Menu
▾
▴
gusdev-gusdev
|
From: <mro...@cs...> - 2006-11-09 16:41:13
|
Steve,
The Core.ProjectInfo table is empty, so I will create a record in
project_id | numeric(4,0) | not null
name | character varying(40) | not null
description | character varying(255) |
release | character varying(20) |
modification_date | timestamp without time zone | not null
user_read | numeric(1,0) | not null
user_write | numeric(1,0) | not null
group_read | numeric(1,0) | not null
group_write | numeric(1,0) | not null
other_read | numeric(1,0) | not null
other_write | numeric(1,0) | not null
row_user_id | numeric(12,0) | not null
row_group_id | numeric(4,0) | not null
row_project_id | numeric(4,0) | not null
row_alg_invocation_id | numeric(12,0) | not null
Indexes:
"pk_projectinfo" primary key, btree (project_id)
with the value "Database Administration" to match my gus.config file, now
I assume that this value correspond to the field "name". Do I need to put
any data in the other fields or is this up to me?
Also before running ISF do I need to put any data in:
- 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
Thanks very much
Michael R
> Michael-
>
> There is a table in gus called Core.ProjectInfo. In contains info abou=
t
> your "project." When you run a plugin, the plugin needs to know what
> the name of your project is so that all the rows you insert will be
> assigned to your project. The plugin discovers the name of your
> project by looking in the gus.config file.
>
> The error message is telling you that the gus.config file is declaring
> your project's name to be "Database Administration" while there is no
> row in Core.ProjectInfo with name set to "Database Administration".
>
> Have you looked at the rows in that table? Is there one with name
> "Database Administration"? On my GUS instance, I have a row with name
> "Database administration" (note the small 'a'). I suspect that this
> row was put in by the gus installer. So perhaps you just need to
> change your config file to that.
>
> steve
>
> mro...@cs... wrote:
>
>>Steve,
>>
>>I understand that you are in charge of ISF.
>>
>>I am trying to run the ISF plugin in a brand new install and I get the
>>following error:
>>
>> No row in Core.ProjectInfo has name =3D Database Administration'. Thi=
s
>> value was found in the project=3D property of your gus.config file.
>> Please
>> be sure it is correct and has been registered in the database
>> **** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit' wi=
th
>> stderr:
>> Operation now in progress**** GUS::PluginMgr::PluginError Failed
>> running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures --
>> commit' with stderr:
>>
>>I already checked my gus.config file and it has the entry
>>
>> project=3DDatabase Administration
>>
>>
>>I would like to know if this and maybe other default values must be
>>inserted into the database before trying to insert data.
>>
>>
>>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.
>>
>>
>>
>>I am sorry if I ask the same question so many times but I am stuck and
>> can
>>not continue until I find an answer.
>>
>>
>>Thank you
>>
>>
>>Michael Robinson
>>Bioinformatics Research Group (Biorg)
>>Florida International University
>>Miami, Florida, USA 33199
>>
>>
>>
>>
>>
>>
>>
>>
>
|
|
From: Steve F. <sfi...@pc...> - 2006-11-09 16:42:16
|
Michael- There is a table in gus called Core.ProjectInfo. In contains info about your "project." When you run a plugin, the plugin needs to know what the name of your project is so that all the rows you insert will be assigned to your project. The plugin discovers the name of your project by looking in the gus.config file. The error message is telling you that the gus.config file is declaring your project's name to be "Database Administration" while there is no row in Core.ProjectInfo with name set to "Database Administration". Have you looked at the rows in that table? Is there one with name "Database Administration"? On my GUS instance, I have a row with name "Database administration" (note the small 'a'). I suspect that this row was put in by the gus installer. So perhaps you just need to change your config file to that. steve mro...@cs... wrote: >Steve, > >I understand that you are in charge of ISF. > >I am trying to run the ISF plugin in a brand new install and I get the >following error: > > No row in Core.ProjectInfo has name = Database Administration'. This > value was found in the project= property of your gus.config file. Please > be sure it is correct and has been registered in the database > **** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit' with > stderr: > Operation now in progress**** GUS::PluginMgr::PluginError Failed > running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures -- > commit' with stderr: > >I already checked my gus.config file and it has the entry > > project=Database Administration > > >I would like to know if this and maybe other default values must be >inserted into the database before trying to insert data. > > >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. > > > >I am sorry if I ask the same question so many times but I am stuck and can >not continue until I find an answer. > > >Thank you > > >Michael Robinson >Bioinformatics Research Group (Biorg) >Florida International University >Miami, Florida, USA 33199 > > > > > > > > |
|
From: Steve F. <sfi...@pc...> - 2006-11-09 16:43:45
|
i thought that the installer loaded default values into that table. how about Core.TableInfo, is it filled? yes, you do have to add the data you describe below steve mro...@cs... wrote: >Steve, > >The Core.ProjectInfo table is empty, so I will create a record in > > project_id | numeric(4,0) | not null > name | character varying(40) | not null > description | character varying(255) | > release | character varying(20) | > modification_date | timestamp without time zone | not null > user_read | numeric(1,0) | not null > user_write | numeric(1,0) | not null > group_read | numeric(1,0) | not null > group_write | numeric(1,0) | not null > other_read | numeric(1,0) | not null > other_write | numeric(1,0) | not null > row_user_id | numeric(12,0) | not null > row_group_id | numeric(4,0) | not null > row_project_id | numeric(4,0) | not null > row_alg_invocation_id | numeric(12,0) | not null >Indexes: > "pk_projectinfo" primary key, btree (project_id) > > > >with the value "Database Administration" to match my gus.config file, now >I assume that this value correspond to the field "name". Do I need to put >any data in the other fields or is this up to me? > >Also before running ISF do I need to put any data in: > > - 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 > > >Thanks very much > >Michael R > > > > > >>Michael- >> >>There is a table in gus called Core.ProjectInfo. In contains info about >>your "project." When you run a plugin, the plugin needs to know what >>the name of your project is so that all the rows you insert will be >>assigned to your project. The plugin discovers the name of your >>project by looking in the gus.config file. >> >>The error message is telling you that the gus.config file is declaring >>your project's name to be "Database Administration" while there is no >>row in Core.ProjectInfo with name set to "Database Administration". >> >>Have you looked at the rows in that table? Is there one with name >>"Database Administration"? On my GUS instance, I have a row with name >>"Database administration" (note the small 'a'). I suspect that this >>row was put in by the gus installer. So perhaps you just need to >>change your config file to that. >> >>steve >> >>mro...