1

Re: Version 0.6 now available.

Version 0.6 of Indicia is now available from the Google Code downloads page, at [utl]http://code.google.com/p/indicia/downloads/list[/url].

As usual there are many bug fixes with a full list of changes available at http://code.google.com/p/indicia/source/list. The most significant changes are a simplification of the process of setting up forms on Drupal, a new class for managing the login process on client websites that don't already have one, reporting and mapping is now much more flexible, a much improved upload process which allows uploads to run from the client website as well as the warehouse and a new modular architecture on the warehouse.

Here is a summary of the changes:

Client helpers

Client helpers now refactored into a base class with subclasses for data entry, mapping, reporting, importing, security and auto-form generation.

Date picker control now uses default date format dd/mm/yyyy

New import_helper class allows csv data import from client websites.

Support for Bing map layers.

New user_helper class provides methods for authenticating a user against the Warehouse users list, from a client website. Also forgotten password functionality. (Thanks to Don Petrie for this).

The map controls now support complete control over the map controls which will appear (new standardControls configuration parameters).

New map layer_list control which can be used to output layer switchers and/or legends.

Map now supports a simple list of WMS layers selected from the GeoServer – also supported in the distribution_map prebuilt forms.

Distribution map prebuilt forms now support specifying a filter on the output using the CQL language.

The image upload control has had several bug fixes so supports a wider range of browsers and browser plugins.

Checkbox controls save their values properly when unchecked.

Reporting

New report_helper class refactors the client report code into one place.

Changes for the Redicia project:
1)    New report_map method for output of reports onto a map.
2)    Reports now support polygon parameters which can be drawn onto a map.
3)    Grid and map reports can now share a single parameters input form, allowing you to “mashup” several reports onto one page to build a dashboard.
4)    New map_occurrences_for_survey xml report file to demonstrate this functionality.
Significant performance improvements for reports which auto-generate the columns for the custom attributes in a survey.

New report_download_link control.

Prebuilt forms

The prebuilt form selection and configuration form is now pure Indicia code rather than a Drupal form, meaning it can be used from outside Drupal.

Prebuilt forms can now return a definition rather than just a title – this allows them to declare descriptions and a link to a help page which is visible when configuring the form.

The prebuilt form configuration now supports calls to the Warehouse’s data services, meaning that parameters such as a taxon list id can be picked from a drop down selector or an autocomplete control rather than having to know the ID. Therefore it is much easier to setup forms.

The mnhnl_bird_transect_walks form reports now include the occurrence ID.

New long-term monitoring forms mnhnl_bats and mnhnl_butterflies, used for monitoring projects in Luxembourg but freely available to all.

New change_identification prebuilt form for changing the identification associated with a record.
Several improvements to the SPIPOLL pollinators prebuilt forms.

New report_map prebuilt form which can be used to draw maps from output of reports that contain a mappable column.

Drupal pages that use a prebuilt form can now specify custom JavaScript, CSS, validation code etc. See http://code.google.com/p/indicia/wiki/DrupalIFormOverrides.

Warehouse

Taxon meaning id is now visible on the taxon edit pages in the Warehouse.

Website administrators can create people records and make them users of their own websites, without needing core admin rights.

Major change to the way that tabbed pages are setup on the Warehouse. All tabs now load on demand.

New architecture for plugins on the Warehouse. Plugins can add tabs, menu items as well as database entities.

New module which allows browsing of warehouse logs from the user interface. Enable the log_browser module to get this functionality.

Rewrite of the csv file import facilities. Imports can now be run from a client website or the warehouse using the new import_helper client helper class. Enable the indicia_svc_import module to allow use of this feature.

New module for support for taxon designations (enable the taxon_designations module on the warehouse for this).

New module for importing taxon names, taxon groups (reporting categories) and designation data from the NBN species dictionary web services (enable the nbn_sync module on the warehouse for this).

When subscribing to a trigger, it is now possible to specify a list of emails to cc the notifications to.

Installation

Better checking for correct directory permissions before installations and upgrades will proceed.

During installation, the email config page now prompts for an email address to send a test to.

Misc

Support for Irish Grid References.

John van Breda
Biodiverse IT

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Re: Version 0.6 now available.

Thanks, John.

I shall be upgrading http://warehouse1.indicia.org.uk and http://testwarehouse.indicia.org.uk tomorrow morning, Thursday 21st April, to this new version. While I do so they will be temporarily unavailable.

Jim Bacon

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Re: Version 0.6 now available.

Hi

I have two apologies to make, although one is hopefully unneccesary.

Firstly, I didn't perform the upgrade at the planned time but have now completed it. If you experienced unexpected problems while the server was down, I am sorry. This happened because a last minute problem arose related to access permissions on our server directory structure.

Secondly, it is now the Thursday night before Easter and our office is locked and bolted for the next four days. Should there be any problems with the upgrade I will not be able to address them until Tuesday. That was an unfortunate lack of foresight on my part. If I have introduced a problem, please bear with us. I hope you all have an enjoyable weekend and are able to spend some time out in the beautiful spring coutryside.

Jim Bacon.

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Re: Version 0.6 now available.

I've just spotted a bug in v0.6.1 - the reports returned from the warehouse are returning all columns as visible, even those which are marked as visible="false" in the XML file. I've fixed it in the code and patched the live warehouse, but if anyone has their own warehouse upgraded to 0.6.1 you can just upgrade the file application/libraries/XmlReportReader.php from the latest copy in Subversion. If you are not using Subversion then you can copy the file content from http://indicia.googlecode.com/svn/core/ … Reader.php.

