ODK to collect species and habitats localities, as pressure and threats to ecosystems

[mathieubossaert]

2021 update of the form

3 enhancements of our main form are detailed here. All made possible by using existing features of collect and thanks to a more attentive reading of the documentation and some guru help

1 - Facilitate and generalize the use of personal settings per form.

In the previous version of the form, we used user's phone number, stored in Collect to allow form customization. Each value from 0 to 9 represents at least ten parameters (see point 3 of the first message of the topic).
This "hack" is quite functional but limited because we can set only one phone number in the app, and not all the forms in the app use the same parameters...

In combination with user settings (user identity and email address defined at Collect's level), we will use the "last saved values" feature, introduced in Collect v1.21.0, to define user settings in each form

Form Logic

The logical is simple :

Each parameters is set to its lasts saved value. If it is the first use of the form, defaults values are set to true or the "Collect user's settings" one when possible (username and email).
here the "default" column of the user name :

coalesce(${last-saved#user_name},${username})

${username} is a field of type "username".

And here for the "geopint" setting (Do you want to create geopoint within the form ?)

coalesce(${last-saved#utiliser_geopoint},’true’)

User will be able to modify each value and next time he will use the form, this last saved value will be the default.

Those settings will be useful to adapt the form :

• show/hide group of question,
• filter select option (filter column : contains(${user_settings},filter))

Here is the extract of the 2021 version of the form relative to user settings and preferences. The empty columns are droped.

type	name	label	calculation	required	appearance	default
begin group	settings	Préférences → Géométries			field-list
select_one boolean	utiliser_geopoint	Saisir des points ?		yes	columns	coalesce(${last-saved#utiliser_geopoint},’true’)
select_one boolean	utiliser_geotrace	Saisir des lignes ?		yes	columns	coalesce(${last-saved#utiliser_geotrace},’true’)
select_one boolean	utiliser_geoshape	Saisir des polygones ?		yes	columns	coalesce(${last-saved#utiliser_geoshape},’true’)
end group
begin group	settings2	Préférences → Thématiques			field-list
select_one boolean	animalia	Données de faune ?		yes	columns	coalesce(${last-saved#animalia},’true’)
select_one boolean	plantae	Données de flore ?		yes	columns	coalesce(${last-saved#plantae},’true’)
select_one boolean	fungi	Données de champignons ?		yes	columns	coalesce(${last-saved#fungi},’true’)
select_one boolean	habitat	Données sur les habitats ?		yes	columns	coalesce(${last-saved#habitat},’true’)
select_one boolean	pression_menace	Pressions / menaces ?		yes	columns	coalesce(${last-saved#pression_menace},’true’)
select_one boolean	observation_generale	Observations générales / jalons ?		yes	columns	coalesce(${last-saved#observation_generale},’true’)
calculate	user_settings		concat(if(${utiliser_geopoint} = 'true','point',''),if(${utiliser_geotrace} = 'true','line',''),if(${utiliser_geoshape} = 'true','polygon',''),if(${animalia} = 'true','animalia',''),if(${plantae} = 'true','plantae',''),if(${fungi} = 'true','fungi',''),if(${habitat} = 'true','habitat',''),if(${pression_menace} = 'true','pression_menace',''),if(${observation_generale} = 'true','observation_generale',''))
end group
begin group	protocole_etude	Protocole et étude			field_list
select_one list_etude	id_etude	Etude		yes	quick search('etudes')
select_one list_protocole	id_protocole	Protocole		yes	quick search('protocoles')
end group

2 - How to select species in a list by typing first letters of its name or a code

This code consists in concatenate the 3 first letters of the genus with the 3 firsts letters of the species (for example the little bird Pheonicurus ochruros is coded with those 6 letters "pho och")

And as a bonus users wanted the list to show first official names, not synonyms : genus firsts, followed by species and in the end subspecies, alphabetically ordered.

This was finally easy to do, even if I didn't had any idea about how to do it before I read once again the serach() function documentation. It mention that you can search in one or more columns - I ignored or forgot that - and also the possibility to arbitrary order the list with a column named "sortby" in the csv file.

\3. "search(csvName, 'startswith', columnsToSearch, searchText)": This  search expression includes all distinct rows that start with the  specified text in the specified column(s) (e.g., "search('hhplotdata',  'startswith', 'respondentname', ${nameprefix})"). The third parameter  specifies either a single column name to search, or a comma-separated  list of column names to search. Rows with matches in any specified  column will be included.

There are just two additional notes on usage:

\1. Choices will be ordered, by default, in the order that they appear in your .csv file. If you want to specify a different ordering, include a numeric column in your .csv file named sortby; choices will be  ordered numerically, according to the sortby column (if present).

So I just had to create a new column in the csv file for the species code (code_espece_key), and another one "sortby" containing the rank of the species once the list is order by official/taxonomic rank/name

SELECT lb_nom_key, cd_nom_key, lb_cd_nom_key, regne as regne_key, groupe, group1_inpn, code_espece_key, rank() OVER(ORDER BY CASE WHEN rang ='GN' THEN 1 else 2 END, CASE WHEN lb_nom_key ILIKE '%nom valide%' THEN 3 ELSE 4 END, lb_nom_key ) AS sortby
FROM total
WHERE ...

the filter columns looks like this :

quick search('espece_animale', 'startswith', 'code_espece_key,lb_nom_key', ${recherche_espece_animale}) 

Select a tax with its name

or its code

3 how to facilitate checking or modifying collected data on the field

In other words how to enhance repeat group naming and form navigation.

Thanks to @LN I was able to reproduce what I did achieved in a simple form.

Problem with repeat group navigation and naming

One issue I can spot is that the localites group ends too early. If you'd like the name of that group to be used for the entire location you're capturing, then you need the group to enclose all questions related to that location. I haven't carefully looked at the observation groups but I wonder whether you might have something similar going on there -- you'll want to make sure that the obs group contains everything about a single observation. It's certainly possible there's a bug with complex n…

Each place (geo-widget question) is now named using creation time (ex. place at 18:06)

And within each location instances, observation are named using the species or habitat name or pressure/threat type

Things to investigate before the field season :

for species lists : having a "last_saved value like" behavior over preloaded data and search() function, or being able to do the same (with search() function) over external csv files (form datasets, select_one from external / select_one_from_file), more standard compliant way) and then query 2 columns (starts with) and order the result in the proposed list.

Here is the new form and its media files (truncated to few lines).
sicen_2021.zip (68.8 KB)

And the sql code to generate taxonomic csv files from the french reference (https://inpn.mnhn.fr/programme/referentiel-taxonomique-taxref)
vue_espece_animale.txt (4.8 KB)