nmdc-runtime 2.9.0__py3-none-any.whl → 2.11.0__py3-none-any.whl

nmdc_runtime/api/swagger_ui/assets/script.js

@@ -0,0 +1,247 @@
+console.debug("Listening for event: nmdcInit");
+window.addEventListener("nmdcInit", (event) => {
+    console.debug("Detected event: nmdcInit");
+
+    // Get the DOM elements we'll be referencing below.
+    const bodyEl = document.querySelector("body");
+
+    // Add the NMDC logo to the top of the page, next to the title.
+    // Note: The logo image will be added as a background image via CSS.
+    const addLogo = () => {
+        console.debug("Adding logo");
+        const headingGroupEl = document.querySelector(".information-container hgroup.main");
+        const titleEl = headingGroupEl.querySelector("h2.title");
+        const openapiSchemaLinkEl = headingGroupEl.querySelector("a.link");
+        const titleWrapperEl = document.createElement("div");
+        const logoEl = document.createElement("div");
+        logoEl.classList.add("nmdc-logo");
+        headingGroupEl.classList.add("nmdc-heading-group");
+        titleWrapperEl.replaceChildren(titleEl, openapiSchemaLinkEl);
+        headingGroupEl.replaceChildren(logoEl, titleWrapperEl);
+    };
+    addLogo();
+
+    // If there is a non-empty access token present in the DOM (see `main.py`), create and add a banner
+    // displaying the token along with buttons to show/hide it and copy it to the clipboard.
+    const accessToken = document.getElementById("nmdc-access-token")?.getAttribute("data-token");
+    if (typeof accessToken === "string" && accessToken.trim().length > 0) {
+        console.debug("Adding token banner");
+
+        // Create the banner.
+        const sectionEl = document.createElement("section");
+        sectionEl.classList.add("nmdc-info", "nmdc-info-token", "block", "col-12");
+        sectionEl.innerHTML = `
+            <p>You are now authorized. Prefer a command-line interface (CLI)? Use this header for HTTP requests:</p>
+            <p>
+                <code>
+                    <span>Authorization: Bearer </span>
+                    <span id="token" data-state="masked">***</span>
+                </code>
+            </p>
+            <p>
+                <button id="token-mask-toggler">Show token</button>
+                <button id="token-copier">Copy token</button>
+                <span id="token-copier-message"></span>
+            </p>
+        `;
+
+        // Mount the banner to the DOM.
+        document.querySelector(".information-container").append(sectionEl);
+
+        // Get references to DOM elements within the banner that was mounted to the DOM.
+        const tokenMaskTogglerEl = document.getElementById("token-mask-toggler");
+        const tokenEl = document.getElementById("token");
+        const tokenCopierEl = document.getElementById("token-copier");
+        const tokenCopierMessageEl = document.getElementById("token-copier-message");
+
+        // Set up the token visibility toggler.
+        console.debug("Setting up token visibility toggler");
+        tokenMaskTogglerEl.addEventListener("click", (event) => {
+            if (tokenEl.dataset.state == "masked") {
+                console.debug("Unmasking token");
+                tokenEl.dataset.state = "unmasked";
+                tokenEl.textContent = accessToken;
+                event.target.textContent = "Hide token";
+            } else {
+                console.debug("Masking token");
+                tokenEl.dataset.state = "masked";
+                tokenEl.textContent = "***";
+                event.target.textContent = "Show token";
+            }
+        });
+
+        // Set up the token copier.
+        // Reference: https://developer.mozilla.org/en-US/docs/Web/API/Clipboard/writeText
+        console.debug("Setting up token copier");
+        tokenCopierEl.addEventListener("click", async (event) => {
+            tokenCopierMessageEl.textContent = "";
+            try {
+                await navigator.clipboard.writeText(accessToken);
+                tokenCopierMessageEl.innerHTML = "<span class='nmdc-success'>Copied to clipboard</span>";
+            } catch (error) {
+                console.error(error.message);
+                tokenCopierMessageEl.innerHTML = "<span class='nmdc-error'>Copying failed</span>";
+            }
+        });
+    }
+
+    /**
+     * Customizes the login form in the following ways:
+     * - Changes the header text of the username/password login form to "User login".
+     * - Changes the header text of the client credentials login form to "Site client login".
+     * - Augments the "Logout" button on the `bearerAuth` login form so that, when it is clicked,
+     *   it clears and expires the `user_id_token` cookie, and reloads the web page.
+     * - Focuses on the username input field whenever the login form appears.
+     * - Adds a "Login with ORCID" widget to the login form.
+     * 
+     * Reference: https://developer.mozilla.org/en-US/docs/Web/API/Document/cookie
+     * 
+     * Prerequisite: The login form must be present in the DOM.
+     */
+    const customizeLoginForm = () => {
+        const modalContentEl = document.querySelector('.auth-wrapper .modal-ux-content');
+        const formHeaderEls = modalContentEl.querySelectorAll('.auth-container h4');
+        formHeaderEls.forEach(el => {
+            switch (el.textContent.trim()) {
+                case "OAuth2PasswordOrClientCredentialsBearer (OAuth2, password)":
+                    console.debug(`Customizing "password" login form header`);
+                    el.textContent = "User login";
+                    break;
+                case "OAuth2PasswordOrClientCredentialsBearer (OAuth2, clientCredentials)":
+                    console.debug(`Customizing "clientCredentials" login form header`);
+                    el.textContent = "Site client login";
+                    break;
+                // Note: This string has a `U+00a0` character before the regular space.
