Reaction full text search results include reactions with no data

[jonrkarr]

Example:

• Search for trehalose
  • HSCJRCZFDFQWRP-RDKQLNKOSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N-->XCCTYIAWTASOJW-XVFCMESISA-N,LABSPYBHMPDTEL-LIZSDCNHSA-N
  • XLYOFNOQVPJJNP-UHFFFAOYSA-N,LABSPYBHMPDTEL-LIZSDCNHSA-N-->NBIIXXVUZAFLBC-UHFFFAOYSA-N,HDTRYLNUVZCQOY-MFAKQEFJSA-N
  • HXXFSFRBOHSIMQ-VFUOTHLCSA-N,WQZGKKKJIJFFOK-DVKNGEFBSA-N-->HDTRYLNUVZCQOY-MFAKQEFJSA-N,NBIIXXVUZAFLBC-UHFFFAOYSA-N
  • HXXFSFRBOHSIMQ-DVKNGEFBSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N-->NBIIXXVUZAFLBC-UHFFFAOYSA-N,LABSPYBHMPDTEL-LIZSDCNHSA-N
  • HDTRYLNUVZCQOY-MFAKQEFJSA-N,GACDQMDRPRGCTN-KQYNXXCUSA-N-->WVFKPISWLUJJIJ-LIZSDCNHSA-N,WHTCPDAXWFLDIH-KQYNXXCUSA-N
  • ZKHQWZAMYRWXGA-KQYNXXCUSA-J,NBSCHQHZLSJFNQ-DVKNGEFBSA-N-->HDTRYLNUVZCQOY-MFAKQEFJSA-N,XTWYTFMLZFPYCI-KQYNXXCUSA-N

[lzy7071]

I am not too sure what it means but here's what I did to replicate the isssue:

• I searched for trehalose using the endpoint /ftx/text_search/num_of_index

• I found the document with rxn_id: 1177 and kinlaw_id: [56592], that's the reaction indicated in the first bullet point.

• There are data associated with the reaction document.

If you were referring to Km or kcat, the has_poi (meaning has parameters, or rate constants, of interest) indicates if reactions have parameter information Km or kcat`. But I think we should return all reactions in the result, regardless of if it has rate constant information or not.

[jonrkarr]

I was referring to search results for trehalose: https://datanator.info/search/trehalose/.

Of the top 10 reaction results, 6 of the links point to pages which don't display any data. Examples:

• https://datanator.info/reaction/HSCJRCZFDFQWRP-RDKQLNKOSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3EXCCTYIAWTASOJW-XVFCMESISA-N,LABSPYBHMPDTEL-LIZSDCNHSA-N
• https://datanator.info/reaction/XLYOFNOQVPJJNP-UHFFFAOYSA-N,LABSPYBHMPDTEL-LIZSDCNHSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,HDTRYLNUVZCQOY-MFAKQEFJSA-N
• https://datanator.info/reaction/HXXFSFRBOHSIMQ-VFUOTHLCSA-N,WQZGKKKJIJFFOK-DVKNGEFBSA-N--%3EHDTRYLNUVZCQOY-MFAKQEFJSA-N,NBIIXXVUZAFLBC-UHFFFAOYSA-N

[jonrkarr]

The issue was that the search results include parameters that the frontend doesn't understand. I fixed most of the cases by extending the front end to support K_I (inhibitory constants) and parameters that use non-canonical units (by adding separate columns for units).

With my changes, the above errors are not longer relevant. Ignore the message above.

We still need to make 1 change to the reaction full text search. The full text search should only cover parameters with the following type or sbo_type:

• 25 (k_cat)
• 186 (V_max)
• 27 (K_M)
• 261 (K_I)

[jonrkarr]

Similar to #86 and #89, upon further reflection, I think its useful for Datanator explicitly communicate the absence of relevant data.

When we have more time, lets add an option to only return reactions that have kinetic measurements -- at least one parameter with (a) value or observed_value != null and (b) type or sbo_type is equal one of the following:

• 25 (k_cat)
• 186 (V_max)
• 27 (K_M)
• 261 (K_I)