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From: Adhemar Z. N. <ad...@cp...> - 2005-09-20 17:55:59
|
<font size=3D"1" style=3D"font-family: courier new,courier,monospace;"><s=
pan
style=3D"font-family: arial,helvetica,sans-serif;"><font size=3D"2">Hello=
<br
/><br />I just downloaded the InsertSequenceFeatures plugin revision 3451
and when I try to run it the following error appears:<br
/></font></span><br />ERROR:<br />Can't locate object method
"ignoreFeature" via package
"GUS::Supported::BioperlFeatMapper" at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenc=
eFeatures.pm
line 753, <GEN39> line 42.<br /><br />STACK TRACE:<br />=A0at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenc=
eFeatures.pm
line 753<br />=A0=A0=A0=A0=A0=A0=A0
GUS::Supported::Plugin::InsertSequenceFeatures::makeImmediateFeature('GUS=
::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x850b8cc)',
'Bio::SeqFeature::Generic=3DHASH(0x9731c10)', 4) called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenc=
eFeatures.pm
line 728<br />=A0=A0=A0=A0=A0=A0=A0
GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Support=
ed::Plugin::InsertSequenceFeatures=3DHASH(0x850b8cc)',
'Bio::SeqFeature::Generic=3DHASH(0x9731c10)', 4) called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenc=
eFeatures.pm
line 368<br />=A0=A0=A0=A0=A0=A0=A0
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plug=
in::InsertSequenceFeatures=3DHASH(0x850b8cc)',
'HASH(0x94c2c94)') called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 469<br />=A0=A0=A0=A0=A0=A0=A0 eval {...} called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 461<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x84d5c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 380<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x84d5c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 288<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x84d5c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 197<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x84d5c20)',
'ARRAY(0x84e9918)') called at /usr/local/SchistoDB/gus_home/bin/ga line
11<br /><br /><br /><span style=3D"font-family:
arial,helvetica,sans-serif;"><font size=3D"2">Do anybody know what is it
about?<br /><br />Thanks<br /><br />Adhemar</font></span></font>
|
|
From: <mro...@cs...> - 2006-10-24 20:44:10
|
Steve,
I am almost ready to insert some bacteria sequences from genebank, and i
have some questions.
a - i found in the gusdev site the following:
From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32
for those of you who are using the beta version of the ISF plugin:
1. i will improve its documentation to indicate what it expects to
already be in the database:
- SequenceOntology (InsertSequenceOntology plugin)
- NCBI Taxon (LoadTaxon plugin)
- External database and release (InsertExternalDatabase and
InsertExternalDatabaseRls plugins)
- at least one row in SequenceType so you can say what type of
sequence you are loading (you can use LoadRow plugin for this=
)
2. i will improve the error messages so that it better detects the
absence of these, and makes it more clear what to do.
About loading SO:
1. can you send the SO term with definition that is too big?
2. i understand about the rollback. we have been discussing how to
undo a plugin. for now, you need to do it with sql.
Thanks for helping us make this plugin better.
steve
We did a new GUS install two weeks ago and i wonder if this applies to me=
,
if it does could you tell me where do i find the documentation that you
mention above.
b - When I do a search in gusdev for "InsertSequenceFeatures" or parts of
it, i get very little replies and somotimes none. Is there another way to
find all documents in gusdev relating to this.
