Harvester updates for mosquito sample classes

[sunray1]

For the mosquito sample classes, the harvester is failing to record data from the API, even though the information is available.

For Bulk Identified/DNA Extracts/Pathogen Extracts/Pinned Vouchers:

• Check Plot/Site information - for bulk identified, there should be no plot, it should only be to site; check this for the others
• Determination date (added recently by NEON) and identifiedBy - none of these are being pulled in even though the information is at the grandparent or the sample level depending on the class
• Sample count - for bulk samples this is getting taken from the first grandparent instead of the sample itself, for pinned vouchers, this is likely hard coded as 1
• Life Stage and reproductive condition - for single samples this exists at the sample level but is not getting recorded

[sunray1]

Related to #325

[kyule]

I did some additional digging here 5/28/24

If we were to "uncomment out" //if(strpos($tableName,'identification')) continue; we would be able to correctly harvest the collector for pinned mosquitos and DNA samples as the API is always providing "National Ecological Observatory Network..." for these samples (likely is because of how the expert identifiers are returning data). However, uncommenting out that line prevents harvesting of other fields that do rely on that table. It would be better if we could get NEON to not include that in the API.

The sorting table is needed in order to get the determination dates and references but relying on info that far up the heirarchy leads to incorrect plot, individual count, etc. Commenting out the line that causes us to skip the barcoding table. Collection date is provided in the barcoding table but not the pinned table so you need to go up to the sorting table for the pinned individual but not its child sample :/

[kyule]

Currently the line to skip the 'identifications' table is commented out, but the line to skip the 'barcoding' table is active. Sample classes like pinned and DNA sample, are therefore able to get the correct taxon for the sample but do not see the identifiedBy, identificationResources, and identificationDate fields because those are located in the barcoding table, etc. They get the taxon and say the determiner, etc, is unknown. Although they would be able to see this information in the parent sample, they already have an identificaiton (albeit incomplete) from the sample itself so $harvestIdentifications is false and the parent sample identification is not used.