bug #8631
closedABCD import fails to put new taxa into the classification, create mediaspecimens, etc
80%
Description
To reproduce:
- import Arenaria_ABCD_one_unit.xml with the below options
at the end the exception as described in #8630 happens.
As result of the import a classification has been created as well as the taxon "Arenaria serpyllifolia L. subsp. serpyllifolia sec. ABCD classic" but
- the taxon is not part of the classification.
- the specimen is not related to the name or taxon
- a media object was created (http://ww2.bgbm.org/herbarium/images/B/10/04/63/63/B_10_0463639.jpg) but is not associated with the specimen. A media specimen should have been created as derivative of the specimen B 10 0463639
- The DNA Sample which was fetched from a BioCase Provider is not a derivative of the specimen
BTW:
- What's the purpose of the text field close to the bottom of the dialog?
Files
| picture367-1.png (59.8 KB) picture367-1.png | |||
| Arenaria_ABCD_one_unit.xml (9.74 KB) Arenaria_ABCD_one_unit.xml | |||
| picture699-1.png (56.9 KB) picture699-1.png | |||
| picture673-1.png (20.1 KB) picture673-1.png | |||
| picture860-1.png (20.2 KB) picture860-1.png | |||
| picture468-1.png (51.2 KB) picture468-1.png |
Related issues
Updated by Andreas Kohlbecker over 4 years ago
Updated by Andreas Kohlbecker over 4 years ago
- Related to bug #8630: ClassCastException when ABCD import has finished added
Updated by Andreas Kohlbecker over 4 years ago
- Related to task #8580: Update documentation to latest revision of the Taxeditor added
Updated by Andreas Kohlbecker over 4 years ago
- Subject changed from ABCD import fails to put new taxa into the classification to ABCD import fails to put new taxa into the classification, create mediaspeciemens, etc
Updated by Andreas Kohlbecker over 4 years ago
- Related to bug #8632: ABCD retrieves DNA Sample from Biocase Provider even if it is not selected in the import configuration added
Updated by Katja Luther over 4 years ago
the media was not imported because of a NPE, this is fixed.
the dna was not associated to the specimen because of wrong associationType parsing when the abcd version is different, this is fixed.
The problem of the taxon appears only for the import from file. It is a lazy loading exception while creating the nomenclatural titleCache of a team during cascading.
Updated by Katja Luther over 4 years ago
- Status changed from New to In Progress
Updated by Katja Luther over 4 years ago
- Target version changed from Unassigned CDM tickets to Release 5.11
The ClassCastException should be solved with the last commit
Updated by Katja Luther over 4 years ago
As a workaround the possibility to search for dna is disabled for file import. For the biocase seach it is still possible to add a dna biocase provider.
There is a test in cdmlib for import from file with dna search, it works.
Updated by Katja Luther over 4 years ago
- Status changed from In Progress to Resolved
- Assignee changed from Katja Luther to Andreas Kohlbecker
Updated by Andreas Kohlbecker over 4 years ago
- Assignee changed from Andreas Kohlbecker to Katja Luther
There are still some problems which are not yet fixed:
- the taxon is not part of the classification.
- the specimen is not related to the name or taxon
and I found some new problems
- after the import the Taxonnavigator is not refreshes, the new classification only becomes visible after closing and re-openening this view, I will add this obeservarion to #8582
- The "Configure Import Dialog" has changed, and has two issues:
- The select field for "Unit ID Mapping" is hardly readable and should be moved, aligned differently so that it is completely visible also in linux
- There is a new select field offering codes, the purpose of this field is unclear, even more unclear since the next page of the import wizard allows to choose the code again.
Updated by Andreas Kohlbecker over 4 years ago
- Related to bug #8582: Taxon Navigator: Classification label not refreshed & new taxa not visible added
Updated by Katja Luther over 4 years ago
- File picture673-1.png picture673-1.png added
Andreas Kohlbecker wrote:
There are still some problems which are not yet fixed:
- the taxon is not part of the classification.
