Class: biosample diagram URL produces 414 URI Too Long error

[pvangay]

https://nmdc-docs-sphinx.readthedocs.io/en/latest/reference/metadata/Biosample.html

I'm not sure if this happened during the generation of it or further upstream.

FYI: @turbomam @ssarrafan

[eecavanna]

As of October 21, 2023, the maybe the same page still shows the same—or a similar—URL.

I looked at the JavaScript console (screenshot below) and saw an error message saying:

414 (Request-URI Too Large)

The offending long URL is:

https://yuml.me/diagram/nofunky%3Bdir:TB/class/%5BTimestampValue%5D,%5BTextValue%5D,%5BQuantityValue%5D,%5BOmicsProcessing%5D,%5BNamedThing%5D,%5BGeolocationValue%5D,%5BDatabase%5D,%5BControlledTermValue%5D,%5BBiosampleProcessing%5D,%5BQuantityValue%5D%3Csubsurface_depth2%200..1-++%5BBiosample%7Ctype:string%20%3F%3Becosystem:string%20%3F%3Becosystem_category:string%20%3F%3Becosystem_type:string%20%3F%3Becosystem_subtype:string%20%3F%3Bspecific_ecosystem:string%20%3F%3Badd_date:string%20%3F%3Bcommunity:string%20%3F%3Bhabitat:string%20%3F%3Bhost_name:string%20%3F%3Bidentifier:string%20%3F%3Blocation:string%20%3F%3Bmod_date:string%20%3F%3Bncbi_taxonomy_name:string%20%3F%3Bproport_woa_temperature:string%20%3F%3Bsalinity_category:string%20%3F%3Bsample_collection_site:string%20%3F%3Bsoluble_iron_micromol:string%20%3F%3BGOLD_sample_identifiers:external_identifier%20*%3BINSDC_biosample_identifiers:external_identifier%20*%3BINSDC_secondary_sample_identifiers:external_identifier%20*%3Bid(i):string%3Bname(i):string%20%3F%3Bdescription(i):string%20%3F%3Balternative_identifiers(i):string%20*%5D,%5BQuantityValue%5D%3Csubsurface_depth%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cdepth2%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cwater_content_soil_meth%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cwater_content%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Ctot_phosp%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Ctot_nitro_content_meth%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Ctot_nitro_content%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Ctot_org_c_meth%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Ctot_org_carb%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Ctot_diss_nitro%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Ctot_depth_water_col%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Ctot_carb%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Ctidal_stage%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Ctillage%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Ctexture_meth%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Ctexture%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Ctemp%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Csulfide%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Csulfate%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cstore_cond%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Csoil_type_meth%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Csoil_type%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Csodium%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cslope_aspect%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cslope_gradient%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Csize_frac_up%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Csize_frac_low%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Csieving%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cseason_precpt%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cseason_temp%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Csamp_vol_we_dna_ext%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Csamp_store_temp%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Csamp_store_loc%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Csamp_store_dur%200..1-++%5BBiosample%5D,%5BControlledTermValue%5D%3Csamp_mat_process%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Csamp_collect_device%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Csalinity_meth%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Csalinity%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Credox_potential%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cprofile_position%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cprevious_land_use_meth%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cprevious_land_use%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cpressure%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cpotassium%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cpool_dna_extracts%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cphosplipid_fatt_acid%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cphaeopigments%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cph_meth%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cph%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cpetroleum_hydrocarb%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cperturbation%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cpart_org_carb%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Coxy_stat_samp%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Corganism_count%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Corg_nitro%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Corg_matter%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cnitrite%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cnitrate%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cn_alkanes%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cmisc_param%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cmicrobial_biomass_meth%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cmicrobial_biomass%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cmean_peak_frict_vel%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cmean_frict_vel%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cmagnesium%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Clocal_class_meth%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Clocal_class%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Clink_climate_info%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Clink_class_info%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Clink_addit_analys%200..1-++%5BBiosample%5D,%5BGeolocationValue%5D%3Clat_lon%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Chorizon_meth%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Chorizon%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cheavy_metals_meth%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cheavy_metals%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cglucosidase_act%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cgeo_loc_name%200..1-++%5BBiosample%5D,%5BTimestampValue%5D%3Cflooding%200..1-++%5BBiosample%5D,%5BTimestampValue%5D%3Cfire%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cfao_class%200..1-++%5BBiosample%5D,%5BTimestampValue%5D%3Cextreme_event%200..1-++%5BBiosample%5D,%5BControlledTermValue%5D%3Cenv_medium%201..1-++%5BBiosample%5D,%5BControlledTermValue%5D%3Cenv_local_scale%201..1-++%5BBiosample%5D,%5BControlledTermValue%5D%3Cenv_broad_scale%201..1-++%5BBiosample%5D,%5BTextValue%5D%3Cenv_package%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Celev%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cdrainage_class%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cdiss_oxygen%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cdiss_org_nitro%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cdiss_org_carb%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cdiss_inorg_phosp%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cdiss_inorg_carb%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cdiss_hydrogen%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cdiss_carb_dioxide%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cdepth%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cdensity%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Ccrop_rotation%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Ccur_vegetation_meth%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Ccur_vegetation%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Ccur_land_use%200..1-++%5BBiosample%5D,%5BTimestampValue%5D%3Ccollection_date%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cchlorophyll%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cchloride%200..1-++%5BBiosample%5D,%5BControlledTermValue%5D%3Cchem_administration%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Ccarb_nitro_ratio%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Ccalcium%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cbromide%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cbishomohopanol%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cbacteria_carb_prod%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cannual_temp%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cannual_precpt%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cammonium%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Caminopept_act%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Cal_sat_meth%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cal_sat%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Calt%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Calkyl_diethers%200..1-++%5BBiosample%5D,%5BTextValue%5D%3Calkalinity_method%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Calkalinity%200..1-++%5BBiosample%5D,%5BQuantityValue%5D%3Cagrochem_addition%200..1-++%5BBiosample%5D,%5BNamedThing%5D%3Cpart%20of%201..*-%20%5BBiosample%5D,%5BBiosampleProcessing%5D-%20has%20input%200..*%3E%5BBiosample%5D,%5BDatabase%5D++-%20biosample%20set%200..*%3E%5BBiosample%5D,%5BOmicsProcessing%5D-%20has%20input(i)%201..*%3E%5BBiosample%5D,%5BNamedThing%5D%5E-%5BBiosample%5D

