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GBIF Integrated Publishing Toolkit (IPT)

The Integrated Publishing Toolkit (IPT) is a free, open source software tool provided by the Global Biodiversity Information Facility (GBIF) and used to publish and share biodiversity datasets through the GBIF network. The IPT can also be configured with a DataCite account in order to assign DOIs to datasets, thus transforming it into a data repository.

Tip

Most users should refer to the user manual for further information, including downloads, installation instructions and details of the latest release.

If you have a GitHub account, you may select "Watch" → "Custom" → "Releases" above to receive a notification from GitHub when there is a new IPT release. These notifications are also sent to the mailing list.

In this repository you can find the source code for the IPT software and its user manual, as well as the issue tracker.

Resources

Acknowledgements

A large number of dedicated volunteers contribute to the success of this software. With your help, the IPT has become a successful tool in use all around the world.

Crowdin is kindly supporting this open source project by giving GBIF a free access to its localization management platform. Crowdin makes it possible to manage a large number of concurrent translations.

ipt's People

Contributors

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ipt's Issues

help link to open in new window

help links for concepts or extensions should open in new window

Original issue reported on code.google.com by wixner on 2008-07-16 15:05:26

extend dwc with geospatial & curatorial

curatorial and geospatial dwc extension are essential and used for most tapir output
models too. 
Also they are one2one mappings, so better integrate them into the occurrence core instead
of 
treating them as seperate extensions.

watch out for too large SQL statements to insert a single row

Original issue reported on code.google.com by wixner on 2008-07-29 08:35:15

strings for dwc properties

use only strings for all dwc properties, but keep additional typed properties that are
tried to be 
filled during the upload. E.g. coordinates


Original issue reported on code.google.com by wixner on 2008-07-09 08:11:08

model tests

toString, hasCode + equals need tests

Original issue reported on code.google.com by wixner on 2008-07-09 08:11:37

RSS feed for all resource

just using the resource metadata

Original issue reported on code.google.com by wixner on 2008-09-03 19:40:37

add tab file dump + taxonomy generation job

when adding an upload job additional jobs should be executed in the same running group:

a) create taxonomy
b) generate dwc star dump file

Original issue reported on code.google.com by wixner on 2008-07-23 21:43:18

TAPIR occurrence interface

implement basic TAPIRlite darwin core services to be harvested by GBIF

Original issue reported on code.google.com by wixner on 2008-07-09 11:02:37

admin pages cannot be accessed

The admin pages cannot be accessed even as admin.
A folder "admin" inside the exploded war creates chaos.

Removing the folder and all runs fine.
Remove this appfuse leftover!

Original issue reported on code.google.com by wixner on 2009-01-29 15:04:46

add #1 admin user

add admin user with account id=1 that is the primary site administrator and used for
other 
metadata. Export as dbunit

Original issue reported on code.google.com by wixner on 2008-09-03 19:51:11

Menus drop down CSS / JS problems

What is the expected output? What do you see instead?

The drop down menus disappear sometimes - bug in the CSS / JS. 
Check with Appfuse to see if updated

Safari, and firefox

This needs fixed before launch proper

Original issue reported on code.google.com by timrobertson100 on 2008-12-05 14:45:00

[Issue Deleted]

...

Original issue reported on code.google.com by NA on NA

webtests for occurrence resources

write webtests to add/edit/delete an occurrence resource

Original issue reported on code.google.com by wixner on 2008-07-11 13:10:09

upload jobs

add upload jobs, show jobs, run upload adding logs

Original issue reported on code.google.com by wixner on 2008-07-09 08:08:47

add logevent admin overview page

link a new page from the admin menu that gives an overview about the logs:

- latest
- by users
- by resources
- by source type/ids


Original issue reported on code.google.com by wixner on 2008-07-17 21:51:20

occurrence REST

add REST services for occurrences via REST plugin?

Original issue reported on code.google.com by wixner on 2008-07-09 08:14:35

add GBIF logo

add gbif logo to header

Original issue reported on code.google.com by wixner on 2008-07-16 15:04:14

file import source

write new csv file based import source. Needs to be uploaded in the webapp before mapping
can 
take place and a reference to this file should be stored in the resource metadata

Original issue reported on code.google.com by wixner on 2008-07-09 08:12:37

hash code stack overflow when uploading the same occurrence resource more than once

[providertoolkit] INFO [Thread-16] WorkerPool.returnObject(75) | Returning worker, so
removing 
Job
Exception in thread "Thread-16" java.lang.StackOverflowError
    at org.gbif.provider.model.DarwinCore.hashCode(DarwinCore.java:659)
    at org.apache.commons.lang.builder.HashCodeBuilder.append(HashCodeBuilder.java:856)
    at org.gbif.provider.model.DarwinCoreLocation.hashCode(DarwinCoreLocation.java:339)
    at org.apache.commons.lang.builder.HashCodeBuilder.append(HashCodeBuilder.java:856)
    at org.gbif.provider.model.DarwinCore.hashCode(DarwinCore.java:661)
    at org.apache.commons.lang.builder.HashCodeBuilder.append(HashCodeBuilder.java:856)
    at org.gbif.provider.model.DarwinCoreLocation.hashCode(DarwinCoreLocation.java:339)
    at org.apache.commons.lang.builder.HashCodeBuilder.append(HashCodeBuilder.java:856)
    at org.gbif.provider.model.DarwinCore.hashCode(DarwinCore.java:661)


Original issue reported on code.google.com by wixner on 2008-07-17 16:07:10

add upload when form + allow repeatable jobs

allow people to schedule jobs for certain times.
add time/date form to uploadAction

Also allow jobs to be repeated every x days, weeks or months
That information should be part of the job, so the job created a new job of
itself as the first thing before it launches.

