API v0.original

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The original version of the BETYdb API was tightly integrated with the BETYdb browser interface. In general, for every BETYdb Web page displaying a list of some kind of database entity (or one particular item from that list), there is a corresponding URL to request that same information in CSV, JSON, or XML format. Usually, this is a simple matter of deleting the ".html" extension from the Web page URL path (if present) and appending ".csv", ".json", or ".xml" to the path instead.

Note: All of the URLs in the examples below are for the BETYdb instance at www.betydb.org. To try the examples at a different BETYdb site, replace "https://www.betydb.org" with the top-level URL for the desired site.

Simple API queries

The simplest kind of API request extracts information from a single database table. Various result formats can be requested. CSV (comma-separated values) format is of particular interest: it is a format that is easy to view and use in any spreadsheet software and in R. Other possible formats are JSON and XML.

In the discussion that follows, most URLs given as examples are clickable; the results of the various HTTP requests represented by these URLs will then be viewable in a browser.

In most of these calls, we will write the URLs to request results in XML format rather than in CSV format. This is mainly for convenience: requests for XML format will usually display the result in the browser whereas requests for CSV format will download a CSV file. If, however, you want to see what the result would be in either of the other two formats, this is easy to do: After clicking the link and seeing the XML result in the browser, go into the browser's address box and manually edit the URL there, replacing the .xml extension with .json or .csv as desired.

A simple example

Data can be requested as a CSV, XML, or JSON file, and data from previously published syntheses can be requested without logging in. In the simplest case, we can use a single key-value pair to filter the table, restricting the result to the set of rows having a given value in a given column. For example, to download all of the trait data for the switch-grass species Panicum virgatum, we must first look up the id number of the Panicum virgatum species. We can do this by querying the species table by sending a request to this URL

/species.xml?scientificname=Panicum+virgatum

and then examining the "id" value of the one species in the result. Once we have the id, we can use it to query the traits table:

/traits.xml?specie_id=938

The reason we must use this two-stage process is that the traits table doesn't contain the species name information directly.

Caveat! There is no guarantee that these id numbers will not change! Although it is unlikely that the id number for Panicum virgatum will change between the time we look it up in the species table and the time we use it to query the traits table, it entirely possible that if we run the query /traits.xml?specie_id=938 a year from now, the result will be for an entirely different species! For this and other reasons, it is worthwhile learning how to do cross-table queries.

Complex API Queries

The API allows more complex queries and faster programmatic access by including multiple search terms in the query string of the URL. This feature is (for example) used to access BETYdb via the Ropensci traits package.

A brief summary of the syntax of URL-based queries:

  • The portion of the URL directly following / determines the primary table being queried and the format of the query result. For example, use /citations.json to get results from the citations table in JSON format and /cultivars.xml to get results from the cultivars table in XML format.

  • As a special case, to query the SQL view traits_and_yields_view, use "search" in place of the table name. For example, /search.json?search=Salix+caprea returns all the rows of this view pertaining to species Salix caprea.

  • The URL /traits.csv will download the entire traits table (or rather, that portion of the table which the current user is permitted to access) in CSV format. To restrict the results, we use a query string, which is the portion of the URL after the question mark. The query string consists of one or more clauses of the form <key>=<value> separated by & characters. For example, to obtain only the portion of the traits table associated with the site having id 99, the species having id 938, and the citation having id 45, we could write /traits.csv?site_id=99&specie_id=938&citation_id=45. Note that restrictions are cumulative: each clause further restricts the result of applying the previous restriction. In general, there is no way of taking the disjunction of multiple clauses—that is, there is not way of "OR-ing" the clauses together (but see the next item).

  • In queries on traits_and_yields_view, in addition to being able to use column names as keys, you can also use the special key search. This matches against multiple columns at once, and the query succeeds if each word in the search string matches any portion of one of the column values in the list of searched columns. Moreover, these matches are not case-sensitive. For full details, see the appendix.

