Species data lost when two calibrations use same specimen

[Ksepka]

Noted for Atlantogenata and Afrotheria calibrations, which use the same fossil (MNHNFr PM69: Eritherium azzouzorum. Atlantogenata is fine, but Afrotheria shows a blank for "fossils used to date this node".

Allof the specimen, locality, and phylogenetic information is saved, but the species name / common name / author & date / PBDB taxon number fields are all blank in edit and view modes.

When I try to re-enter Eritherium azzouzorum here and save, I get this error message

Error in query: INSERT INTO fossiltaxa SET TaxonName = 'Eritherium azzouzorum' ,CommonName = '' ,TaxonAuthor = '' ,PBDBTaxonNum = ''|Duplicate entry 'Eritherium azzouzorum' for key 2

Exactly the same issue occurs in the case Protostomia and Ecdysozoa which use the same fossil (Rusophycus). Protostomia is fine, but Ecdysozoa lacks the species info block and it cannot be re-entered.

[jimallman]

Thanks @Ksepka, I'll chase this down today and report here.

[jimallman]

When I try to re-enter Eritherium azzouzorum here and save, I get this error message

I believe this is the problem; as the error message says ("Duplicate entry 'Eritherium azzouzorum' for key 2"), this taxon is already in the fossiltaxa table. We should not be re-entering an existing fossil taxon, just selecting it using the auto-complete widget shown here:

I've selected this fossil in the Afrotheria calibration and saved the change. Please take a look and confirm that this is correct. If so, try the same fix in the Ecdysozoa calibration and see if it behaves as described here.

Aside from the terse error message, this is the expected behavior.

[Ksepka]

Traveling this weekend will try as soon as I have internet.

Sent from my iPhone

On Oct 16, 2014, at 8:48 PM, Jim Allman notifications@github.com wrote:

When I try to re-enter Eritherium azzouzorum here and save, I get this error message

I believe this is the problem; as the error message says ("Duplicate entry 'Eritherium azzouzorum' for key 2"), this taxon is already in the fossiltaxa table. We should not be re-entering an existing fossil taxon, just selecting it using the auto-complete widget shown here:

I've selected this fossil in the Afrotheria calibration and saved the change. Please take a look and confirm that this is correct. If so, try the same fix in the Ecdysozoa calibration and see if it behaves as described here.

Aside from the terse error message, this is the expected behavior.

— Reply to this email directly or view it on GitHub.

[jimallman]

@Ksepka, I think I understand how things went wrong in your original report above. I've fixed the code that saves a previous fossil species when linking a fossil to multiple calibrations.

[jimallman]

FYI - I'm testing these fixes with this test calibration, which is in Private Draft state and has two linked fossils.

[Ksepka]

Looks like it is working now - just need to open and re-save each calibration (did this for Atlantogenata and Afrotheria and both now work).

[jimallman]

Great! @Ksepka, please close these issues once you're satisfied with the fix.