Remove .dev substring from api.dev.microbiomedata.org URLs (#309)

* Update auth.md docs

* Remove `.dev` substring from `api.dev.microbiomedata.org` URLs

---------

Co-authored-by: eecavanna <134325062+eecavanna@users.noreply.github.com>

demo/metadata_discovery/indexing.ipynb

@@ -68,13 +68,13 @@
     "import requests\n",
     "\n",
     "docs = []\n",
-    "rv = requests.get(\"https://api.dev.microbiomedata.org/biosamples?page=1&per_page=200\")\n",
+    "rv = requests.get(\"https://api.microbiomedata.org/biosamples?page=1&per_page=200\")\n",
     "docs.extend(rv.json()['results'])\n",
-    "rv = requests.get(\"https://api.dev.microbiomedata.org/biosamples?page=2&per_page=200\")\n",
+    "rv = requests.get(\"https://api.microbiomedata.org/biosamples?page=2&per_page=200\")\n",
     "docs.extend(rv.json()['results'])\n",
-    "rv = requests.get(\"https://api.dev.microbiomedata.org/biosamples?page=3&per_page=200\")\n",
+    "rv = requests.get(\"https://api.microbiomedata.org/biosamples?page=3&per_page=200\")\n",
     "docs.extend(rv.json()['results'])\n",
-    "rv = requests.get(\"https://api.dev.microbiomedata.org/biosamples?page=4&per_page=200\")\n",
+    "rv = requests.get(\"https://api.microbiomedata.org/biosamples?page=4&per_page=200\")\n",
     "docs.extend(rv.json()['results'])\n",
     "len(docs)"
    ]

docs/howto-guides/author-changesheets.md

@@ -45,9 +45,9 @@ flowchart LR;
         * If you are modifying/replacing the value of a key in a document which has a *list* structure, then specifying a single value in the *value* column of the changesheet will be interpreted as a single element list. If you wanted to replace it with a multi-element list, then you can specify the individual elements of that list value in a pipe (`|`) delimited fashion in the *value* column of the changesheet
 
 
-3. The third step is to use the validation endpoint from the runtime API which you can find [here](https://api.dev.microbiomedata.org/docs#/metadata/validate_changesheet_metadata_changesheets_validate_post). Click on *Try it out*, and upload your TSV file. You should see a `200` successful response for proper validation.
+3. The third step is to use the validation endpoint from the runtime API which you can find [here](https://api.microbiomedata.org/docs#/metadata/validate_changesheet_metadata_changesheets_validate_post). Click on *Try it out*, and upload your TSV file. You should see a `200` successful response for proper validation.
 
-4. The fourth and final step in the protocol is to actually submit the changesheet using the submission endpoint from the nmdc-runtime API which you can find [here](https://api.dev.microbiomedata.org/docs#/metadata/submit_changesheet_metadata_changesheets_submit_post). For this, you must be logged in using your username/password (click on any lock icon) and authorized to submit changesheets. Click on *Try it out*, and upload your TSV file. Similar to the validation endpoint, you should see a `200` successful response on execution the request. For an example submission changesheet, see [here](https://github.com/microbiomedata/nmdc-runtime/blob/main/metadata-translation/notebooks/data/changesheet-without-separator3.tsv).
+4. The fourth and final step in the protocol is to actually submit the changesheet using the submission endpoint from the nmdc-runtime API which you can find [here](https://api.microbiomedata.org/docs#/metadata/submit_changesheet_metadata_changesheets_submit_post). For this, you must be logged in using your username/password (click on any lock icon) and authorized to submit changesheets. Click on *Try it out*, and upload your TSV file. Similar to the validation endpoint, you should see a `200` successful response on execution the request. For an example submission changesheet, see [here](https://github.com/microbiomedata/nmdc-runtime/blob/main/metadata-translation/notebooks/data/changesheet-without-separator3.tsv).
 
 !!! note
     The submission endpoint runs the validation endpoint prior to actually submitting the data.

docs/howto-guides/claim-and-run-jobs.md

@@ -1,19 +1,19 @@
 # Claim and Run Jobs
 
-The Runtime advertises jobs to be done, where a [Job](https://api.dev.microbiomedata.org/docs#/jobs)
-is a [Workflow](https://api.dev.microbiomedata.org/docs#/workflows) paired with a chosen input
-[Object](https://api.dev.microbiomedata.org/docs#/objects). See [Guide - Create Workflow Triggers To
+The Runtime advertises jobs to be done, where a [Job](https://api.microbiomedata.org/docs#/jobs)
+is a [Workflow](https://api.microbiomedata.org/docs#/workflows) paired with a chosen input
+[Object](https://api.microbiomedata.org/docs#/objects). See [Guide - Create Workflow Triggers To
 Spawn Jobs](guide-create-triggers.md) to learn how to arrange for jobs of interest to be
 automatically available when relevant new workflow inputs are available.
 