  • URLs can not contain spaces. If the value you are querying against contains a space, substitute + or %20 in the URL. Thus, in our very first example above we had to write the query URL as /species.csv?scientificname=Panicum+virgatum. We could not have written it as /species.csv?scientificname=Panicum virgatum and expect to get the result we wanted.

Cross-table queries

It is possible to write queries involving multiple tables. Compared with the full expressive power of SQL, this ability is somewhat limited. Nevertheless, most common queries of interest should be possible. Here is a short outline of the scope and syntax of such queries:

  • In any multiple-table query, there is always a "primary" table. This corresponds to the name directly following the hostname portion of the URL. For example, in a query of the form /yields.csv?specie_id=938&..., "yields" is the primary table of the query.

  • Other tables involved in the query must be related to the primary table in one of the following three ways:

    1. The primary table has a foreign key column that refers to the other table. For example, the citation_id column of the yields table refers to the citations table, so we can include the citations table in any query on the yields table.

    2. The other table has a foreign key referring to the primary table. For example, we could involve the cultivars table in any query where species is the primary table because the cultivars table has a specie_id column.

    3. There is a join table connecting the primary table to the other table. For example, because the citations_sites table joins the citations table with the sites table, a query with citations as the primary table is allowed to include the sites table. Visit /schemas to view a list of the tables (including join tables) of BETYdb. Click on a table name to see a list of its columns.

  • For each "other" table involved in the query, there must be a clause in the query string of the URL of the form include[]=other. The "other" portion of this clause is either (1) the name of the other table, or (2) the singular form of the name of the other table. Which of these two to use depends on whether a row of the primary table may be associated with multiple rows of the other table (case 1) or whether a row of the primary table is always associated with at most one row of the associated table (case 2). An easy rule of thumb here is to use the singular form if the primary table has a foreign key column referring to the other table and to use the actual (plural) table name otherwise. Note you must include the square brackets after "include"!

  • "include[]-ing" another table in a query allows the query to filter query results based on column values in that other table. But to do so, the "key" portion of the filter clause must be of the form <other-table-name>.<column-name>. (Note that for keys referring to column values in the primary table, using the table name qualifier is optional.)

  • "include[]-ing" another table in a query has another effect in the case of XML and JSON-formatted results: The associated row(s) from the included table are included with each entity of the primary table the query returns. For example, consider the query /cultivars.xml?species.genus=Salix&include[]=specie. Not only will this return all cultivars for any species with genus Salix, it will return detailed species information for each cultivar returned. Contrast this with the CSV-format query /cultivars.csv?species.genus=Salix&include[]=specie. This returns the same cultivars as before, but we only get the information contained in the cultivars table. In particular, while we will get the value of specie_id for each returned cultivar, we won't get the corresponding species name.

A few points need to be made about how cross-table queries work.

  1. Suppose the primary table is in a many-to-one relationship with the other table. Then if we include a clause of the form <other-table-name>.<column-name>=value, a row of the primary table is selected precisely when <other-table-name>.<column-name>=value for at least one associated row from the other table. For example, in the query https://www.betydb.org/citations.xml?author=Clifton-Brown&include[]=sites&sites.city=Lisbon, the citations returned will be all and only those where the author is Clifton-Brown and where at least one of the associated sites is in the city Lisbon.

  2. As mentioned above, in the case of XML and JSON-formatted results, full information is given about associated rows from the other table(s). In the example just given, for each citation of Clifton-Brown associated with some site(s) in Lisbon, we will see full information about those sites in the results. Other sites associated with the same citation but not in Lisbon, however, will not be shown.

  3. You can add an include[]=other clause without any corresponding filter clauses. This will not filter out any results but will add in information from the other table (except when the return format is CSV). For example, the query https://www.betydb.org/citations.xml?author=Clifton-Brown&include[]=sites shows the same citations as the query https://www.betydb.org/citations.xml?author=Clifton-Brown. But it will, in addition, show full information about all of the sites associated with each of the selected citations.

