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Topic: Records Reporting Species names

It's been pointed out that species name reporting has changed. We have a group recording veteran trees. There were some records put it as lime or poplar and these would report as Tilia in the Scientific Name and Lime in the Common Name or Populus and Poplar. However the common name is now left blank. Other species such as oak are still being listed as Quercus and Oak.

Is this because of change or is it an error?

Graham Hawker
Thames Valley Environmental Records Centre

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Re: Records Reporting Species names

Hi Graham

Can you tell us what report you are running to get these results?
Is there a URL we can look at to see the problem?

Thanks,
Jim Bacon.

3 (edited by Graham Hawker 12-12-2017 12:30:44)

Re: Records Reporting Species names

Hi Jim

I'm downloading records from our recording website sightings.tverc.org. I guess you won't be able to see it yourself without an admin login.

The page is set to use the standard library report:

Occurrences Download (Standard Filters)

If you need to look further I can set you up to give you access.

Graham Hawker
Thames Valley Environmental Records Centre

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Re: Records Reporting Species names

Hi Graham,

Here is what I have found out so far.

The Occurrences Download (standard filters) report obtains the Species and Common Name columns from the preferred_taxon and default_common_name fields of the cache_taxa_taxon_list table.

Your survey has recorded against the following taxa_taxon_list_id which have no default_common_name. The first two columns are the entered values and the second two are the corresponding preferred values.

+--------------------+------------+------------------------------+-----------------+
| taxa_taxon_list_id | taxon      | preferred_taxa_taxon_list_id | preferred_taxon |
+--------------------+------------+------------------------------+-----------------+
| 71589              | Cedrus     | 71589                        | Cedrus          |
+--------------------+------------+------------------------------+-----------------+
| 307125             | Poplar     | 74024                        | Populus         |
+--------------------+------------+------------------------------+-----------------+
| 38222              | Eucalyptus | 38222                        | Eucalyptus      |
+--------------------+------------+------------------------------+-----------------+
| 301431             | Lime       | 246834                       | Tilia           |
+--------------------+------------+------------------------------+-----------------+
| 160383             | Fraxinus   | 160383                       | Fraxinus        |
+--------------------+------------+------------------------------+-----------------+

The SQL that generates the cache table is in $config['taxa_taxon_lists']['update'] of modules/cache_builder/config/cache_builder.php

It gets the default_common_name from the taxon identified by the common_taxon_id field of the taxa_taxon_list table for the preferred_taxa_taxon_list_id. We can look these up.

+------------------------------+-----------------+-----------------+---------------------+---------+
| preferred_taxa_taxon_list_id | preferred_taxon | common_taxon_id | default_common_name | deleted |
+------------------------------+-----------------+-----------------+---------------------+---------+
| 71589                        | Cedrus          |                 |                     |         |
+------------------------------+-----------------+-----------------+---------------------+---------+
| 74024                        | Populus         | 74026           | Poplar              | true    |
+------------------------------+-----------------+-----------------+---------------------+---------+
| 38222                        | Eucalyptus      |                 |                     |         |
+------------------------------+-----------------+-----------------+---------------------+---------+
| 246834                       | Tilia           | 246836          | Lime                | true    |
+------------------------------+-----------------+-----------------+---------------------+---------+
| 160383                       | Fraxinus        |                 |                     |         |
+------------------------------+-----------------+-----------------+---------------------+---------+

Cedrus, Eucalyptus and Fraxinus have no common_taxon_id. Populus and Tilia do but the corresponding taxon records have been deleted. Poplar and Lime do, of course, exist in the species list but with taxon_id of 287888 and 290750. From the update times in the database it would appear that the current Lime and Poplar entries were added on 23/10/2013, that the original entries were marked as deleted at the same time but that the link from the preferred taxon was not updated.

Why have you observed a change now? All of the above-mentioned cache records were updated at the beginning of October (2017). I'm not sure by what method they were updated or when they might previously have been updated. However, they would have been updated on 23/10/2013 and, at that time, the fact that the linked common names were deleted was ignored by the cache builder. This was fixed in July 2014. It is possible that the recent cache update has applied code changes from 2014 which have revealed a flaw in the taxon list that has been there since 2013! Let me just reassure you that there is no problem with the species records - there is just a broken link between names in the species list so they don't join up properly when reporting. I can find 208 species names showing this problem.

I will raise as issue regarding this because, not only do we need to look at how we tidy up the database but also the synchronisation with the UK Species Inventory may need checking in case it has caused this problem in the first place.

Thanks to your hawk-eyed reporter and to you for passing this on.

Jim Bacon.

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Re: Records Reporting Species names

Issue raised at https://github.com/Indicia-Team/warehouse/issues/283

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Re: Records Reporting Species names

Thanks Jim

Graham Hawker
Thames Valley Environmental Records Centre