-You can list open jobs via [`GET /jobs`](https://api.dev.microbiomedata.org/docs#/jobs/list_jobs_jobs_get). To
+You can list open jobs via [`GET /jobs`](https://api.microbiomedata.org/docs#/jobs/list_jobs_jobs_get). To
 claim a job, [`POST` to
-`/jobs/{job_id}:claim`](https://api.dev.microbiomedata.org/docs#/jobs/claim_job_jobs__job_id__claim_post). The
-response will be an [Operation](https://api.dev.microbiomedata.org/docs#/operations) to track job
+`/jobs/{job_id}:claim`](https://api.microbiomedata.org/docs#/jobs/claim_job_jobs__job_id__claim_post). The
+response will be an [Operation](https://api.microbiomedata.org/docs#/operations) to track job
 execution and send updates to the system.
 
 [`PATCH
-/operations/{op_id}`](https://api.dev.microbiomedata.org/docs#/operations/update_operation_operations__op_id__patch)
+/operations/{op_id}`](https://api.microbiomedata.org/docs#/operations/update_operation_operations__op_id__patch)
 is how to report state transitions for the job execution. If a job execution has been completed
 successfully, has failed, or has been aborted, the `done` field for the operation must be set to
 `true`.
@@ -26,11 +26,11 @@ and run jobs are available in the codebase in
   submit metadata as Objects and associate them with the `metadata-in` Object Type. This in turn
   triggers the creation of Jobs (for the `metadata-in-1.0.0` Workflow) to validate and ingest the
   metadata. Because these jobs are not too intensive wrt data or compute, the Runtime itself hosts a
-  [Site](https://api.dev.microbiomedata.org/docs#/sites) that claims and runs these jobs. *
+  [Site](https://api.microbiomedata.org/docs#/sites) that claims and runs these jobs. *
 
 * `claim_and_run_apply_changesheet_jobs` senses new jobs to apply changesheets, that is, to apply
   surgical updates to existing metadata. Users submit changesheets via [`POST
-  /metadata/changesheets:submit`](https://api.dev.microbiomedata.org/docs#/metadata/submit_changesheet_metadata_changesheets_submit_post),
+  /metadata/changesheets:submit`](https://api.microbiomedata.org/docs#/metadata/submit_changesheet_metadata_changesheets_submit_post),
   which creates an Object on behalf of the user, annotates it with the `metadata-changesheet` Object
   Type. A registered trigger then creates a corresponding `apply-changesheet-1.0.0` job, which this
   sensor senses, allowing the Runtime Site to claim and run the job.

docs/howto-guides/create-triggers.md

@@ -1,14 +1,14 @@
 # Create Workflow Triggers To Spawn Jobs
 
-Jobs represent work to be done. Specifically, a [Job](https://api.dev.microbiomedata.org/docs#/jobs)
-is a request to run a [Workflow](https://api.dev.microbiomedata.org/docs#/workflows) given a certain
-[Object](https://api.dev.microbiomedata.org/docs#/objects) as its input. The Runtime system will
+Jobs represent work to be done. Specifically, a [Job](https://api.microbiomedata.org/docs#/jobs)
+is a request to run a [Workflow](https://api.microbiomedata.org/docs#/workflows) given a certain
+[Object](https://api.microbiomedata.org/docs#/objects) as its input. The Runtime system will
 spawn a new Job when:
 
-1. An [Object](https://api.dev.microbiomedata.org/docs#/objects),
-2. is assigned an [Object Type](https://api.dev.microbiomedata.org/docs#/object_types),
-3. which is associated with a [Workflow](https://api.dev.microbiomedata.org/docs#/workflows),
-4. through a [Trigger](https://api.dev.microbiomedata.org/docs#/triggers).
+1. An [Object](https://api.microbiomedata.org/docs#/objects),
+2. is assigned an [Object Type](https://api.microbiomedata.org/docs#/object_types),
+3. which is associated with a [Workflow](https://api.microbiomedata.org/docs#/workflows),
+4. through a [Trigger](https://api.microbiomedata.org/docs#/triggers).
 
