Cannot access remote data on Some Systems

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What steps will reproduce the problem?

Using software based on the WFDB library, such as the WFDB Toolbox for MATLAB, 
it should be possible to read PhysioBank data directly from PhysioNet (i.e., 
without downloading files first). For example, after starting MATLAB and 
installing the WFDB Toolbox, this command should not result in an error:

%%This will attempt to read data from PhysioNet servers using libcurl.
%%It assumes that you have never loaded the record mitdb/100 in your machine
%%before (otherwise it could be cached in your system and still work).
[tm,signal]=rdsamp('mitdb/100');size(signal)

What is the expected output? What do you see instead?

This command should produce this output:

ans =

       21600           2

For reasons we have not yet determined, this command fails on some machines, 
producing this output instead:

Warning: Could not get signal information. Attempting to read signal
without buffering.
> In rdsamp at 107
Command exited with non-zero status!!
Error using rdsamp (line 152)
Java exception occurred:
java.lang.NullPointerException
at org.physionet.wfdb.Wfdbexec.execToDoubleArray(Unknown Source)


 If this happens, any WFDB toolbox commands that attempt to access remote data will fail similarly. If you are experiencing this problem, please help us to find its cause by running the command 'wfdbtest()' from the MATLAB command prompt. Copy and paste the output into an email, and send it to: [email protected].

We have been able to observe this problem on one of two apparently identically 
configured Windows 7 machines; on the second machine, the problem does not 
occur. The toolbox is normally able to behave as a web client to retrieve data 
from the PhysioNet server by using the libcurl library (DLL). Our best guess 
about the cause of the problem is that the Java virtual machine (JVM) invoked 
by the toolbox functions is unable to load libcurl, either because the JVM is 
not looking in the correct location, or because a security setting prevents the 
JVM from loading libcurl.

Solution: Whether or not you encounter the problem described above, you can 
always use the WFDB Toolbox for MATLAB to read data files within the current 
directory or a subdirectory of it. There are several ways to download data 
files from PhysioNet, described below.

    To download a single record, you can use your web browser. Navigate to http://physionet.org/physiobank/database and follow the links to the data set of interest. For example, you will find the MIT-BIH Arrhythmia Database at http://physionet.org/physiobank/database/mitdb/. In most cases, a record is stored in multiple files with the same base name (the record name) and different suffixes, and you will generally need to download all of them for any record of interest. For example, record 100 of the MIT-BIH Arrhythmia Database includes a short text header file (100.hea), a longer binary signal file (100.dat), and a medium-length binary annotation file (100.atr).

    To download an entire database (a set of records), there are several efficient methods. Two of the recommended methods are described in the PhysioNet FAQ, at: http://physionet.org/faq.shtml#downloading-databases and http://physionet.org/faq.shtml#zip-tar. These methods are recommended because they can update previously downloaded databases quickly, and because they can complete interrupted downloads efficiently. The first method is preferred if you can use it, because it has the lowest impact on the PhysioNet servers.

    The WFDB toolbox (version 0.9.5 and later) provides the PHYSIONETDB function for downloading the header and signal files (but not the annotation files) of a database. For example, download all of the .hea and .dat files of the MIT-BIH Arrhythmia Database from the MATLAB prompt using the command:

        rc=physionetdb('mitdb',1);

Original issue reported on code.google.com by [email protected] on 9 Jan 2014 at 3:14

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Original comment by [email protected] on 9 Jan 2014 at 3:49

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Original comment by [email protected] on 9 Jan 2014 at 6:51

• Added labels: Priority-High, Milestone-Release1.0
• Removed labels: Priority-Critical

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Original comment by [email protected] on 18 Jan 2014 at 5:19

• Changed state: Started

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Issue 41 has been merged into this issue.

Original comment by [email protected] on 27 May 2014 at 8:50

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Hi Ikaro,

I have just installed the latest version from WFDB (0.9.8) on my problematic 
system. Attached are the error messages, I hope it helps.

Best regards,

Fernando

Original comment by [email protected] on 18 Dec 2014 at 1:23

Attachments:

• log.txt