PALMS+User's+Guide+-+FAQs

=Frequently Asked Questions (FAQs)=

Quick Links:

 * General Questions
 * Problems connecting to PALMS
 * Problems connecting to PALMS with Firefox (Diffie-Hellman key error)
 * Timezones, daylight savings time and date/time formats
 * Problems uploading datasets to PALMS
 * Problems with batch uploader
 * Problems running calculations
 * PALMS output variables (columns in CSV file)
 * Calculation log files
 * CSV files
 * KML files



Q: How do I print a page from this wiki?
A: On the toolbar in the top right corner of the page, click the box containing "..." to reveal the "more page options". Then select "Print". A printer-friendly page will be displayed. Use your browser's Print button to print the page. Or you can select "Download PDF" to create and print a PDF version of the page.

Q: How do I report bugs, suggest improvements or request new features?
A: We welcome your comments. Follow this link and fill out the form.

Q: How can I learn of new additions to this wiki?
A: Click on "Recent Changes" in the blue box on the upper left side of the screen. This will show all changes to the wiki, however minor. To follow major changes, click the "News" link in the blue navigation sidebar. It is updated when a major change is made.

**Q: Can I receive email notification of new additions?**
A: Yes, wiki members can receive email notification. On the toolbar in the top right corner of the page, click the box containing "..." to reveal the "more page options". Then select "Notify". In the "Pages" box, enter "News" and click next. Then click the "Page Edits" check box and click Update. You will receive an email whenever the News pages is updated to reflect a noteworthy change.



Problems connecting to PALMS with Firefox (Diffie-Hellman Key error)
With the Firefox #39 update, by default Firefox will no longer access websites that show weaknesses in the Diffie-Hellman key exchange used by the SSL encryption algorithms. The PALMS websites exhibits such weakness. We have updated the SSL libraries, but the problem still remains. Until it is resolved, you can access PALMS using Chrome or Internet Explorer. Or, you can change the default configuration of FireFox 39 to work with PALMS using the following procedure in this document.





Q: I can not connect to PALMS. My browser reports that the server was not found.
A: Your browser can not locate or connect to the PALMS server
 * Check that you have an Internet connection by visiting some other website.
 * Verify that you are using the correct URL: https://palms.ucsd.edu:8443/PALMS/

Q: I can not connect to PALMS. My browser reports "SSL Handshake Failed. The SSL handshake with host palms.ucsd.edu failed."
A: Your browser has located the PALMS server but your network's firewall is blocking port 8443. Please ask your network administrator to add a rule to the firewall to allow access to palms.ucsd.edu using ports 8443, 81 and 9001.

Q: I can not connect to PALMS. My browser reports that the connection has timed out.
A: Your browser has located the PALMS server but it is not responding. Please try again. If this condition lasts longer than 5 minutes, please report it to a PALMS administrator.

Q: What's the meaning of the message....
A: When PALMS detects a networking problem, it responses with a message that describes the issue: > PALMS did not respond in a timely manner to your last operation. Please try again. > > PALMS most likely detected a system error and is re-starting. Please try your operation again. If this condition lasts longer than 5 minutes, please report it to a PALMS administrator. > > After 4 hours of inactivity, you have been logged out of PALMS. Click your browser's refresh button and log-in again. > > This is a rare network configuration problem. Please report it to a PALMS administrator. You will not be able to proceed until it is fixed. > > PALMS experienced difficulty communicating with the server that validates your username and password. This problem may be temporary. Please enter your username and password again. If this condition lasts longer that 5 minutes, please report it to a PALMS administrator.
 * //The PALMS server is not responding.//
 * //The PALMS server is temporarily unavailable.//
 * //Your PALMS session has expired.//
 * //The PALMS server can not be found.//
 * //An error occurred connecting to the authentication server.//

Q: When working in PALMS, pressing the web browser's BACK button returns me to the log-in page. Is that normal?
A: Yes, that is the normal behavior. PALMS is a two-page, web application (written in JavaScript), not a collection of web pages. From the browser's viewpoint, the log-in page is the previous page.

Q: The wiki NEWS page states that a new version of the web application is available, but when I access PALMS, I'm getting the older version. What should I do?
A: The version number and build date are displayed in the upper, left corner of the screen. If it's not the latest version, that's because your browser has cached the application and is using the old version. Click your browser's RELOAD button (usually a circular arrow). The newest version will be loaded from the server.

**Q: I am getting the message "Not enough storage is available to complete this operation". What should I do?**
A: This message is unique to Internet Explorer. The browser is running low on memory. Exit the browser completely (exit the program) and start again. If the problem persists, consider using Firefox.

**Q: I am getting the message "Stop running this script?". What should I do?**
A: The PALMS application uses JavaScript and some operations (listing a large number of items, or displaying a grid or chart) take longer than the browser expects. **In all cases, click No.** (Do not stop running the script.) If the problem persists, consider using Firefox.