- the specimen is not related to the name or taxon
and I found some new problems
- after the import the Taxonnavigator is not refreshes, the new classification only becomes visible after closing and re-openening this view, I will add this obeservarion to #8582
- The "Configure Import Dialog" has changed, and has two issues:
- The select field for "Unit ID Mapping" is hardly readable and should be moved, aligned differently so that it is completely visible also in linux
- There is a new select field offering codes, the purpose of this field is unclear, even more unclear since the next page of the import wizard allows to choose the code again.
that the field for Unit ID Mapping is hardly readable seems to be a OS problem with windows it looks like this:
Updated by Katja Luther over 4 years ago
the nomenclatural code selection page is removed
Updated by Katja Luther over 4 years ago
Andreas Kohlbecker wrote:
There are still some problems which are not yet fixed:
- the taxon is not part of the classification.
- the specimen is not related to the name or taxon
I think this is related to the lazy loading exception during the import. There is now a import report at the end of the import, there these exceptions should be shown.
Updated by Katja Luther over 4 years ago
Katja Luther wrote:
Andreas Kohlbecker wrote:
There are still some problems which are not yet fixed:
- the taxon is not part of the classification.
- the specimen is not related to the name or taxon
maybe there is no "preferred" flag for one of the determinations (if there is only one determination this is the preferred determination), if this is missing the import does not create the taxon node and relation from the taxon and specimen.
Updated by Andreas Kohlbecker over 4 years ago
Katja Luther wrote:
the nomenclatural code selection page is removed
Did you add a label to the code selection field?
Updated by Andreas Kohlbecker over 4 years ago
Katja Luther wrote:
Andreas Kohlbecker wrote:
- The "Configure Import Dialog" has changed, and has two issues:
- The select field for "Unit ID Mapping" is hardly readable and should be moved, aligned differently so that it is completely visible also in linux
- There is a new select field offering codes, the purpose of this field is unclear, even more unclear since the next page of the import wizard allows to choose the code again.
that the field for Unit ID Mapping is hardly readable seems to be a OS problem with windows it looks like this:
I don't share this view that is an OS problem. I checked a coupld of dialogs with selects in eclipse and in dBeaver and none of the dialogs has this problem.
To me it looks like the width of the select elements is determined by the code selection field (At least in QT/GTK driven desktop environments).
The way the label is added to the select is a bit special in this import dialog as in all other cases the label prepends the select:
label: [select]
Updated by Andreas Müller over 4 years ago
- % Done changed from 0 to 40
Can you please leave a note if this is easy to fix? Otherwise please move to new ticket as the layout is not really part of the original ticket description
Updated by Katja Luther over 4 years ago
- File picture860-1.png picture860-1.png added
Andreas Müller wrote:
Can you please leave a note if this is easy to fix? Otherwise please move to new ticket as the layout is not really part of the original ticket description
the label and the combo box are now in one line:
@AK: could you please check, whether the combo box is displayed correctly on linux?
Updated by Andreas Müller over 4 years ago
- Assignee changed from Katja Luther to Andreas Kohlbecker
Updated by Andreas Müller over 4 years ago
- Subject changed from ABCD import fails to put new taxa into the classification, create mediaspeciemens, etc to ABCD import fails to put new taxa into the classification, create mediaspecimens, etc
Updated by Patrick Plitzner over 4 years ago
- File picture468-1.png picture468-1.png added
This is how it looks for me. Started the editor from the IDE.
Updated by Andreas Müller over 4 years ago
- Status changed from Resolved to Feedback
- Assignee changed from Andreas Kohlbecker to Katja Luther
So the layout still needs some update for linux, I guess.
Updated by Katja Luther over 4 years ago
- Assignee changed from Katja Luther to Patrick Plitzner
@Patrick could you have another look, whether it looks better now. It is difficult to check for me because with windows it looks ok.
Updated by Patrick Plitzner over 4 years ago
- Assignee changed from Patrick Plitzner to Katja Luther
I made some changes myself. Looks fine on Linux. Please test on windows.
Updated by Andreas Müller over 4 years ago
It look ok now. Only change I suggest: let the "Biocase provider for DNA" dropdown start at the same horizontal position as all other dropdowns.
@Andreas K.: Can you also check if it looks ok on your Linux?
Updated by Andreas Müller over 4 years ago
Andreas Müller wrote:
It look ok now. Only change I suggest: let the "Biocase provider for DNA" dropdown start at the same horizontal position as all other dropdowns.
@Andreas K.: Can you also check if it looks ok on your Linux?
upps, sorry, I tested the preference page, not the file import. However, the little change in the preference would also be nice ...
Updated by Andreas Kohlbecker over 4 years ago
It looks ok in KDE!
The ticket can be closed.
Updated by Katja Luther over 4 years ago
- Status changed from Feedback to Closed