@cs... wrote: >> >> >> >>>Steve, >>> >>>I understand that you are in charge of ISF. >>> >>>I am trying to run the ISF plugin in a brand new install and I get the >>>following error: >>> >>>No row in Core.ProjectInfo has name = Database Administration'. This >>>value was found in the project= property of your gus.config file. >>>Please >>>be sure it is correct and has been registered in the database >>>**** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit' with >>>stderr: >>>Operation now in progress**** GUS::PluginMgr::PluginError Failed >>>running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures -- >>>commit' with stderr: >>> >>>I already checked my gus.config file and it has the entry >>> >>>project=Database Administration >>> >>> >>>I would like to know if this and maybe other default values must be >>>inserted into the database before trying to insert data. >>> >>> >>>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. >>> >>> >>> >>>I am sorry if I ask the same question so many times but I am stuck and >>>can >>>not continue until I find an answer. >>> >>> >>>Thank you >>> >>> >>>Michael Robinson >>>Bioinformatics Research Group (Biorg) >>>Florida International University >>>Miami, Florida, USA 33199 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> > > > |
|
From: <mro...@cs...> - 2006-11-09 19:09:50
|
Steve, The Core.TableInfo is also empty. Since the installer did not load the default values, at http://www.gusdb.org/documentation/older/vbidoc.pdf i looked in page 17 "Loading Data Into Gus" (i realize this is for versio= n 3.0 but since we do not have a similar documentation for version 3.5) i was wondering if i can follow those instructions to do "Initial Population" of the tables they refer to, or is there any other place that i can find the same information for the current version. Thank you Michael R > i thought that the installer loaded default values into that table. > > how about Core.TableInfo, is it filled? > > yes, you do have to add the data you describe below > > steve > > mro...@cs... wrote: > >>Steve, >> >>The Core.ProjectInfo table is empty, so I will create a record in >> >> project_id | numeric(4,0) | not null >> name | character varying(40) | not null >> description | character varying(255) | >> release | character varying(20) | >> modification_date | timestamp without time zone | not null >> user_read | numeric(1,0) | not null >> user_write | numeric(1,0) | not null >> group_read | numeric(1,0) | not null >> group_write | numeric(1,0) | not null >> other_read | numeric(1,0) | not null >> other_write | numeric(1,0) | not null >> row_user_id | numeric(12,0) | not null >> row_group_id | numeric(4,0) | not null >> row_project_id | numeric(4,0) | not null >> row_alg_invocation_id | numeric(12,0) | not null >>Indexes: >> "pk_projectinfo" primary key, btree (project_id) >> >> >> >>with the value "Database Administration" to match my gus.config file, n= ow >>I assume that this value correspond to the field "name". Do I need to p= ut >>any data in the other fields or is this up to me? >> >>Also before running ISF do I need to put any data in: >> >> - 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 >> >> >>Thanks very much >> >>Michael R >> >> >> >> >> >>>Michael- >>> >>>There is a table in gus called Core.ProjectInfo. In contains info abo= ut >>>your "project." When you run a plugin, the plugin needs to know what >>>the name of your project is so that all the rows you insert will be >>>assigned to your project. The plugin discovers the name of your >>>project by looking in the gus.config file. >>> >>>The error message is telling you that the gus.config file is declaring >>>your project's name to be "Database Administration" while there is no >>>row in Core.ProjectInfo with name set to "Database Administration". >>> >>>Have you looked at the rows in that table? Is there one with name >>>"Database Administration"? On my GUS instance, I have a row with nam= e >>>"Database administration" (note the small 'a'). I suspect that this >>>row was put in by the gus installer. So perhaps you just need to >>>change your config file to that. >>> >>>steve >>> >>>mro...@cs... wrote: >>> >>> >>> >>>>Steve, >>>> >>>>I understand that you are in charge of ISF. >>>> >>>>I am trying to run the ISF plugin in a brand new install and I get th= e >>>>following error: >>>> >>>>No row in Core.ProjectInfo has name =3D Database Administration'. Th= is >>>>value was found in the project=3D property of your gus.config file. >>>>Please >>>>be sure it is correct and has been registered in the database >>>>**** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit' >>>> with >>>>stderr: >>>>Operation now in progress**** GUS::PluginMgr::PluginError Failed >>>>running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures -- >>>>commit' with stderr: >>>> >>>>I already checked my gus.config file and it has the entry >>>> >>>>project=3DDatabase Administration >>>> >>>> >>>>I would like to know if this and maybe other default values must be >>>>inserted into the database before trying to insert data. >>>> >>>> >>>>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 th= e >>>> absence of these, and makes it more clear what to do. >>>> >>>> >>>> >>>>I am sorry if I ask the same question so many times but I am stuck an= d >>>>can >>>>not continue until I find an answer. >>>> >>>> >>>>Thank you >>>> >>>> >>>>Michael Robinson >>>>Bioinformatics Research Group (Biorg) >>>>Florida International University >>>>Miami, Florida, USA 33199 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >> >> >> > |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X