Q: When creating a study, what timezone do I choose?
A: Chose the timezone that includes the majority of your participants. For participants not in this timezone, you will have the opportunity to change their timezone when you add them to the study.

Q: My timezone isn't listed. What should I do?
A: PALMS accommodates most of the major timezones, but it not the full set of 561 possible zones. Choose a timezone with the characteristics of the desired timezone. And contact a PALMS administrator and we'll add your specific timezone.

Q: What about daylight savings time?
A: PALMS automatically adjusts for daylight savings time. Select the time zone appropriate for your participants.

Q: How are timezones used in PALMS?
A: PALMS stores time as the participant's local time. For example, a timestamp of 09:00:00 is 9AM for the participant. The Actigraph / ActiLife / Actical products follow this convention. GPS devices store times in UTC (Coordinated Universal Time) which is GMT and does not change during the summer. The PALMS uploaders for GPS devices automatically converts the GPS UTC to the participant's local time for storage and processing.

Q: What date formats are used by PALMS?
A: The Actigraph / ActiLife / Actical products export dates according to the locale setting of your computer, either month/day/year (MM/dd/yyyy) or day/month/year (dd/MM/yyyy). When adding devices to your study, please select the device uploader with the correct format for your locale. PALMS exports all date / times as yyyy-mm-dd hh:mm:ss. Hours are in 24 hour time.

Q: When opening a CSV file in Excel, the dateTime column appears wrong. It only shows minutes:seconds.0.
A: PALMS outputs date/times as year-month-day hour:minutes:seconds.milliseconds (yyyy-mm-dd hh:mm:ss.s). Unfortunately, when Excel reads a CSV file containing that format, Excel makes a poor choice in the display format for the column. To change the format: > Note: you can scroll down and click on the option "m/d/yyyy h:mm", then append ":ss" We recommend saving the spreadsheet as a Excel Workbook (.xls) in order to preserve your formatting choices.
 * 1) Select the entire column
 * 2) Select Format > Cells... in the menu bar.
 * 3) In the Number tab, click on custom.
 * 4) In the text box labeled, Type:, enter the desired format.
 * 1) Click OK.



Q: What's the difference between uploading and inserting?
A: Uploading datasets to PALMS is a two step process: First the file is uploaded to the server. While this is happening the "uploading" message is displayed. Once complete, the "file uploaded" message is displayed.

Then the data is read from the file and inserted into the PALMS repository. While this is happening, the "inserting" message is displayed. When successfully completed, the dataset is marked as "available". If an error occurred during the insertion, the dataset is marked as "rejected". Clicking on the dataset will display an error message containing the reason the dataset was rejected.

Q: Why is my file taking so long to upload and/or insert?
A: In general, the larger the file the more time required to upload and insert. Upload time is dependent on the speed of your internet connection. Insert time is dependent on the number of data samples in your file. PALMS can currently process 3700 samples per second. Five days of accelerometer data sampled every second generates 432,000 samples which requires 116 seconds to process.

Q: What do I do when a dataset is rejected?
A: Datasets are usually rejected because the file uploaded is not in the proper format expected by PALMS or the file contained an invalid entry. Clicking on the rejected message will display the cause of the rejection in a message window. Verify that you followed the procedures for downloading the data from the device. Compare the contents of the file to the file format documentation. Usually the problem occurs within the first 50 lines of the file. It is recommended that you delete the rejected datasets once you determine the cause of the error.

Q: My Qstarz (raw) data set was rejected. The error message was "Unparseable date: /--/-- --:--:--". What should I do?
A:The Qstarz Raw Data Manager sometimes outputs such a line when the device is turned off. Using a text editor such as NotePad++ (not a spreadsheet), search for "--/--". Delete the offending line(s), save the file (best under a new name) and upload the edited file to PALMS.

Q: My Qstarz (raw) data set was rejected. The SAT INFO (SID-SNR) field contains dates! What happened?
A:The CSV file was edited in Excel and Excel interpreted some of the values as dates. The value 8-12 will be changed to aug-12. Do NOT use Excel (or any spreadsheet to edit and save CSV files. If you need to edit a CSV file, use a text editor such as NotePad++.

Q: My dataset was rejected. The error message was "Stored data contains one observation set(s) overlapping with observation data." What does this mean?
A: The data file that you are uploading contains a date / time that already exists in the database. If the data file to be uploaded contains all the the data already in the database, then delete the dataset from PALMS and upload the file again. If it contains only some of the data, edit the data file and upload the file again.

Q: I've edited my CSV file in Excel and now it will not import in to PALMS. Why?
A: Excel often changes the formatting of dates, times and numbers. PALMS expects data columns in specific formats and will reject the dataset as invalid. If you need to edit a CSV file, use a text editor such as NotePad++.