  4. Even if the singular form of the table name must be used in the include[]=other clause, the actual table name must be used in the <other-table-name>.<column-name>=value filtering clause.

Some examples will make the query syntax clearer. In all of these examples, you can interchange .json with .xml or .csv depending on the format that you want.

Examples

  1. Return all trait data for "Panicum virgatum" without having to know its species id number:

    /traits.xml?include[]=specie&species.scientificname=Panicum+virgatum

    This will return exactly the same traits as the query in simple example above that used the specie_id number, but with the species information included. (If CSV format is used instead, exactly the same result files are returned).

  2. Note that the result of the previous query contains much redundancy: full information about species Panicum virgatum is included with each trait returned. The following query will show the Panicum virgatum species information only once:

    /species.xml?scientificname=Panicum+virgatum&include[]=traits

    This returns a single result from the species table—the row information for Panicum virgatum—but nested inside this result is a list of all trait rows associated with that species.

    In CSV mode, this option is not available to us. CSV format only shows information extracted from the primary table. In CSV mode, an "include[]=other_table" clause is useless unless you are going to filter the returned results using column values in the included table.

  3. Return all citations in JSON format (replace .json with .xml or .csv for those formats):

    /citations.json

  4. Return all yield data for the genus Miscanthus:

    /yields.xml?include[]=specie&species.genus=Miscanthus

    If we're only interested in Miscanthus having species name "sinensis", we can do:

    /yields.xml?include[]=specie&species.genus=Miscanthus&species.species=sinensis

    As in the first example, this query will show the same species information multiple times—once for each yield.

    Once again, we may remedy this by making species the primary table:

    /species.xml?genus=Miscanthus&include[]=yields /species.xml?genus=Miscanthus&species=sinensis&include[]=yields

    These each return a list of Miscanthus species, and each species item itself contains a list of yields for that species. In these query results, each species is only listed once.

  5. Return all yield data associated with the citation Heaton 2008:

    /citations.xml?include[]=yields&author=Heaton&year=2008

    To get this information in CSV format, we have to use yields as the primary table:

    /yields.csv?include[]=citation&citations.author=Heaton&citations.year=2008

    Note that we use the singular form "citation" in the include clause (since there is one citation per yield), but the qualified column names "citations.author" and "citations.year" must always use the actual database table name.

  6. Find species associated with the salix plant functional type:

    /pfts.xml?include[]=specie&pfts.name=salix

    You can also do the query like so:

    /species.xml?include[]=pfts&pfts.name=salix

    The results of these two queries contain essentially the same information. And to emphasize that we only need to interchange the primary and included table names to get from one query to the other, we have used the fully-qualified column name "pfts.name" in both (though just "name" would suffice in the first).

    The form of the result of the two queries is rather different. It is instructive to compare them. The first form is better for use with XML and JSON. It doesn't repeat the same PFT information over and over again inside each species listing. But the second form is the only one we can use with CSV format if we want to get any species information at all.

  7. Return all citations with their associated sites:

    /citations.xml?include[]=sites

    (Note that we use the plural form "sites" in the include clause since each citation may be associated with many sites.)

  8. Return all citations with their associated sites and yields:

    /citations.xml?include[]=sites&include[]=yields

    Note that this will take considerable time since the information for all yields rows will be displayed. If the query times out, try adding a restriction such as year=1990:

    /citations.xml?year=1990&include[]=sites&include[]=yields

    Note also that the result of this query will not tell us which site is associated with which yield.

  9. Return all citations by author Lewandowski in the journal European Journal of Agronomy along with their associated sites and yields:

    /citations.xml?journal=European+Journal+of+Agronomy&author=Lewandowski&include[]=sites&include[]=yields

  10. Return citation 1 in JSON format:

    /citations/1.json

    Alternatively, we can do:

    /citations.json?id=1

    This second result is slightly different: It returns a JSON array with a single item instead of the item itself.

