#19 Output to stdout broken (invalid XML) due to log message

[Archie Cobbs]

Attempting to convert a Bruker file to standard output using --outdir - results in invalid XML, because the first line output is a log message.

Command being run:

msconvert.exe --32 --zlib --filter "peakPicking true 1-" --outdir - 'C:\Users\Archie Cobbs\Desktop\HL60.d\analysis.baf' >xx.mzML

Resulting content in xx.mzML... note log message on the first line:

2018-04-06 16:54:43.175982 [tid=0x1208] [INFO ] bdal.io.baf2sql: Generating new SQLite cache in analysis directory: C:\Users\Archie Cobbs\Desktop\HL60.d\analysis.sqlite
<?xml version="1.0" encoding="utf-8"?>
<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
  <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="HL60" version="1.1.0">
 ...

Happens in version 3.0.11885.

[Archie Cobbs]

I suppose it's obvious, but the proper fix is to send all log messages to standard error, not standard output.

[Brian Pratt]

Hi Archie,

Thanks for the report. Unfortunately that log message is coming from the
Bruker reader DLL, and we can't readily control that behavior. (MSConvert
already directs informational messages to stderr when stdout is the output
stream.)

You'll have to work out a solution that doesn't involve stdout, or possibly
run the conversion twice to provoke the creation of that sqlite file when
needed.

Brian

On Fri, Apr 6, 2018 at 5:32 PM, Archie Cobbs archiecobbs@users.sourceforge.net wrote:

I suppose it's obvious, but the proper fix is to send all log messages to
standard error, not standard output.

---

• [bugs:#19] https://sourceforge.net/p/proteowizard/bugs/19/ Output to
  stdout broken (invalid XML) due to log message*

Status: open
Group: v1.0_(example)
Created: Fri Apr 06, 2018 10:01 PM UTC by Archie Cobbs
Last Updated: Fri Apr 06, 2018 10:01 PM UTC
Owner: nobody

Attempting to convert a Bruker file to standard output using --outdir -
results in invalid XML, because the first line output is a log message.

Command being run:

msconvert.exe --32 --zlib --filter "peakPicking true 1-" --outdir - 'C:\Users\Archie Cobbs\Desktop\HL60.d\analysis.baf' >xx.mzML

Resulting content in xx.mzML... note log message on the first line:

2018-04-06 16:54:43.175982 [tid=0x1208] [INFO ] bdal.io.baf2sql: Generating new SQLite cache in analysis directory: C:\Users\Archie Cobbs\Desktop\HL60.d\analysis.sqlite

<indexedmzml xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemalocation="http://psi.hupo.org/ms/mzml &lt;a href=" http:="" psidev.info="" files="" ms="" mzml="" xsd="" mzml1.1.2_idx.xsd"="">http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
<mzml xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemalocation="http://psi.hupo.org/ms/mzml &lt;a href=" http:="" psidev.info="" files="" ms="" mzml="" xsd="" mzml1.1.0.xsd"="">http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="HL60" version="1.1.0">
...</mzml></indexedmzml>

Happens in version 3.0.11885.

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[Archie Cobbs]

OK. I've worked around it by ignoring all characters prior to the first '<'.

If you have any contacts with the Bruker team (perhaps Daniel Kruegler?), they might be interested to see this issue.

Thanks.