Q: My data imported successfully, but the dates are shown in the early years of first century (00xx). Why?
A: The dates were exported with 2-digit years, instead of 4 digit years. Open the .CSV file with a text editor and verify the date format.
 * Was the CSV file edited in Excel? Excel often changes the formatting of dates, times and numbers (see above).
 * Check the program that create the .CSV file -- does it have a data format option? If so, select a 4-digit year.
 * It could possibly be caused by the date format default in the "Regional and Language" settings on your computer. To verify (in Windows):
 * Open the Control Panel
 * Select "Regional and Language Options"
 * On the "Regional Options" tab, verify the format of the "Short date" field.

Q: I've tried all of the suggestions listed here and I'm still having problems. What should I do?
A: Please email a sample file to us at palms@ucsd.edu with a description of your problem. Include the name of your PALMS study, the make and model of your device and the software (with version number) that created the file. We'll analyze the file and propose a solution.



Q: I received the message saying I needed Java and/or the Java Plug-in. What do I do?
A: Both Java and the Java Plug-in for your browser are required. Refer to installation instructions contained on this page.



Q: What calculation(s) do I use?
A: In general you will always use the PALMS calculation entitled "GPS, Activity, HR - Process and Merge". **When starting a study, always use the current version of the calculation.** Details can be found here.

Q: What's is the meaning of the message "No subjects in study "?
A: You attempted to run a calculation before adding participants and datasets to the study.

Q: What's is the meaning of the status "Failed: Execute... "?
A: The calculation failed to execute successfully, Viewing the log file (by clicking the open book icon) will contain error details. Delete the result set, correct the error and run the calculation again.

Q: Why is my result set empty (count = 0)?
A: The calculation execute successfully, but there was not data to process. Or the parameters were set in such a way that all data was filtered and ignored. Viewing the log file (by clicking the open book icon) will contain details. Delete the result set, correct the parameters and run the calculation again.

Q: Why is my calculation taking so long to execute?
A: Calculation time is a function of the number of participants and the number of samples for each participant. You can check the progress of a running calculation by clicking on the Results tab at the top of the screen. The columns "Count" and "% Complete" are updated as the calculation completes processing each participant's data. Count is the total number of rows written to the resultset. % Complete is the participants completed / total number of participants in the calculation.



Q:How are activity bouts numbered? Why should the first bout be numbered 10003?
A: Activity bouts numbering starts at 1. Sedentary periods start at 10001. If the bout is zero, that means there was activity, but not enough to meet either criteria. A bout number zero with an activity value -2 indicates the person was not wearing the accelerometer. An activity value of -1 indicates no accelerometer data was collected at that time

 Bouts and Sedentary periods are numbered from the beginning of the accelerometer data. In this case, there was accelerometer data collected before the GPS data, so the first sedentary bout was numbered 10003. If in the Merge Options, you were to un-check “Merge data to GPS” all of the accelerometer data would be visible.



Q:What's a GUID?
A: Globally Unique Identifiers (GUIDs) are assigned by the PALMS software to each study, participant, dataset and resultset. These values are contained in the log file to help the PALMS staff troubleshoot and solve software problems. You can ignore them.



Q: I click the "export CSV" icon and nothing happened.
A:Your browser may be set to disable pop-ups. If it is, allow popups from https:// palms.ucsd.edu and click the icon again and wait for the download dialog box. Note for large result sets, it may take several minutes for the dialog box to appear. If you are using Internet Explorer, see this page for more information.

Q: When opening a CSV file in Excel, the dateTime column appears wrong. It only shows minutes:seconds.0.
A: Please refer to the discussion on timezones and date/time formats above.

Q: When opening a CSV file in Excel, I get the message "File not loaded completely."
A: Excel 2003 has a limit of 65,536 rows. Clicking "OK" will truncate the file to that limit. Excel 2007 and 2010 has a limitation of 1,048,576 rows. In PALMS, the "Count" column in the results table contains the number of rows in the result set (and thus the CSV file).



Q: I click the "export KML" icon and nothing happened.
A:Your browser may be set to disable pop-ups. If it is, allow popups from https:// palms.ucsd.edu and click the icon again and wait for the download dialog box. Note for large result sets, it may take several minutes for the dialog box to appear. If you are using Internet Explorer, see this page for more information.

Q: When opening a KML file in Google Earth, I'm getting a "error parsing..." error. What should I do?
A: Please email us a copy of KML file if possible and we'll investigate. In the Google Earth menu bar, click on Tools, then "Options". Click the General tab. In the KML Error Handling box, click the "Silently accept all unrecognized data" radio button, and click OK. Attempt to open the KML file again in Google Earth.

Q: When opening a KML file, I'm getting the error "No results - empty KML file". What should I do?
A: PALMS experienced a problem while generating the KML file and returned a file containing no data. Attempt to generate the KML file again in PALMS by clicking on the KML icon for the desired result set.

Q:Why am I receiving the message "This result set can not be exported as a KML file..."?
A: The resultset you are attempting to export does not contain a latitude and longitude columns and thus can not be mapped. It can be exported as a CSV file.