 <figure markdown style="max-width: 25em">
   ![Job Triggering](../img/job-triggering.png)

docs/nb/get_data.ipynb

@@ -56,7 +56,7 @@
     "import requests\n",
     "from toolz import keyfilter, merge, concat\n",
     "\n",
-    "HOST = \"https://api.dev.microbiomedata.org\"\n",
+    "HOST = \"https://api.microbiomedata.org\"\n",
     "\n",
     "def get_json(path, host=HOST, **kwargs):\n",
     "    r = requests.get(host + path, **kwargs)\n",

docs/nb/queue_and_trigger_data_jobs.ipynb

@@ -80,7 +80,7 @@
     "\n",
     "assert (\n",
     "    ENV[\"NMDC_RUNTIME_HOST\"] == \n",
-    "    \"https://api.dev.microbiomedata.org\"\n",
+    "    \"https://api.microbiomedata.org\"\n",
     ")\n",
     "\n",
     "HOST = ENV[\"NMDC_RUNTIME_HOST\"]\n",

docs/tutorials/auth.md

@@ -2,7 +2,7 @@
 
 ## Log in as a User
 
-Open <https://api.dev.microbiomedata.org/docs> and click on the `Authorize` button near the top of
+Open <https://api.microbiomedata.org/docs> and click on the `Authorize` button near the top of
 the page:
 
 ![auth button](../img/auth-button.png)
@@ -22,7 +22,7 @@ Once authorized, hit `Close` to get back to the interactive API documentation:
     You need to be already logged in to create a new user.
     Also, only users `aclum`, `dwinston`, `scanon`, and `scholia` can create new users at this time.
 
-Go to [POST /users](https://api.dev.microbiomedata.org/docs#/users/create_user_users_post), and
+Go to [POST /users](https://api.microbiomedata.org/docs#/users/create_user_users_post), and
 click the `Try it out` button. In the request body, the only required fields are `username` and
 `password`. If you know the `id`s of any sites you would like the new user to administer, enter
 those as an array value for the `site_admin` field.
@@ -39,7 +39,7 @@ behalf of the site. This is used for managing certain API resources -- rather th
 responsible for a resource, a site is, and users that administer the site can come and go.
 
 Once logged in, you can use [GET
-/users/me](https://api.dev.microbiomedata.org/docs#/users/read_users_me_users_me__get) to see the
+/users/me](https://api.microbiomedata.org/docs#/users/read_users_me_users_me__get) to see the
 `id`s of sites you can administer. Example response:
 
 ```json
@@ -54,12 +54,12 @@ Once logged in, you can use [GET
 ```
 
 You can create your own sites via [POST
-/sites](https://api.dev.microbiomedata.org/docs#/sites/create_site_sites_post). If the `id` you
+/sites](https://api.microbiomedata.org/docs#/sites/create_site_sites_post). If the `id` you
 request already exists, you will get an error response. Do not worry about setting `capability_ids`;
 those can be set later.
 
 Once you have identified a site for which to generate credentials, use [POST
-/sites/{site_id}:generateCredentials](https://api.dev.microbiomedata.org/docs#/sites/generate_credentials_for_site_client_sites__site_id__generateCredentials_post)
+/sites/{site_id}:generateCredentials](https://api.microbiomedata.org/docs#/sites/generate_credentials_for_site_client_sites__site_id__generateCredentials_post)
 to do so. The response will look something like
 
 ```json
@@ -73,7 +73,7 @@ Save this information like you saved your username and password.
 
 ## Log in as a Site
 
-Click on the `Authorize` button near the top of <https://api.dev.microbiomedata.org/docs>. You may
+Click on the `Authorize` button near the top of <https://api.microbiomedata.org/docs>. You may
 need to `Logout` first. Scroll all the way down to the second form, the one with only two fields,
 `client_id` and `client_secret`:
 

docs/tutorials/json.md

@@ -15,8 +15,8 @@ This represents a set of [nmdc:Biosample](https://microbiomedata.github.io/nmdc-
 objects. There is just one, with an `id` of `42`.
 
 Let's validate it. Go to the [POST
-/metadata/json:validate](https://api.dev.microbiomedata.org/docs#/metadata/validate_json_metadata_json_validate_post)
-endpoint at <https://api.dev.microbiomedata.org/docs> and click "Try it out":
+/metadata/json:validate](https://api.microbiomedata.org/docs#/metadata/validate_json_metadata_json_validate_post)
+endpoint at <https://api.microbiomedata.org/docs> and click "Try it out":
 
 ![Try it Out](../img/validate-json-try-it-out.png)
 
@@ -31,14 +31,14 @@ to reproduce the request on the command line:
 ![Validation Response](../img/validate-json-response.png)
 
 Let's see what a "valid" response looks like. The [GET
-/nmdcschema/{collection_name}/{doc_id}](https://api.dev.microbiomedata.org/docs#/metadata/get_from_collection_by_id_nmdcschema__collection_name___doc_id__get)
+/nmdcschema/{collection_name}/{doc_id}](https://api.microbiomedata.org/docs#/metadata/get_from_collection_by_id_nmdcschema__collection_name___doc_id__get)
 endpoint allows us to get the NMDC-schema-validated JSON object for one of the NMDC metadata
 collections:
 
 ![Get one valid](../img/validate-json-get-one-valid.png)
 
 For example,
-[https://api.dev.microbiomedata.org/nmdcschema/biosample_set/gold:Gb0115217](https://api.dev.microbiomedata.org/nmdcschema/biosample_set/gold:Gb0115217)
+[https://api.microbiomedata.org/nmdcschema/biosample_set/gold:Gb0115217](https://api.microbiomedata.org/nmdcschema/biosample_set/gold:Gb0115217)
 is
 
