Recent changes to bugs

Startup Failure

2004-06-09T18:57:27Z

Earlier today I tried downloading the new version of OME in
java. After doing this, I ran the shoola.jar file. At this point I
thought it was smooth sailing because the window asking for
a username and a password came up. I looked on the OME
website and it didn't say anything about username and
password registry, so I figured any username and password
would do. After entering this, I enountered the following
errors:

Abnormal termination due to an uncaught exception.
java.lang.RuntimeException: Internal error.
at
org.openmicroscopy.shoola.env.data.OMEDSGateway.handle
Exception(OMEDSGateway.java:117)
at
org.openmicroscopy.shoola.env.data.OMEDSGateway.retriev
eListData(OMEDSGateway.java:304)
at
org.openmicroscopy.shoola.env.data.STSAdapter.getAvailabl
eImageTypes(STSAdapter.java:99)
at
org.openmicroscopy.shoola.agents.browser.BrowserAgent.se
tContext(BrowserAgent.java:246)
at
org.openmicroscopy.shoola.env.Container.startService(Conta
iner.java:276)
at
org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializ
er.java:191)
at
org.openmicroscopy.shoola.env.Container.runStartupProcedu
re(Container.java:112)
at
org.openmicroscopy.shoola.env.Container.access$000(Contai
ner.java:78)
at
org.openmicroscopy.shoola.env.Container$1.run(Container.ja
va:154)
at java.lang.Thread.run(Thread.java:554)
Caused by: java.lang.IllegalArgumentException: Have not
logged in
at
org.openmicroscopy.ds.XmlRpcCaller.dispatch(XmlRpcCaller.
java:387)
at
org.openmicroscopy.ds.InstantiatingCaller.dispatchList(Insta
ntiatingCaller.java:143)
at
org.openmicroscopy.ds.DataFactory.retrieveList(DataFactory
.java:430)
at
org.openmicroscopy.shoola.env.data.OMEDSGateway.retriev
eListData(OMEDSGateway.java:302)
... 8 more
Exception in thread "Initializer"

Now I don't know if this is due to the fact that I did not
register my username and password, but since I don't know
how to register, can you please help me? Thank you.

Feature Import fails

2003-12-03T17:10:37Z

This test fails at Import:
execute 'Feature test chain', Export All, dropdb, Import
Export / Import round trip works for the same dataset
when Feature test chain is not ran. I do not know if
this test ever passed, or if this is a recent breakage.
A rough inspection indicates OME2OME-CA.xslt and
OME/ImportExport/HierarchyImport.pm may need modifications.

bootstrap loops indefinately

2003-10-03T20:03:30Z

running the ./bootstrapOME.pl script gives me:

hasa() is deprecated in favour of has_a(). Using it
instead. at /usr/local/share/perl/5.8.0/OME/Image.pm
line 32

indefinately. If i change the script to:
#!/usr/bin/perl -w
print "Foo\n";
...

foo is never printed. For some reason there seems to be
an infinate loop somewhere in a BEGIN statement. I'll
try reinstalling.

System: Debian Sarge

laurichj@bioinfo.ucr.edu

Update installation instructions

2003-04-23T15:49:02Z

1) Due to last Saturday's changes to bootstrapOME.pl,
the file OME/SessionManager.pm needs to be visible to
bootstrapOME when it is run. If it isn't, the error
"Can't locate OME/SessionManager.pm in @INC" is output.
bootstrapOME also expects its SQL configuration files
to be present in the current directory. If they
aren't, the misleading error "DBD::Pg::st execute
failed: ERROR: Relation "attribute_seq" does not
exist" is output. To satisfy both requirements, the
first paragraph in the Finishing Up section of
SBDD/contents/instructions/p2.htm needs to be modified
to something like: "Change to the OME/src/SQL
directory, and enter the line perl -I ../perl2
./bootstrapOME.pl"

2) In the same paragraph, note that the script needs to
be run as root OR as the user who will be the OME
administrator.

OME/repository must be writable by Apache

2003-04-18T22:50:30Z

The SBDD should instruct the admin that OME/repository
must be writable by the apache process, else importing
tifs will mysteriously fail (even the logs in
apache/logs/error_log only report that print could not
print to a closed file handle.).

Possible solutions are either chmod 777 OME/repository
or adding the apache user to the ome group and chmod 775.

This could possibly be taken care of in bootstrap.pl.
Alternatively, I've written a supplemental installation
script which takes care of most of the last page of
SBDD: moving files, setting permissions, etc... It
would need testing, the developers are welcome to
release it as part of the OME package under the GPL.

Prevent multiple imports

2003-03-18T17:15:17Z

The importer will accept the same input file multiple
times. Need to wire up the detection of a repeat import
attempt via the import file's SHA1 digest.

Viewer

2003-03-18T15:09:43Z

Want to view an image.
Problem in Image.pm

Error Message:
Deep recursion on subroutine "OME::Image:Dimension"
line 101 in Image.pm

Bug due to the image I want to see??

test2

2003-03-13T18:24:00Z

a wee little test bug to see who gets notified

Access

2003-03-13T10:06:08Z

Note that Login is currently meaningless in the system.
Once you know you that patterns, is easy to get to any
page in the system. For example, try just pointitng
browser to:

http://.../serve.pl?Page=OME::Web::Home

or DatasetSearch

or any of the others.

Is true that eventually some of the functions will
break, when accessed in this way, but a not ogged in
user can do alot before this point.

Importer bug

2003-03-13T09:47:24Z

Import function cannot distinguish between image and
non-image files in a directory. Thus if user chooses a
full directory, if one of the files there is not an
image (a log file from, or other metadata file), the
Importer faitfully attempts to import and then breaks.
This can llead to a partially completed DB transaction?