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bug #8533

missing collector and fieldnumber in abcd import

Added by Katja Luther 2 months ago. Updated 14 days ago.

Status:
Closed
Priority:
Highest
Assignee:
Category:
cdmadapter
Target version:
Start date:
09/10/2019
Due date:
% Done:

100%

Severity:
critical
Found in Version:

Description

when importing specimen/dna as associated units where the gathering event information is not complete in one of the derived units the already existing value should not be overwritten by a null value.

dna_sample.xml View (16.1 KB) Patrick Plitzner, 09/18/2019 03:22 PM

picture953-1.png View (32.9 KB) Katja Luther, 09/18/2019 04:34 PM

picture607-1.png View (44.8 KB) Katja Luther, 09/19/2019 09:45 AM

tissue_sample.xml View (12.2 KB) Patrick Plitzner, 09/30/2019 01:41 PM


Related issues

Related to Edit - feature request #8549: while abcd import problems should be logged more in detail New 09/17/2019

Associated revisions

Revision a3a55498 (diff)
Added by Katja Luther 2 months ago

ref #8533: check for all fields in gatheringEvent whether it is set already

Revision 9b1e9a85 (diff)
Added by Katja Luther 2 months ago

ref #8533: minor

History

#1 Updated by Katja Luther 2 months ago

  • Status changed from New to Resolved
  • Assignee changed from Katja Luther to Patrick Plitzner

problems like this should be handled more in detail and the user should be informed about this problems. Therefore I create a new ticket and close this one (#8549).

Please review whether the problem of the missing information is fixed.

#2 Updated by Katja Luther 2 months ago

  • % Done changed from 0 to 60

#3 Updated by Katja Luther 2 months ago

#4 Updated by Patrick Plitzner 2 months ago

  • Status changed from Resolved to Feedback
  • Assignee changed from Patrick Plitzner to Katja Luther

I attached the two sample file: one is the DNA unit the other one the associated tissue sample.

I tested on nightly rem_conf_am and searched for DB 40073 in the specimen import search. It imported the DnaSample and the TissueSample correctly but it did neither import the author (Hutchison) nor the collecting number (1980) which are both available in the tissue sample abcd.

#5 Updated by Patrick Plitzner 2 months ago

#6 Updated by Katja Luther 2 months ago

the collector problem is solved, but the fieldnumber is not delivered. I debugged and also looked at the output and there is no fieldnumber (see the attached file).

#7 Updated by Katja Luther 2 months ago

ah there is another problem, the gathering agent for the tissue is Hutchison and for the tissue sample Lautner

#8 Updated by Patrick Plitzner 2 months ago

Katja Luther wrote:

the collector problem is solved, but the fieldnumber is not delivered. I debugged and also looked at the output and there is no fieldnumber (see the attached file).

The field number is in the tissue sample file (CollectorsFieldNumber)

<abcd21:Gathering>
              <abcd21:DateTime>
                <abcd21:DateText>18.08.1957</abcd21:DateText>
              </abcd21:DateTime>
              <abcd21:Agents>
                <abcd21:GatheringAgentsText>Hutchison</abcd21:GatheringAgentsText>
              </abcd21:Agents>
              <abcd21:LocalityText>Junín. Prov. Tarma, Chanchamayotal zwischen San Ramón und La Merced an vertikalen Felsen oberhalb der Straße.</abcd21:LocalityText>
              <abcd21:Country>
                <abcd21:Name>Peru</abcd21:Name>
                <abcd21:ISO3166Code>PE</abcd21:ISO3166Code>
              </abcd21:Country>
              <abcd21:NamedAreas>
                <abcd21:NamedArea>
                  <abcd21:AreaClass language="en">Continent</abcd21:AreaClass>
                  <abcd21:AreaName language="en">Middle and South America</abcd21:AreaName>
                </abcd21:NamedArea>
              </abcd21:NamedAreas>
              <abcd21:Notes language="en" />
            </abcd21:Gathering>
            <abcd21:CollectorsFieldNumber>1980</abcd21:CollectorsFieldNumber>
            <abcd21:RecordURI>http://herbarium.bgbm.org/object/BGT0023581</abcd21:RecordURI>

#9 Updated by Patrick Plitzner 2 months ago

Katja Luther wrote:

ah there is another problem, the gathering agent for the tissue is Hutchison and for the tissue sample Lautner

Hmm, I guess we have to move this to another issue for discussion

#10 Updated by Katja Luther 2 months ago

Patrick Plitzner wrote:

Katja Luther wrote:

the collector problem is solved, but the fieldnumber is not delivered. I debugged and also looked at the output and there is no fieldnumber (see the attached file).