Maybe make that a separate method of the Launchable interface?
so it runs in a different transaction?

Original issue reported on code.google.com by wixner on 2008-07-16 12:46:50

admin deleting user fails - transaction

Data Access Failure

Write operations are not allowed in read-only mode (FlushMode.NEVER/MANUAL): Turn your

Session into FlushMode.COMMIT/AUTO or remove 'readOnly' marker from transaction definition.

Original issue reported on code.google.com by wixner on 2009-01-30 12:21:18

viewing by class

What steps will reproduce the problem?
1. viewing Pontaurus "occurrences by family" here
http://ipt.gbif.org/occResourceStatsByTaxon.html?resource_id=1&zoom=true&type=4
2. selecting view by "class" produces "Yikes"


What version of the provider software are you using? The version should be
displayed in the footer of any page.

Version 1.0beta


What browser are you using?

Firefox 3.0.3 on Windows XP


Original issue reported on code.google.com by eotuama on 2009-01-29 20:13:29

adding occ resources db connection bug

entering a db connection after creating a new occ resource produces a blank
screen

Original issue reported on code.google.com by wixner on 2008-07-16 15:03:24

upload event created wrong

upload event gets created twice and with wrong data. fix uploadjob

Original issue reported on code.google.com by wixner on 2008-08-04 09:07:02

archive EML document versions

EML is generated on the fly currently. Write all metadata changes to EML files which
are archived and 
point back to last version and the latest version

Original issue reported on code.google.com by wixner on 2009-01-15 14:09:13

add GBIF logo

add gbif logo to header

Original issue reported on code.google.com by wixner on 2008-07-16 15:04:14

show upload log events

show upload log events

Original issue reported on code.google.com by wixner on 2008-07-09 08:09:14

upload event graph should work with 1 upload only

if uploaded only once no graph is visible.
to change that always add a current datetime "fake upload" with the current record
num

Original issue reported on code.google.com by wixner on 2008-08-04 09:08:30

BCI validation

validate collection codes against BCI webservices. Maybe also alow to register new collecitons
or 
institutions?

Original issue reported on code.google.com by wixner on 2008-09-01 12:09:28

load existing EML documents

instead of authoring from scratch load existng document

Original issue reported on code.google.com by wixner on 2009-01-15 13:59:16

mapping of controlled terms

allow mapping of values for controlled terms.
after mapping the concept try to do a select distinct so one can map original terms
to target terms

Original issue reported on code.google.com by wixner on 2008-08-10 22:24:35

wrap jobs in transactions

investigate e whether all jobs should be wrapped in a transaction. might not be needed
and causes 
troubles (DI) with the spring generated proxy objects

Original issue reported on code.google.com by wixner on 2008-07-17 08:29:04

SourceID linking to localhost

What steps will reproduce the problem?
1. view any record page, e.g.,
http://ipt.gbif.org/occDetail.html?resource_id=1&guid=2cd768ea-5b79-4599-a28a-ae97280ce69f

2. click on SourceID points to localhost


What version of the provider software are you using? The version should be
displayed in the footer of any page.

Version 1.0beta

What browser are you using?

Firefox 3.0.3 on Win XP


Original issue reported on code.google.com by eotuama on 2009-01-29 20:37:39

merge by inst+coll chart & top10 into taxa

use drop down to select by institution or collection.
merge top10 taxa with other taxon class drop down
reduces number of charts

Original issue reported on code.google.com by wixner on 2008-08-12 09:09:36

provide upgrade script for releases after 1.0

Future changes in the cache db after release 1.0 require an upgrade script to migrate
existing data 
folders

Original issue reported on code.google.com by wixner on 2009-01-29 15:29:41

Integrate Geoserver

add geoserver so that
a) we have a map for all data per resource
b) a map per species
c) there is WFS per resource

Original issue reported on code.google.com by wixner on 2008-07-09 08:13:56

Investigate how to serve static files more efficiently

currently all static files (data.zip. logo.gif, eml.xml, etc) are served through servlets,
mostly the 
DataAction one. It would be nice to not have to bother tomcat with this task.

Original issue reported on code.google.com by wixner on 2009-01-26 13:55:49

auto enhance metadata based on data

for Data Resources (checklists & occurrences) the IPT should provide a button to update
the 
resource metadata with derived data. In order to prevend overwrites for manually added
good data, 
provide 3 checkboxes initially to overwrite taxonomic, geospatial or temporal data.



Original issue reported on code.google.com by wixner on 2009-01-15 14:01:52

"Resource being updated" interceptor

write portal interceptor that redirects to a "sorry, this resource is currently being
updated" page if 
the requested resource is running a job

Original issue reported on code.google.com by wixner on 2008-08-10 22:22:40

add BCI "widget" for distinct collections

investigate how to integrate BCI for all distinct collection codes.

http://www.silverbiology.com/services/biocol/basic.html

Original issue reported on code.google.com by wixner on 2008-09-09 08:53:43

Use proper http client for TAPIR templates

Currently it will not follow redirects etc. 
Pull out the simple version and use commons httpclient

Original issue reported on code.google.com by timrobertson100 on 2009-01-26 07:18:13

use table.column name for mapping

use tablename.column_name for storing the concept mappings instead of the
colum index. So a changed SQL view statement doesnt crash an existing mapping.

Original issue reported on code.google.com by wixner on 2008-07-16 15:06:51

Internet Explorer renders horribly

hardly anything can be seen correctly with IE6&7.
All blocks are wrongly placed. CSS and potentially some html has to be adapted to work
wiht IE too.
Major work

Original issue reported on code.google.com by wixner on 2009-01-28 18:48:43

fixed value mapping stored wrong

fixed values stored as columnnames not values. fix mapping action

Original issue reported on code.google.com by wixner on 2008-08-04 09:06:17

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