Thank you
Michael R
|
|
From: Steve F. <sfi...@pc...> - 2006-10-24 20:59:44
|
the only documentation is what you get by running the plugin w/ --help i can (try to) answer questions as they come up. it may turn out that the best way to proceed is an orientation by phone. steve mro...@cs... wrote: >Steve, > >I am almost ready to insert some bacteria sequences from genebank, and i >have some questions. > >a - i found in the gusdev site the following: > > From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32 > for those of you who are using the beta version of the ISF plugin: > 1. i will improve its documentation to indicate what it expects to > already be in the database: > - SequenceOntology (InsertSequenceOntology plugin) > - NCBI Taxon (LoadTaxon plugin) > - External database and release (InsertExternalDatabase and > InsertExternalDatabaseRls plugins) > - at least one row in SequenceType so you can say what type of > sequence you are loading (you can use LoadRow plugin for this) > > 2. i will improve the error messages so that it better detects the > absence of these, and makes it more clear what to do. > > About loading SO: > 1. can you send the SO term with definition that is too big? > > 2. i understand about the rollback. we have been discussing how to > undo a plugin. for now, you need to do it with sql. > > Thanks for helping us make this plugin better. > > steve > >We did a new GUS install two weeks ago and i wonder if this applies to me, >if it does could you tell me where do i find the documentation that you >mention above. > >b - When I do a search in gusdev for "InsertSequenceFeatures" or parts of >it, i get very little replies and somotimes none. Is there another way to >find all documents in gusdev relating to this. > >Thank you > >Michael R > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: <mro...@cs...> - 2006-10-25 18:02:43
|
Steve, When changes are made to the plugins in GUS (improvements, bugs etc) do you have "patches" (like in windows programs) that can be applied to GUS, or how it is handle? Thanks Michael R > john- > > this GUS user, michael, has downloaded and installed the latest GUS. > > your new PluginError.pm is giving him problems. see below. > > steve > > mro...@cs... wrote: > >>Steve, >> >>Thanks for the phone orientation offer, tomorrow will be great, I am on >> my >>way to a 3 hour class. >> >>In the meantime I run: >> >> mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/Supported/Plugin 9% >> ga GUS::Supported::Plugin::InsertSequenceFeatures >> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml >> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk >> --fileFormat genbank >> --extDbName "Pseudomonas_aeruginosa" >> --extDbRlsVer "1000" >> --soCvsVersion "1.1.4" >> --commit >> >> >>and got: >> >> Base class package "Error" is empty. >> (Perhaps you need to 'use' the module which defines that package >> first.) >> at /home/acrl-storage-1/gusdb-dev/GUS/gus_home/ >> lib/perl/GUS/PluginMgr/PluginError.pm line 2 >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/bin/ga line 7. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/bin/ga line 7. >> >> >>I examined the errors by looking in the programs and all errors have >>something in common: >> >> use GUS::PluginMgr::GusApplication; #at ga.pm line 7 >> use GUS::PluginMgr::Plugin; #at GusApplication.pm line 27 >> use GUS::PluginMgr::PluginError; #at Plugin.pm line 29 >> use base qw(Error); #at PluginError.pm line 2 >> >> >>It probably is a stupid mistake on my part, but I can not see >> >>All help will be very much appreciated. >> >> >>Thanks again >> >>Michael >> >> >> >> >> >>>the only documentation is what you get by running the plugin w/ --help >>> >>>i can (try to) answer questions as they come up. >>> >>>it may turn out that the best way to proceed is an orientation by phon= e. >>> >>>steve >>> >>>mro...