diff --git a/nmdc_runtime/api/main.py b/nmdc_runtime/api/main.py index 6f5986c4..4e9013b3 100644 --- a/nmdc_runtime/api/main.py +++ b/nmdc_runtime/api/main.py @@ -222,11 +222,8 @@ { "name": "metadata", "description": """ -The [metadata endpoints](https://api.microbiomedata.org/docs#/metadata) can be used to get and filter metadata from -collection set types (including [studies](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Study.html), -[biosamples](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Biosample.html), -[data objects](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/DataObject.html), and -[activities](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Activity.html)).
+The [metadata endpoints](https://api.microbiomedata.org/docs#/metadata) can be used to get and filter metadata from collection set types (including studies, biosamples, planned processes, and data objects as discussed in the __find__ section). +
The __metadata__ endpoints allow users to retrieve metadata from the data portal using the various GET endpoints that are slightly different than the __find__ endpoints, but some can be used similarly. As with the __find__ endpoints, @@ -236,9 +233,6 @@ uses [MongoDB-like language querying](https://www.mongodb.com/docs/manual/tutorial/query-documents/). The applicable parameters of the __metadata__ endpoints, with acceptable syntax and examples, are in the table below. -
-More Details - | Parameter | Description | Syntax | Example | | :---: | :-----------: | :-------: | :---: | | collection_name | The name of the collection to be queried. For a list of collection names please see the [Database class](https://microbiomedata.github.io/nmdc-schema/Database/) of the NMDC Schema | String | `biosample_set` | @@ -248,25 +242,20 @@ | projection | Indicates the desired attributes to be included in the response. Helpful for trimming down the returned results | Comma-separated list of attributes that belong to the documents in the collection being queried | `name, ecosystem_type` | | doc_id | The unique identifier of the item being requested. For example, the identifier of a biosample or an extraction | Curie e.g. `prefix:identifier` | `nmdc:bsm-11-ha3vfb58` |

-
+ """, }, { "name": "find", "description": """ -The [find endpoints](https://api.microbiomedata.org/docs#/find:~:text=Find%20NMDC-,metadata,-entities.) are provided with -NMDC metadata entities already specified - where metadata about [studies](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Study.html), -[biosamples](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Biosample.html), -[data objects](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/DataObject.html), and -[activities](https://nmdc-documentation.readthedocs.io/en/latest/reference/metadata/Activity.html) can be retrieved using GET requests. +The [find endpoints](https://api.microbiomedata.org/docs#/find:~:text=Find%20NMDC-,metadata,-entities.) are provided with NMDC metadata entities already specified - where metadata about [studies](https://w3id.org/nmdc/Study), [biosamples](https://w3id.org/nmdc/Biosample), [data objects](https://w3id.org/nmdc/DataObject/), and [planned processes](https://w3id.org/nmdc/PlannedProcess/) can be retrieved using GET requests. +
Each endpoint is unique and requires the applicable attribute names to be known in order to structure a query in a meaningful way. Please note that endpoints with parameters that do not have a red ___* required___ label next to them are optional.
The applicable parameters of the ___find___ endpoints, with acceptable syntax and examples, are in the table below. -
More Details - | Parameter | Description | Syntax | Example | | :---: | :-----------: | :-------: | :---: | | filter | Allows conditions to be set as part of the query, returning only results that satisfy the conditions | Comma separated string of attribute:value pairs. Can include comparison operators like >=, <=, <, and >. May use a `.search` after the attribute name to conduct a full text search of the field that are of type string. e.g. `attribute:value,attribute.search:value` | `ecosystem_category:Plants, lat_lon.latitude:>35.0` | @@ -280,9 +269,9 @@ | study_id | The unique identifier of a study | Curie e.g. `prefix:identifier` | `nmdc:sty-11-34xj1150` | | sample_id | The unique identifier of a biosample | Curie e.g. `prefix:identifier` | `nmdc:bsm-11-w43vsm21` | | data_object_id | The unique identifier of a data object | Curie e.g. `prefix:identifier` | `nmdc:dobj-11-7c6np651` | -| activity_id | The unique identifier for an NMDC workflow execution activity | Curie e.g. `prefix:identifier` | `nmdc:wfmgan-11-hvcnga50.1`|
+| planned_process_id | The unique identifier for an NMDC planned process | Curie e.g. `prefix:identifier` | `nmdc:wfmgan-11-hvcnga50.1`| +
-
""", },