1 (edited by Syrphus 01-04-2014 09:33:11)

Topic: Laminaria puzzle

I notice that Laminaria saccharina does not seem to be associated with any higher taxa in a report, as below.

Fields ouput are, in order

Recommended Taxon Name without Sub-genus
Recommended Common Name/Taxon Group
Taxon Family
Taxon Order
Taxon Class
Taxon Phylum
Taxon Kingdom
Taxon Group

Two adjacent records are:
Laminaria hyperborea Kelp Laminariaceae Laminariales Phaeophyceae    Ochrophyta Chromista chromist   
Laminaria saccharina  chromist                                              chromist

For saccharina, only the Taxon Group shows - twice, as the group and the 'common name'.  That too is odd - is Sugar Kelp not one of a few standard common names?

Murdo

2

Re: Laminaria puzzle

I should have been clearer about this - the problem arose in running a saved report in R6.

M.

3

Re: Laminaria puzzle

I can't duplicate this, which is always of concern. Do you know what the Taxon_List_Item key is of the record(s) or which list the original entry comes from.

Mike Weideli

4

Re: Laminaria puzzle

Thanks, Mike.

The code is (generated originally through the wizard, and then saved):

<?xml version="1.0"?>
<Report><SQL>SELECT  Distinct Taxon_Occurrence.Taxon_Occurrence_Key AS Occurrence_Key, 'T' AS Type
FROM ((Taxon_Occurrence LEFT JOIN Sample ON Taxon_Occurrence.sample_Key = Sample.Sample_Key ) LEFT JOIN Survey_Event ON Survey_Event.Survey_Event_Key = Sample.Survey_Event_Key ) LEFT JOIN Survey ON Survey.Survey_Key = Survey_Event.Survey_Key
WHERE Survey.Survey_Key NOT IN (SELECT Survey_Key FROM User_Survey_Restriction USR WHERE  USR.Name_Key = 'CI0001660000016Y') AND ((Survey.Survey_Key IN ('CI0001660000002P')))</SQL><additional_filters><confidential state="0"/><unchecked state="0"/><invalid state="0"/><zero_abundance state="0"/></additional_filters><Attributes><Attribute visible="True" type="Standard" key="JNCCDEV100000004" position="17"/><Attribute visible="True" type="Standard" key="JNCCDEV100000014" position="16"/><Attribute visible="True" type="Measurement" key="NBNSYS0000000003" position="15" context="SAMPLE_DATA"/><Attribute visible="True" type="Standard" key="NBNSYS0000000019" position="14"/><Attribute visible="True" type="Standard" key="NBNSYS0000000024" position="13"/><Attribute visible="True" type="Standard" key="NBNSYS0000000027" position="12"/><Attribute visible="True" type="Standard" key="NBNSYS0000000049" position="11"/><Attribute visible="True" type="Standard" key="NBNSYS0000000053" position="10"/><Attribute visible="True" type="Standard" key="NBNSYS0000000063" position="9"/><Attribute visible="True" type="Standard" key="NBNSYS0000000064" position="8"/><Attribute visible="True" type="Standard" key="NBNSYS0000000088" position="7"/><Attribute visible="True" type="Standard" key="SRA0000400000023" position="6"/><Attribute visible="True" type="Standard" key="SRA0000400000024" position="5"/><Attribute visible="True" type="Standard" key="SRA0000400000025" position="4"/><Attribute visible="True" type="Standard" key="SRA0000400000026" position="3"/><Attribute visible="True" type="Standard" key="SRA0000400000027" position="2"/><Attribute visible="True" type="Standard" key="SRA0000400000028" position="1"/><Attribute visible="True" type="Standard" key="SRA0000400000029" position="0"/></Attributes></Report>

The various keys are:
TAXON_LIST_ITEM_KEY    TAXON_VERSION_KEY    TAXON_KEY    dbo_TAXON.ITEM_NAME
NBNSYS0000170217    NBNSYS0000175995    NBNSYS0000175995    Laminaria saccharina

The list is SEAWEEDS (the only preferred list with L. sacc.).  I added a dummy record through 'add a species record' and called the report again on that one alone, and the same result appeared.

M.

5

Re: Laminaria puzzle

The problem could be in the Dictionary or in the way the report wizard is working.  If possible could you please run the attached xml report. It will show whether  or not Indes_Taxon_Hierrechy is correctly populated.  It runs from  Systems Reports/Dictionary Test. Should give the hierarchy for Laminaria saccharina. I am testing this on a dictionary at  versiom 00000025

Post's attachments

JNCC_Dictionary_Test1.xml 978 b, 3 downloads since 2014-04-01 

You don't have the permssions to download the attachments of this post.
Mike Weideli

6

Re: Laminaria puzzle

Well, not illuminating, if I have done the right thing, Mike.

I put the file into User Files/Reports, then found it in the R6 Menu: Reports - Run... - System reports.

It returned no records, just the two field headings taxon_name and Hierarchy.

I am on 6.22 and dictionary 25.  Upgraded last week and rebuilt indexes as per the recipe.

M.

7

Re: Laminaria puzzle

Returning nothing is a result, but it means we need to dig a bit deeper.

Mike Weideli

8

Re: Laminaria puzzle

I don't know if this helps the digging, Mike, but G5 shows the preferred name for L. sacc. to be

Name:    Saccharina latissima
Authority:    (Linnaeus)
Common Name:    Sugar Kelp
Taxon Version Key:    NHMSYS0020744386
Rank:    Species
Name Form:    Well-formed
Output Group:    chromist
Taxon Reference:    Saccharina latissima (Linnaeus) [Sugar Kelp], NHMSYS0020744386,

with synonyms

Laminaria saccharina (Linnaeus) J.V. Lamouroux
Sea Belt
Poor Man’s Weather Glass
Sugar Kelp

R6 has Saccharina as a genus in the Additional names and the EA checklists, but no species (why would you list a genus but no contained species?).

So it would seem there is more to this than appeared yesterday.

M.

9

Re: Laminaria puzzle

I am begining to suspect that at some point your dictionary has got out of step, The last change  Saccharina latissima/  L. sacc was in January 2011 to NameServer. This is prior to the new version of the Dictionary upgrade Kit which corrected a bug, which was causing some changes to be ignored.

I can do a report which will check to see if something has gone wrong with these species, but as a rough check you should  have  280527 records in NameServer and  108607 in the Organism table.

Mike Weideli

10

Re: Laminaria puzzle

I am OK for Organism, but short in NameServer with only 280039.

If you remember, I did have a glitch with an upgrade last year, but then all seemed to be OK after restoring the backup and starting again.  Maybe something went awry unnoticed.

M.

11

Re: Laminaria puzzle

Most probably nothing you have done, but something in the  old Dictionary upgrade kit. There are two options.

1.Try to work out what has gone wrong and make the adjustments . It may be just in NameServer, but because the tables  are linked changes can have knock on effect so it is difficult to say where this will end up.
2. Let me have a copy of your database and I will give you back a dictionary upgrade to bring you into line. It doesn't take me very long  and I can work from a backup up or a detached database. I don't touch your data, just work out a special dictionary upgrade to bring you into line and give  this to you to run. You can continue to use Recorder while this is being done .  Happy to sign a confidentially agreement if required.

Mike Weideli