[eecavanna]

That URL is 8507 characters long.

Here is some guidance about URL lengths: https://stackoverflow.com/a/417184

[eecavanna]

Hi @kwdavenport, I noticed this ticket is assigned to you and I don't know if you are working on the project anymore. Do you plan to work on this? If I don't hear back within the next few days, I'll reassign it.

[ssarrafan]

Hi @kwdavenport, I noticed this ticket is assigned to you and I don't know if you are working on the project anymore. Do you plan to work on this? If I don't hear back within the next few days, I'll reassign it.

@eecavanna Karen is no longer working on NMDC. Can we re-assign this to @yxu-lanl ?

[eecavanna]

Thanks. That works for me.

[turbomam]

The issue here is the number of slots assigned to Biosample. If there is some clever short-term way to shrink the URLs that generate the Mermaid diagrams for this class, then yes, let's do that. But it is not a good long terms solution, and I don't think this issue belongs in this repo.

I have asked @sujaypatil96, who essentially owns the LinkML documentation page generator, to add some test that says "if the number of slots ins greater than X, the the Mermaid diagram will not be generated", but that never rose to the top of his sizable priority list.

There has also been discussion of using some diagram creator other than Mermaid for LinkML class documentation pages. @sujaypatil96 might be able to weigh in on that, or we could consult with @sierra-moxon.

Finally, there had been some discussion about refactoring Biosample as part of the December schema refactoring in Berkeley, but I believe that has been de-prioritized.

cc @cmungall @mslarae13 @aclum @mbthornton-lbl

[turbomam]

I would say that since we switched from YUML to Mermaid, there isn't a 414 error anymore. But the Biosample Mermaid diagram just isn't useful. If it can be made useful, let's do that. Otherwise let's just disable Mermaid generation for classes than have over N slots.

[mslarae13]

I agree with @turbomam I think we should just disable the diagram. It's not useful & close this issue.