 ```json
@@ -129,7 +129,7 @@ Hooray!
 ## Get a List of NMDC-Schema-Compliant Documents
 
 The [GET
-/nmdcschema/{collection_name}](https://api.dev.microbiomedata.org/docs#/metadata/list_from_collection_nmdcschema__collection_name__get)
+/nmdcschema/{collection_name}](https://api.microbiomedata.org/docs#/metadata/list_from_collection_nmdcschema__collection_name__get)
 endpoint allows you to get a filtered list of documents from one of the NMDC Schema collections:
 
 ![List from collections](../img/list-from-collection.png)
@@ -152,7 +152,7 @@ returned at a time. A much larger `max_page_size` is fine for programs/scripts,
 web browser less responsive when using the interactive documentation.
 
 The response body for [our
-request](https://api.dev.microbiomedata.org/nmdcschema/biosample_set?filter=%7B%22part_of%22%3A%20%22gold%3AGs0114663%22%7D&max_page_size=20)
+request](https://api.microbiomedata.org/nmdcschema/biosample_set?filter=%7B%22part_of%22%3A%20%22gold%3AGs0114663%22%7D&max_page_size=20)
 has two fields, `resources` and `next_page_token`:
 
 ```json

docs/tutorials/metadata-in.md

@@ -63,14 +63,14 @@ $ stat -f "%z bytes" fake_biosample.json
 }
 ```
 
-After a [POST /objects](https://api.dev.microbiomedata.org/docs#/objects/create_object_objects_post)
+After a [POST /objects](https://api.microbiomedata.org/docs#/objects/create_object_objects_post)
 with the above as the request body, I get back a response object with an `id` that looks like
 `sys0***`.
 
 ## Annotate the DRS object with the "metadata-in" type
 
 Now, go to [PUT
-/objects/{object_id}/types](https://api.dev.microbiomedata.org/docs#/objects/replace_object_types_objects__object_id__types_put)
+/objects/{object_id}/types](https://api.microbiomedata.org/docs#/objects/replace_object_types_objects__object_id__types_put)
 and ensure the types array for the object is `["metadata-in"]`. This lets the Runtime know that you
 intend for this object to be ingested as NMDC metadata.
 
@@ -100,7 +100,7 @@ Here's an example of the general Runs view after our new metadata has been inges
 ![metadata-in-dagit-runs](../img/metadata-in-dagit-runs.png)
 
 And indeed it has been ingested! See
-<https://api.dev.microbiomedata.org/nmdcschema/biosample_set/fake> (unless we already deleted it --
+<https://api.microbiomedata.org/nmdcschema/biosample_set/fake> (unless we already deleted it --
 see section below).
 
 ## Removing a JSON document
@@ -118,7 +118,7 @@ see section below).
     Any to-be-deleted documents are backed up to a separate database immediately prior to deletion.
 
 A call to [POST
-/queries:run](https://api.dev.microbiomedata.org/docs#/queries/run_query_queries_run_post) with the
+/queries:run](https://api.microbiomedata.org/docs#/queries/run_query_queries_run_post) with the
 body
 
 ```json