@cs... wrote: >>> >>> >>> >>>>Steve, >>>> >>>>I am almost ready to insert some bacteria sequences from genebank, an= d >>>> i >>>>have some questions. >>>> >>>>a - i found in the gusdev site the following: >>>> >>>>From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32 >>>>for those of you who are using the beta version of the ISF plugin: >>>> 1. i will improve its documentation to indicate what it expects to >>>> already be in the database: >>>> - SequenceOntology (InsertSequenceOntology plugin) >>>> - NCBI Taxon (LoadTaxon plugin) >>>> - External database and release (InsertExternalDatabase and >>>> InsertExternalDatabaseRls plugins) >>>> - at least one row in SequenceType so you can say what type = of >>>> sequence you are loading (you can use LoadRow plugin for >>>>this) >>>> >>>> 2. i will improve the error messages so that it better detects the >>>> absence of these, and makes it more clear what to do. >>>> >>>> About loading SO: >>>> 1. can you send the SO term with definition that is too big? >>>> >>>> 2. i understand about the rollback. we have been discussing how t= o >>>> undo a plugin. for now, you need to do it with sql. >>>> >>>> Thanks for helping us make this plugin better. >>>> >>>> steve >>>> >>>>We did a new GUS install two weeks ago and i wonder if this applies t= o >>>>me, >>>>if it does could you tell me where do i find the documentation that y= ou >>>>mention above. >>>> >>>>b - When I do a search in gusdev for "InsertSequenceFeatures" or part= s >>>> of >>>>it, i get very little replies and somotimes none. Is there another wa= y >>>> to >>>>find all documents in gusdev relating to this. >>>> >>>>Thank you >>>> >>>>Michael R >>>> >>>> >>>>-------------------------------------------- >>>> >>>> > |
|
From: <mro...@cs...> - 2006-10-27 12:21:58
|
Steve, I am sorry to be a pain, but I was wondering if you have received any new= s from John concerning the PluginError.pm Thank you Michael > john- > > this GUS user, michael, has downloaded and installed the latest GUS. > > your new PluginError.pm is giving him problems. see below. > > steve > > mro...@cs... wrote: > >>Steve, >> >>Thanks for the phone orientation offer, tomorrow will be great, I am on >> my >>way to a 3 hour class. >> >>In the meantime I run: >> >> mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/Supported/Plugin 9% >> ga GUS::Supported::Plugin::InsertSequenceFeatures >> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml >> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk >> --fileFormat genbank >> --extDbName "Pseudomonas_aeruginosa" >> --extDbRlsVer "1000" >> --soCvsVersion "1.1.4" >> --commit >> >> >>and got: >> >> Base class package "Error" is empty. >> (Perhaps you need to 'use' the module which defines that package >> first.) >> at /home/acrl-storage-1/gusdb-dev/GUS/gus_home/ >> lib/perl/GUS/PluginMgr/PluginError.pm line 2 >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/bin/ga line 7. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/bin/ga line 7. >> >> >>I examined the errors by looking in the programs and all errors have >>something in common: >> >> use GUS::PluginMgr::GusApplication; #at ga.pm line 7 >> use GUS::PluginMgr::Plugin; #at GusApplication.pm line 27 >> use GUS::PluginMgr::PluginError; #at Plugin.pm line 29 >> use base qw(Error); #at PluginError.pm line 2 >> >> >>It probably is a stupid mistake on my part, but I can not see >> >>All help will be very much appreciated. >> >> >>Thanks again >> >>Michael >> >> >> >> >> >>>the only documentation is what you get by running the plugin w/ --help >>> >>>i can (try to) answer questions as they come up. >>> >>>it may turn out that the best way to proceed is an orientation by phon= e. >>> >>>steve >>> >>>mro...@cs... wrote: >>> >>> >>> >>>>Steve, >>>> >>>>I am almost ready to insert some bacteria sequences from genebank, an= d >>>> i >>>>have some questions. >>>> >>>>a - i found in the gusdev site the following: >>>> >>>>From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32 >>>>for those of you who are using the beta version of the ISF plugin: >>>> 1. i will improve its documentation to indicate what it expects to >>>> already be in the database: >>>> - SequenceOntology (InsertSequenceOntology plugin) >>>> - NCBI Taxon (LoadTaxon plugin) >>>> - External database and release (InsertExternalDatabase and >>>> InsertExternalDatabaseRls plugins) >>>> - at least one row in SequenceType so you can say what type = of >>>> sequence you are loading (you can use LoadRow plugin for >>>>this) >>>> >>>> 2. i will improve the error messages so that it better detects the >>>> absence of these, and makes it more clear what to do. >>>> >>>> About loading SO: >>>> 1. can you send the SO term with definition that is too big? >>>> >>>> 2. i understand about the rollback. we have been discussing how t= o >>>> undo a plugin. for now, you need to do it with sql. >>>> >>>> Thanks for helping us make this plugin better. >>>> >>>> steve >>>> >>>>We did a new GUS install two weeks ago and i wonder if this applies t= o >>>>me, >>>>if it does could you tell me where do i find the documentation that y= ou >>>>mention above. >>>> >>>>b - When I do a search in gusdev for "InsertSequenceFeatures" or part= s >>>> of >>>>it, i get very little replies and somotimes none. Is there another wa= y >>>> to >>>>find all documents in gusdev relating to this. >>>> >>>>Thank you >>>> >>>>Michael R >>>> >>>> >>>>-------------------------------------------- >>>> >>>> > |