The field number is in the tissue sample file (CollectorsFieldNumber)

<abcd21:Gathering>
              <abcd21:DateTime>
                <abcd21:DateText>18.08.1957</abcd21:DateText>
              </abcd21:DateTime>
              <abcd21:Agents>
                <abcd21:GatheringAgentsText>Hutchison</abcd21:GatheringAgentsText>
              </abcd21:Agents>
              <abcd21:LocalityText>Junín. Prov. Tarma, Chanchamayotal zwischen San Ramón und La Merced an vertikalen Felsen oberhalb der Straße.</abcd21:LocalityText>
              <abcd21:Country>
                <abcd21:Name>Peru</abcd21:Name>
                <abcd21:ISO3166Code>PE</abcd21:ISO3166Code>
              </abcd21:Country>
              <abcd21:NamedAreas>
                <abcd21:NamedArea>
                  <abcd21:AreaClass language="en">Continent</abcd21:AreaClass>
                  <abcd21:AreaName language="en">Middle and South America</abcd21:AreaName>
                </abcd21:NamedArea>
              </abcd21:NamedAreas>
              <abcd21:Notes language="en" />
            </abcd21:Gathering>
            <abcd21:CollectorsFieldNumber>1980</abcd21:CollectorsFieldNumber>
            <abcd21:RecordURI>http://herbarium.bgbm.org/object/BGT0023581</abcd21:RecordURI>

I know, but if you have a look at the file attached, there is only "Gathering" and then "RecordURI", no CollectorsFieldNumber

#11 Updated by Katja Luther 2 months ago

  • Status changed from Feedback to In Progress
  • Target version changed from Release 5.10 to Release 5.11

I think we have to move this to 5.11

#12 Updated by Patrick Plitzner 2 months ago

  • Severity changed from normal to critical

ok, this seems to be a bigger problem.

If you compare your debug output with the two files it seems like it has mixed the information together.

For example

                  <abcd21:AreaName language="en">North America</abcd21:AreaName>

comes from the DnaSample and

            <abcd21:RecordURI>http://herbarium.bgbm.org/object/BGT0023581</abcd21:RecordURI>

comes from the tissue sample.

Maybe the Abcd206XMLFieldGetter does not reset its state correctly when handling a new unit and instead just merges all the information it can get together.

#13 Updated by Katja Luther 2 months ago

  • File picture715-1.png added

Patrick Plitzner wrote:

ok, this seems to be a bigger problem.

If you compare your debug output with the two files it seems like it has mixed the information together.

For example

                  <abcd21:AreaName language="en">North America</abcd21:AreaName>

comes from the DnaSample and

            <abcd21:RecordURI>http://herbarium.bgbm.org/object/BGT0023581</abcd21:RecordURI>

comes from the tissue sample.

Maybe the Abcd206XMLFieldGetter does not reset its state correctly when handling a new unit and instead just merges all the information it can get together.

I checked the two files again and the tissue sample has UnitID B GT 0023581 and the associated unit of the dnaSample is B GT 0023612, so they do not belong together.
and the field unit of B GT 0023612 has no fieldNumber:


