Open Microscopy Environment

Hi,

I use the command tiffcomment (http://downloads.openmicroscopy.org/bio-formats/5.0.0/) that runs into the warning shown below. I have seen that it should help to use the option "-no-upgrade" to get rid of these warnings, but this option is unknown to the command.

Furthermore there is no option like "--help" / "-h"

Can you help me?

Frank



%>./tiffcomment OME-artifical-datasets/single-channel2.ome.tif | ./xmlindent

Failed to compare version numbersjava.net.SocketTimeoutException: connect timed out at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:384) at java.net.Socket.connect(Socket.java:546) at sun.net.NetworkClient.doConnect(NetworkClient.java:173) at sun.net.www.http.HttpClient.openServer(HttpClient.java:409) at sun.net.www.http.HttpClient.openServer(HttpClient.java:530) at sun.net.www.http.HttpClient.
<init>
(HttpClient.java:240) at sun.net.www.http.HttpClient.New(HttpClient.java:321) at sun.net.www.http.HttpClient.New(HttpClient.java:338) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:935) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:876) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:801) at loci.formats.UpgradeChecker.newVersionAvailable(UpgradeChecker.java:230) at loci.formats.UpgradeChecker.newVersionAvailable(UpgradeChecker.java:176) at loci.formats.tools.TiffComment.main(TiffComment.java:65)

Unfortunately, tiffcomment doesn't yet take the -no-upgrade argument like bfconvert does.

If you're using Bio-Formats 5.0.0 or later, you can set NO_UPDATE_CHECK instead:

Code: Select all

$ env NO_UPDATE_CHECK=1 ./tiffcomment


Cheers,
~Josh

Hi Josh,

it seems that it does not help (in tcsh). See below.

Frank


%>env NO_UPDATE_CHECK=1 ./tiffcomment OME-artifical-datasets/time-series.ome.tif
Failed to compare version numbers
java.net.SocketTimeoutException: connect timed out
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:384)
at java.net.Socket.connect(Socket.java:546)
at sun.net.NetworkClient.doConnect(NetworkClient.java:173)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:409)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:530)
at sun.net.www.http.HttpClient.<init>(HttpClient.java:240)
at sun.net.www.http.HttpClient.New(HttpClient.java:321)
at sun.net.www.http.HttpClient.New(HttpClient.java:338)
at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:935)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:876)
at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:801)
at loci.formats.UpgradeChecker.newVersionAvailable(UpgradeChecker.java:230)
at loci.formats.UpgradeChecker.newVersionAvailable(UpgradeChecker.java:176)
at loci.formats.tools.TiffComment.main(TiffComment.java:65)
<?xml version="1.0" encoding="UTF-8" standalone="no"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://ome-xml.org/wiki/OmeTiff. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2013-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:93057338-e834-4c00-be8d-c0227a167c38" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2013-06 http://www.openmicroscopy.org/Schemas/O ... 06/ome.xsd"><Image ID="Image:0" Name="time-series"><AcquisitionDate>2013-06-19T13:02:13</AcquisitionDate><Pixels DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="7" SizeX="439" SizeY="167" SizeZ="1" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="time-series.ome.tif">urn:uuid:93057338-e834-4c00-be8d-c0227a167c38</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="1" PlaneCount="1"><UUID FileName="time-series.ome.tif">urn:uuid:93057338-e834-4c00-be8d-c0227a167c38</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="0" IFD="2" PlaneCount="1"><UUID FileName="time-series.ome.tif">urn:uuid:93057338-e834-4c00-be8d-c0227a167c38</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="0" IFD="3" PlaneCount="1"><UUID FileName="time-series.ome.tif">urn:uuid:93057338-e834-4c00-be8d-c0227a167c38</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="0" IFD="4" PlaneCount="1"><UUID FileName="time-series.ome.tif">urn:uuid:93057338-e834-4c00-be8d-c0227a167c38</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="0" IFD="5" PlaneCount="1"><UUID FileName="time-series.ome.tif">urn:uuid:93057338-e834-4c00-be8d-c0227a167c38</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="0" IFD="6" PlaneCount="1"><UUID FileName="time-series.ome.tif">urn:uuid:93057338-e834-4c00-be8d-c0227a167c38</UUID></TiffData></Pixels></Image></OME>
107%>

In tcsh, can you try with:

Code: Select all

  setenv NO_UPDATE_CHECK 1
  echo "$NO_UPDATE_CHECK"
  ./tiffcomment ...


Cheers,
~Josh

I am sorry to say that, but it stays the same although I set the environment variable in the shell.

Frank

Hmmm....what does "bfconvert -version" say? In my case it's:

Code: Select all

$ bfconvert -version
Version: 5.0.0
VCS revision: cd2a5db
Build date: 7 March 2014


Cheers,
~Josh.

That's it! Thank you! Have a nice weekend.

I was using v4.4.10 and build 15 Jan 2014


Frank

You too!
~Josh