|
From: Mark S. H. <mh...@ug...> - 2006-10-27 13:20:46
|
I'm coming in late to this thread but it looks like you need to install the Error module from CPAN. http://search.cpan.org/~shlomif/Error-0.17008/lib/Error.pm I had to install version 0.17006, the latest 0.17008 version didn't compile for me out of the box. -M On Oct 27, 2006, at 8:21 AM, mro...@cs... wrote: > Steve, > > I am sorry to be a pain, but I was wondering if you have received > any news > from John concerning the PluginError.pm > > Thank you > > > Michael > > > >> john- >> >> this GUS user, michael, has downloaded and installed the latest GUS. >> >> your new PluginError.pm is giving him problems. see below. >> >> steve >> >> mro...@cs... wrote: >> >>> Steve, >>> >>> Thanks for the phone orientation offer, tomorrow will be great, I >>> am on >>> my >>> way to a 3 hour class. >>> >>> In the meantime I run: >>> >>> mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/ >>> gus_home/lib/perl/GUS/Supported/Plugin 9% >>> ga GUS::Supported::Plugin::InsertSequenceFeatures >>> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml >>> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk >>> --fileFormat genbank >>> --extDbName "Pseudomonas_aeruginosa" >>> --extDbRlsVer "1000" >>> --soCvsVersion "1.1.4" >>> --commit >>> >>> >>> and got: >>> >>> Base class package "Error" is empty. >>> (Perhaps you need to 'use' the module which defines that package >>> first.) >>> at /home/acrl-storage-1/gusdb-dev/GUS/gus_home/ >>> lib/perl/GUS/PluginMgr/PluginError.pm line 2 >>> >>> BEGIN failed--compilation aborted at >>> /home/acrl-storage-1/gusdb-dev/GUS/ >>> gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2. >>> >>> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/ >>> GUS/ >>> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >>> >>> BEGIN failed--compilation aborted at >>> /home/acrl-storage-1/gusdb-dev/GUS/ >>> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >>> >>> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/ >>> GUS/ >>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >>> >>> BEGIN failed--compilation aborted at >>> /home/acrl-storage-1/gusdb-dev/GUS/ >>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >>> >>> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/ >>> GUS/ >>> gus_home/bin/ga line 7. >>> >>> BEGIN failed--compilation aborted at >>> /home/acrl-storage-1/gusdb-dev/GUS/ >>> gus_home/bin/ga line 7. >>> >>> >>> I examined the errors by looking in the programs and all errors have >>> something in common: >>> >>> use GUS::PluginMgr::GusApplication; #at ga.pm line 7 >>> use GUS::PluginMgr::Plugin; #at GusApplication.pm line 27 >>> use GUS::PluginMgr::PluginError; #at Plugin.pm line 29 >>> use base qw(Error); #at PluginError.pm line 2 >>> >>> >>> It probably is a stupid mistake on my part, but I can not see >>> >>> All help will be very much appreciated. >>> >>> >>> Thanks again >>> >>> Michael >>> >>> >>> >>> >>> >>>> the only documentation is what you get by running the plugin w/ >>>> --help >>>> >>>> i can (try to) answer questions as they come up. >>>> >>>> it may turn out that the best way to proceed is an orientation >>>> by phone. >>>> >>>> steve >>>> >>>> mro...@cs... wrote: >>>> >>>> >>>> >>>>> Steve, >>>>> >>>>> I am almost ready to insert some bacteria sequences from >>>>> genebank, and >>>>> i >>>>> have some questions. >>>>> >>>>> a - i found in the gusdev site the following: >>>>> >>>>> From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32 >>>>> for those of you who are using the beta version of the ISF plugin: >>>>> 1. i will improve its documentation to indicate what it >>>>> expects to >>>>> already be in the database: >>>>> - SequenceOntology (InsertSequenceOntology plugin) >>>>> - NCBI Taxon (LoadTaxon plugin) >>>>> - External database and release (InsertExternalDatabase >>>>> and >>>>> InsertExternalDatabaseRls >>>>> plugins) >>>>> - at least one row in SequenceType so you can say what >>>>> type of >>>>> sequence you are loading (you can use LoadRow plugin for >>>>> this) >>>>> >>>>> 2. i will improve the error messages so that it better >>>>> detects the >>>>> absence of these, and makes it more clear what to do. >>>>> >>>>> About loading SO: >>>>> 1. can you send the SO term with definition that is too