The Auspice server handles requests to 3 API endpoints made by the Auspice client:
/charon/getAvailable
(returns a list of available datasets and narratives)/charon/getDataset
(returns the requested dataset)/charon/getNarrative
(returns the requested narrative)
URL query arguments:
prefix
(optional) - the pathname of the requesting page in Auspice. ThegetAvailable
handler can use this to respond according appropriately. Unused by the default Auspice handler.
JSON Response (on success):
{
"datasets": [
{
"request": "[required] The pathname of a valid dataset. \
Will become the prefix of the getDataset request.",
"buildUrl": "[optional] A URL to display in the sidebar representing \
the build used to generate this analysis.",
"secondTreeOptions": "[optional] A list of requests which should \
appear as potential second-trees in the sidebar dropdown"
},
// ...
],
"narratives": [
{"request": "URL of a narrative. Will become the prefix in a getNarrative request"},
// ...
]
}
Failure to return a valid JSON will result in a warning notification shown in Auspice.
URL query arguments:
prefix
(required) - the pathname of the requesting page in Auspice. Use this to determine which dataset to return.type
(optional) -- if specified, then the request is for an additional file (e.g. "tip-frequencies"), not the main dataset.
JSON Response (on success):
The JSON response depends on the file-type being requested.
If the type is not specified, i.e. we're requesting the "main" dataset JSON then see this JSON schema. Note that the Auspice client cannot process v1 (meta / tree) JSONs -- see below <server-api-importing-code-from-auspice>
for how to convert these.
Alternative file type reponses are to be documented.
Alternative responses:
A 204
reponse will cause Auspice to show its splash page listing the available datasets & narratives. Any other non-200 reponse behaves similarly but also displays a large "error" message indicating that the dataset was not valid.
URL query arguments:
prefix
(required) - the pathname of the requesting page in Auspice. Use this to determine which narrative to return.type
(optional) - the format of the data returned (see below for more information). Current valid values are "json" and "md". If no type is specified the server will use "json" as a default (for backwards compatibility reasons). Requests to this API from the Auspice client are made withtype=md
.
Response (on success):
The response depends on the type
specified in the query.
If a markdown format is requested, then the narrative file is sent to the client unmodified to be parsed on the client.
If a JSON is requested then the narrative file is parsed into JSON format by the server. For Auspice versions prior to v2.18 this was the only expected behavior. The transformation from markdown (i.e. the narrative file itself) to JSON is via the parseNarrativeFile()
function (see below for how this is exported from Auspice for use in other servers). Here, roughly, is the code we use in the auspice server for this transformation:
const fileContents = fs.readFileSync(pathName, 'utf8');
if (type === "json") {
const blocks = parseNarrative(fileContents);
res.send(JSON.stringify(blocks).replace(/</g, '\\u003c'));
}
Note
While the Auspice client (from v2.18 onwards) always requests the type=md
, it will attempt to parse the response as JSON if markdown parsing fails, in an effort to remain backwards compatible with servers which may be using an earlier API.
The provided Auspice servers -- i.e. auspice view
and auspice develop
both have a --handlers <JS>
option which allows you to define your own handlers. The provided JavaScript file must export three functions, each of which handles one of the GET requests described above and must respond accordingly (see above for details).
function name | arguments | API endpoint |
---|---|---|
getAvailable | req, res | /charon/getAvailable |
getDataset | req, res | /charon/getDataset |
getNarrative | req, res | /charon/getNarrative |
For information about the req
and res
arguments see the express documentation for the request object and response object, respectively.
You can see nextstrain.org's implementation of these handlers here.
Here's a pseudocode example of an implementation for the getAvailable
handler which may help understanding:
const getAvailable = (req, res) => {
try {
/* collect available data */
res.json(data);
} catch (err) {
const errorMessage = `error message to display in client`;
console.log(errorMessage); /* printed by the server, not the client */
return res.status(500).type("text/plain").send(errorMessage);
}
};
The servers included in Auspice contain lots of useful code which you may want to use to either write your own handlers or entire servers. For instance, the code to convert v1 dataset JSONs to v2 JSONs (which the client requires) can be imported into your code so you don't have to reinvent the wheel!
Currently
const auspice = require("auspice");
returns an object with two properties:
Signature:
const v2json = convertFromV1({tree, meta})
where tree
is the v1 tree JSON, and meta
the v1 meta JSON.
Returns:
An object representing the v2 JSON defined by this schema.
Warning
This function is deprecated as of vXXX. You can now send the untransformed contents of the narrative file (markdown) for client-side parsing. See above <server-api-charon-getnarrative>
for more details.
Signature:
const blocks = parseNarrativeFile(fileContents);
where fileContents
is a string representation of the narrative Markdown file.
Returns:
An array of objects, each entry representing a different narrative "block" or "page". Each object has properties
__html
-- the HTML to render in the sidebar to form the narrativedataset
-- the dataset associated with this blockquery
-- the query associated with this block