          <abcd21:Unit>
            <abcd21:UnitGUID>http://herbarium.bgbm.org/object/BGT0023612</abcd21:UnitGUID>
            <abcd21:SourceInstitutionID>B</abcd21:SourceInstitutionID>
            <abcd21:SourceID>Herbarium Berolinense</abcd21:SourceID>
            <abcd21:UnitID>B GT 0023612</abcd21:UnitID>
            <abcd21:Identifications>
              <abcd21:Identification>
                <abcd21:Result>
                  <abcd21:TaxonIdentified>
                    <abcd21:HigherTaxa>
                      <abcd21:HigherTaxon>
                        <abcd21:HigherTaxonName>CACTACEAE</abcd21:HigherTaxonName>
                        <abcd21:HigherTaxonRank>familia</abcd21:HigherTaxonRank>
                      </abcd21:HigherTaxon>
                    </abcd21:HigherTaxa>
                    <abcd21:ScientificName>
                      <abcd21:FullScientificNameString>Selenicereus dorschianus Ralf Bauer</abcd21:FullScientificNameString>
                      <abcd21:NameAtomised>
                        <abcd21:Botanical>
                          <abcd21:GenusOrMonomial>Selenicereus</abcd21:GenusOrMonomial>
                          <abcd21:FirstEpithet>dorschianus</abcd21:FirstEpithet>
                          <abcd21:AuthorTeam>Ralf Bauer</abcd21:AuthorTeam>
                        </abcd21:Botanical>
                      </abcd21:NameAtomised>
                    </abcd21:ScientificName>
                  </abcd21:TaxonIdentified>
                </abcd21:Result>
                <abcd21:PreferredFlag>1</abcd21:PreferredFlag>
              </abcd21:Identification>
            </abcd21:Identifications>
            <abcd21:RecordBasis>PreservedSpecimen</abcd21:RecordBasis>
            <abcd21:KindOfUnit>tissue</abcd21:KindOfUnit>
            <abcd21:Gathering>
              <abcd21:DateTime>
                <abcd21:DateText>04.02.2001</abcd21:DateText>
              </abcd21:DateTime>
              <abcd21:Agents>
                <abcd21:GatheringAgentsText>Lautner</abcd21:GatheringAgentsText>
              </abcd21:Agents>
              <abcd21:LocalityText>Jalisco. zwischen Conception de Buenas Aires und Union de Guadelupe an der Jal 410.</abcd21:LocalityText>
              <abcd21:Country>
                <abcd21:Name>Mexico</abcd21:Name>
                <abcd21:ISO3166Code>MX</abcd21:ISO3166Code>
              </abcd21:Country>
              <abcd21:NamedAreas>
                <abcd21:NamedArea>
                  <abcd21:AreaClass language="en">Continent</abcd21:AreaClass>
                  <abcd21:AreaName language="en">North America</abcd21:AreaName>
                </abcd21:NamedArea>
              </abcd21:NamedAreas>
              <abcd21:Altitude>
                <abcd21:MeasurementOrFactAtomised>
                  <abcd21:LowerValue>2150 m</abcd21:LowerValue>
                </abcd21:MeasurementOrFactAtomised>
              </abcd21:Altitude>
              <abcd21:Notes language="en" />
            </abcd21:Gathering>
            <abcd21:RecordURI>http://herbarium.bgbm.org/object/BGT0023612</abcd21:RecordURI>
          </abcd21:Unit>

#14 Updated by Katja Luther 2 months ago

the imported field unit for B GT 0023581 has collector and fieldNumber see attached file (picture607-1.png)

#15 Updated by Katja Luther 2 months ago

  • File deleted (picture715-1.png)

#16 Updated by Katja Luther about 2 months ago

  • Status changed from In Progress to Resolved
  • Assignee changed from Katja Luther to Patrick Plitzner

as the used example was about two different field units I close this ticket. Please make a last review for closing the ticket.

#18 Updated by Patrick Plitzner about 2 months ago

  • File deleted (tissue_sample.xml)

#19 Updated by Patrick Plitzner about 2 months ago

I uploaded the correct tissue sample file and will test again.

#20 Updated by Patrick Plitzner 16 days ago

  • Target version changed from Release 5.11 to Release 5.12

#21 Updated by Andreas Müller 16 days ago

  • Target version changed from Release 5.12 to Release 5.11

Why did you move it to 5.12. It has status resolved and should therefore be reviewed in 5.11 milestone. If there is a reason for moving please mention it.

#22 Updated by Patrick Plitzner 14 days ago

  • Status changed from Resolved to Closed
  • Assignee changed from Patrick Plitzner to Katja Luther
  • % Done changed from 60 to 100

Why did you move it to 5.12. It has status resolved and should therefore be reviewed in 5.11 milestone. If there is a reason for moving please mention it.

Sorry, I overlooked the content of this ticket.

Tested the import again and the FieldUnit data is now correctly imported.

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