  11. Return citation 1 in JSON format with its associated sites:

    /citations/1.json?include[]=sites

  12. Return citation 1 in JSON format with its associated sites and yields:

    /citations/1.json?include[]=sites&include[]=yields

Regarding the last three examples, although the syntax for returning data associated with a single entity (citation 1 in these examples) is very convenient, in general it is best not to rely on fixed id numbers for entities. "The citation in Agronomy Journal with author Adler" is a more reliable locator than "The citation with id 1".

Avoiding Cross-Table Queries: Using the Traits and Yields View

The database view traits_and_yields_view provides summary information about traits and yields: It combines information from the traits and the yields tables, and it includes information from six associated tables—namely, the sites, species, citations, treatments, variables, and users tables. Whereas the traits and the yields tables contain only pointers to these tables (foreign keys in the form of id numbers), the traits_and_yields_view directly contains information associated with a trait or yield, such as the name of the species of the plant whose trait was measured, the name of the measured variable, and the author and year of the citation associated with the trait or yield. This means that in many cases, a query of the traits_and_yields_view may be used to extract information that otherwise would require a complex cross-table query.

Furthermore, looser match rules are possible by using the special key called search instead of a column name. For example,

/search.xml?search=cottongrass

will return all traits and yields for which the common name of the species includes the word "cottongrass". To get the same rows using commonname as the key, we would have to do three separate searches:

/search.xml?commonname=tussock+cottongrass

/search.xml?commonname=white+cottongrass

/search.xml?commonname=tall+cottongrass

This is because when we use a column name as the search key, the value must match the column value exactly, including the letter case and the number of spaces between words.

Including Unchecked Data in the Traits and Yields View

By default, searches on traits_and_yields_view return only checked data. The Web interface now has a checkbox labelled "include unchecked records" that the user may check to override this default. To do the same thing through the API, the user must include a clause of the form include_unchecked=true in the query string. (Any of "TRUE", "yes", "YES", "y", "Y", "1", "t", "T" may be used in place of "true" here.)

A Few Notes about Searching the Traits and Yields View

  1. The base URL to use is /search

  2. You can use column name keys only when the result format is XML or JSON. If the result format is CSV or HTML, any query-string clause of the form <columnname>=<value> is ignored.

  3. The query-string clauses of the form search=<value> and include_unchecked=true may be used with all result formats.

  4. If multiple search=<value> clauses are included, only last one is used. Don't do this! To search on multiple terms, separate them in the query string by + signs. For example, /search.xml?search=LTER+cottongrass&include_unchecked=true will likely find traits and yields results for cottongrass species at LTER (Long-term Ecological Research) sites, including those that have not been checked.

  5. As noted in the Web Interface Search section, each word in the value of a search=<value> clause must match one of the columns sitename, city, scientificname, commonname, cultivar author, trait, trait_description, citation_year, or entity in order for a given row to be included in the search result. Recall that a word in the value of the search string matches a column value if it is textually included in it.

  6. Remember that values for column name keys are treated very differently from the way the value of the search key is treated. In particular, the value is treated as one unit. Consider the difference between these two examples: In the search

    /search.xml?commonname=white+willow

    the search string "white willow" is treated as a unit, and this search will return only rows pertaining to the species with commonname "white willow". But in the search

    /search.xml?search=white+willow

    the words "white" and "willow" are considered separately. So this search will, in addition, return (for example) rows for white ash at a site called Willow Creek (US-WCr) because "white" matches the species name and "willow" matches the site name.

Using the command-line program curl as an example, we could issue the curl command

curl -u <your login>:<your password> "{{book.BETYdb_URL}}/species.xml?scientificname=Panicum+virgatum"

instead of visiting the given URL in a Web browser. Or, using an API key instead of the -u option, we could use the command

curl "{{book.BETYdb_URL}}/species.xml?scientificname=Panicum+virgatum?key=<your API key>"