create the dataset, and then using Manage to delete to dataset. What is the reason these participants will not disappear? Thanks, Scott

Unexpected Error when deleting folders or subfolders

Sat Dec 01 06:08:52 PST 2018

Hi, When I use the Admin>Folder>Management and try to delete any folder or subfolder I receive "500: Unexpected Server Error" following the confirm deletion page. Nothing is deleted. This is on Firefox 63.0.3 on Windows. Thanks, Scott

branch of existing Labkey notebook for new lab

Mon Jul 16 14:45:19 PDT 2018

Hello, I am a member of David O'Connor's group from UW Madison. I am branching into my own space and Dave has helped me be setting up a labkey lab notebook under his master agreement, but said I needed to link it to server space before doing it. I will be working with my pediatrics department IT people to set up this storage and am wondering how this is actually done. Thanks, Emma

Trying to create a survey with trial version

Thu Jun 14 12:25:47 PDT 2018

Hi. I am trying to create a survey with the trial version, but cannot see how I can 'Under Modules, place a checkmark next to Survey' or 'Add a Survey Designs web part'. I was able to 'Create a new Lists web part' and import some data.

Assay type/Assay design

Wed May 23 13:52:42 PDT 2018

Hi, i am trying to use my LabKey trial version to set up an assay to analyse Luminex data. I am following the Luminex assay tutorial level 1, and it tells me to select 'Luminex' in my assay type under New Assay Design. I am unable o locate this feature, and can only see a 'General' assay type. Please help!!!

Registering for a Trial

Mon Feb 12 10:56:16 PST 2018

Tell us about your experience registering for a trial. Were you successful? Did the UI function as you expected? Did you need any additional directions to be successful?

Exploring the Example Project

Mon Feb 12 10:55:25 PST 2018

Tell us about your experience exploring the example project. Were you successful? Did the UI function as you expected? Did you need any additional documentation to be successful?