big? >>>>> >>>>> 2. i understand about the rollback. we have been discussing >>>>> how to >>>>> undo a plugin. for now, you need to do it with sql. >>>>> >>>>> Thanks for helping us make this plugin better. >>>>> >>>>> steve >>>>> >>>>> We did a new GUS install two weeks ago and i wonder if this >>>>> applies to >>>>> me, >>>>> if it does could you tell me where do i find the documentation >>>>> that you >>>>> mention above. >>>>> >>>>> b - When I do a search in gusdev for "InsertSequenceFeatures" >>>>> or parts >>>>> of >>>>> it, i get very little replies and somotimes none. Is there >>>>> another way >>>>> to >>>>> find all documents in gusdev relating to this. >>>>> >>>>> Thank you >>>>> >>>>> Michael R >>>>> >>>>> >>>>> -------------------------------------------- >>>>> >>>>> >> > > > > ---------------------------------------------------------------------- > --- > Using Tomcat but need to do more? Need to support web services, > security? > Get stuff done quickly with pre-integrated technology to make your > job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: <mro...@cs...> - 2006-10-24 20:45:15
|
Steve,
I am almost ready to insert some bacteria sequences from genebank, and i
have some questions.
a - i found in the gusdev site the following:
From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32
for those of you who are using the beta version of the ISF plugin:
1. i will improve its documentation to indicate what it expects to
already be in the database:
- SequenceOntology (InsertSequenceOntology plugin)
- NCBI Taxon (LoadTaxon plugin)
- External database and release (InsertExternalDatabase and
InsertExternalDatabaseRls plugins)
- at least one row in SequenceType so you can say what type of
sequence you are loading (you can use LoadRow plugin for this=
)
2. i will improve the error messages so that it better detects the
absence of these, and makes it more clear what to do.
About loading SO:
1. can you send the SO term with definition that is too big?
2. i understand about the rollback. we have been discussing how to
undo a plugin. for now, you need to do it with sql.
Thanks for helping us make this plugin better.
steve
We did a new GUS install two weeks ago and i wonder if this applies to me=
,
if it does could you tell me where do i find the documentation that you
mention above.
b - When I do a search in gusdev for "InsertSequenceFeatures" or parts of
it, i get very little replies and somotimes none. Is there another way to
find all documents in gusdev relating to this.
Thank you
Michael R
|
|
From: Steve F. <sfi...@pc...> - 2005-09-20 17:58:45
|
Adhemar-
You need to update all of $PROJECT_HOME/GUS/Supported, not just that one
file.
steve
Adhemar Zerlotini Neto wrote:
> Hello
>
> I just downloaded the InsertSequenceFeatures plugin revision 3451 and
> when I try to run it the following error appears:
>
> ERROR:
> Can't locate object method "ignoreFeature" via package
> "GUS::Supported::BioperlFeatMapper" at
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 753, <GEN39> line 42.
>
> STACK TRACE:
> at
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 753
>
> GUS::Supported::Plugin::InsertSequenceFeatures::makeImmediateFeature('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x850b8cc)',
> 'Bio::SeqFeature::Generic=HASH(0x9731c10)', 4) called at
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 728
>
> GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x850b8cc)',
> 'Bio::SeqFeature::Generic=HASH(0x9731c10)', 4) called at
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 368
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x850b8cc)',
> 'HASH(0x94c2c94)') called at
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 469
> eval {...} called at
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 461
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x84d5c20)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 380
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x84d5c20)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 288
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x84d5c20)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /usr/local/SchistoDB/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 197
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x84d5c20)',
> 'ARRAY(0x84e9918)') called at /usr/local/SchistoDB/gus_home/bin/ga line 11
>
>
> Do anybody know what is it about?
>
> Thanks
>
> Adhemar ------------------------------------------------------- SF.Net
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