John van Breda
Biodiverse IT

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Re: Version 0.6 now available.

I have applied two more patches to warehouse1 and testwarehouse.

The first, r2635, removes the requirement for the scientific field to be included when adding species.

The second, r2638 plusr2640, ensures correct uploading of species lists.

Jim Bacon.

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Re: Version 0.6 now available.

Hi,

I tried upgrading my warehouse to 0.6.1 but I am getting following error messages:

in the warehouse:
Database configuration
Database configuration options need to be set allowing the Indicia Warehouse to access your database. Indicia will then install the required database tables for you.
Fix the other issues listed on this page before proceeding to configure and install the database.

in drupal:
302 - Found

http://localhost/test/indicia/index.php/setup_check

Fatal error: Uncaught exception 'Exception' with message 'Invalid response received from Indicia Warehouse. Array ( [result] => [output] => HTTP/1.1 302 Found Date: Thu, 12 May 2011 14:24:00 GMT Server: Apache/2.2.14 (Unix) DAV/2 mod_ssl/2.2.14 OpenSSL/0.9.8l PHP/5.3.1 mod_perl/2.0.4 Perl/v5.10.1 X-Powered-By: PHP/5.3.1 Location: http://localhost/test/indicia/index.php/setup_check Content-Length: 144 Content-Type: text/html; charset=UTF-8 <h1>302 - Found</h1><p><a href="http://localhost/test/indicia/index.php/setup_check">http://localhost/test/indicia/index.php/setup_check</a></p> [errno] => 0 ) ' in /Applications/XAMPP/xamppfiles/htdocs/test/portalbb/sites/all/modules/iform/client_helpers/data_entry_helper.php:3663 Stack trace: #0 /Applications/XAMPP/xamppfiles/htdocs/test/portalbb/sites/all/modules/iform/client_helpers/data_entry_helper.php(5011): data_entry_helper::get_population_data(Array) #1 /Applications/XAMPP/xamppfiles/htdocs/test/portalbb/sites/all/modules/iform/client_helpers/prebuilt_form in /Applications/XAMPP/xamppfiles/htdocs/test/portalbb/sites/all/modules/iform/client_helpers/data_entry_helper.php on line 3663


I was looking for the database file, but couldn't find the one for the pgsql configuration. I just found one for the mysql configuration?
Did I miss something?

Thank you,
Gaby

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Re: Version 0.6 now available.

oh, I think I found the problem which is a very mac-specific one. I was missing some files while copying to run the update.

greetings,
gaby

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Re: Version 0.6 now available.

Hi

I have applied another patch to Warehouse1 and Testwarehouse. This involves changing the file application/libraries/Attribute_Value_ORM.php to match the version from r2600.

Without this patch, all custom boolean attributes are stored with the value true regardless of the submitted value.

This condition existed on our servers between about 6pm on 21st April, 2011 and about 8.30am on 16th May.

I will endeavour to mark these records with a comment and inform the relevant surveys which samples are affected.

My apologies to the 5 surveys for the 151 affected records.

Jim.

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Re: Version 0.6 now available.

Hi

Following on from my previous posting, I used sample comments to indicate which records were affected by the boolean attributes bug. However, while sample comments existed within the data model, the warehouse interface did not display them. I have added the necessary code to display them and patched the warehouse.

Due to changes in the development trunk I have had to create a branch in the repository to store this update. Since I was doing that, I have also committed the other fixes mentioned in this thread to the branch. As a result, it is currently the most stable version of the warehouse.

Jim Bacon.

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Re: Version 0.6 now available.

Just for the record, warehouse1 and testwarehouse have been patched with the update contained in r2723. This fixes a problem with spreadsheet file uploads.
A corresponding update, r2724, should be applied to client websites wanting to use this facility.

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Re: Version 0.6 now available.

Three more patches have been applied to warehouse1 and the testwarehouse recently. These have all been recorded in the 0.6.2 branch of the repository. They address the following issues:
- edits to termlist terms not being saved.
- file not found exception when creating triggers.
- problem processing complex columns in reports.

Jim Bacon

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Re: Version 0.6 now available.

I have applied patches r2789 to r2796 to warehouse1 and testwarehouse. These address problems that existed with filtering and sorting custom attributes.

Jim Bacon.

13 (edited by Jim Bacon 10-08-2011 16:08:16)

Re: Version 0.6 now available.

Hi

I have applied patch r2911 and r2912 to the test server and the live server. The first is a minor bug fix. The other adds a zero_abundance field to the occurrence table. This allows Indicia to support surveys that record absences in a consistent manner.

Jim Bacon

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Re: Version 0.6 now available.

Hi

I have upgraded the OpenLayers javascript library on both the testwarehouse and warehouse1 from version 2.8 to 2.10. If you see any anomalous behaviour, such as the layer switcher appearing on the left rather than the right of the map panel, then try clearing your browser cache. The next release of the Indicia Warehouse will come with this version or higher.

This upgrade was performed to help compatibility with Apple products. Can I also draw your attention to r2565 as well.  Ensure you patch your client_helpers with this for your date pickers to work on these products.

Jim Bacon.

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Re: Version 0.6 now available.

Hi

I have just patched warehouse1 and testwarehouse with r2990. This alleviates a problem that manifested itself as a FastCGI error message on our Windows servers when making certain web service calls to the warehouse.

Jim Bacon.