+                case "bearerAuth  (http, Bearer)":
+                    const buttonEls = el.closest(".auth-container").querySelectorAll("button");
+                    buttonEls.forEach(buttonEl => {
+                        if (buttonEl.textContent.trim() === "Logout") {
+                            console.debug(`Augmenting "bearerAuth" form logout button`);
+                            buttonEl.addEventListener("click", () => {
+                                console.debug("Clearing and expiring `user_id_token` cookie");
+                                document.cookie = "user_id_token=; max-age=0; path=/;";
+                                // Reload the web page so that any in-memory authentication state is reset.
+                                // Note: If we had full control over the Swagger UI code, we would just
+                                //       manipulate that state directly instead of reloading the page.
+                                console.debug("Reloading web page");
+                                window.location.reload();
+                            });
+                        }
+                    });
+                    break;
+                default:
+                    console.debug(`Unrecognized header: ${el.textContent}`);
+            }
+        });
+        // Add a "Login with ORCID" widget to the login form.
+        //
+        // TODO: Consider disabling this when the user is already logged in.
+        //
+        // TODO: Consider moving this up next to (or into) the regular "User login" form,
+        //       once our system administrators have implemented a practical process for
+        //       managing "allowances" of users whose usernames are ORCID IDs. Putting it
+        //       at the bottom of the modal (I think) makes it less likely people will use it.
+        //
+        console.debug("Adding ORCID Login widget to login form");
+        const orcidLoginUrl = document.getElementById("nmdc-orcid-login-url")?.getAttribute("data-url");
+        const orcidLoginWidgetEl = document.createElement("div");
+        orcidLoginWidgetEl.classList.add("auth-container", "nmdc-orcid-login");
+        orcidLoginWidgetEl.innerHTML = `
+            <h4>User login with ORCID</h4>
+            <div class="nmdc-orcid-login-icon-link">
+                <img src="/static/ORCID-iD_icon_vector.svg" height="16" width="16"/>
+                <a href="${orcidLoginUrl}">Login with ORCID</a>
+            </div>
+        `;
+        modalContentEl.appendChild(orcidLoginWidgetEl);
+
+        console.debug("Focusing on username field if present");
+        const usernameInputEl = modalContentEl.querySelector("input#oauth_username");
+        if (usernameInputEl !== null) {
+            usernameInputEl.focus();
+        }
+    };
+    console.debug("Setting up event listener for customizing login form");
+    //
+    // Listen for a "click" event on the `body` element, check whether the element that was clicked
+    // was the "Authorize" button (or one of its descendants), and if so, customize the modal login
+    // form that will have been mounted to the DOM by the time the "click" event propagated to the
+    // `body` element and our event handler was called.
+    //
+    // Note: We attach this event listener to the `body` element because that's the lowest-level
+    //       element where we found that mounting it doesn't cause our event handler to run too early
+    //       (i.e. doesn't cause it to run _before_ the event handlers that mount the modal login form
+    //       to the DOM have run). Our event handler needs that form to be mounted so it can access
+    //       its elements.
+    //       
+    //       If we were to attach it to a lower-level element (e.g. directly to the "Authorize" button),
+    //       we would have to, for example, make its body a `setTimeout(fn, 0)` callback in order to
+    //       defer its execution until all the event handlers for the "click" even have run.
+    //
+    bodyEl.addEventListener("click", (event) => {
+        // Check whether the clicked element was the "Authorize" button or any of its descendants.
+        if (event.target.closest(".auth-wrapper > .btn.authorize:not(.modal-btn)") !== null) {
+            customizeLoginForm();
+        }
+    });
+
+    // If the `<ellipses-button>` custom HTML element is available, set up the tag
+    // description details togglers.
+    //
+    // Note: At the time of this writing, all of our tag descriptions begin with a
+    //       single-paragraph summary of the tag. Some of the tag descriptions have
+    //       additional paragraphs that provide more _details_ about the tag. In an
+    //       attempt to keep the Swagger UI page "initially concise" (only showing
+    //       more information when the user requests it), for the tag descriptions
+    //       that have additional paragraphs, we add a toggler button that the user
+    //       can press to toggle the visibility of the additional paragraphs.
+    //
+    if (customElements.get("ellipses-button")) {
+        console.debug("Setting up tag description details togglers");
+        const tagSectionEls = bodyEl.querySelectorAll(".opblock-tag-section");
+        Array.from(tagSectionEls).forEach(el => {
+
+            // Check whether the description contains more than one element (i.e. paragraph).
+            const descriptionEl = el.querySelector("h3 > small > .renderedMarkdown");
+            if (descriptionEl.children.length > 1) {
+
+                // Wrap the additional elements (i.e. paragraphs) in a hidable `<div>`.
+                const detailsEl = document.createElement("div");
+                detailsEl.classList.add("tag-description-details", "hidden");
+                Array.from(descriptionEl.children).slice(1).forEach(el => {
+                    detailsEl.appendChild(el);
+                });
+                descriptionEl.replaceChildren(descriptionEl.firstChild, detailsEl);
+
+                // Add a button that, when clicked, toggles the visibility of the tag
+                // description details (but does not propagate the click event upward,
+                // so the visibility of the containing tag section isn't toggled).
+                const toggleButtonEl = document.createElement("ellipses-button");
+                toggleButtonEl.textContent = "Show details"; // populates the "slot"
+                descriptionEl.firstChild.appendChild(toggleButtonEl);
+                toggleButtonEl.addEventListener("click", (event) => {
+                    detailsEl.classList.toggle("hidden");
+                    event.stopPropagation();
+
+                    // Update the button's "is-open" attribute so the button's icon changes.
+                    if (toggleButtonEl.getAttribute("is-open") === "true") {
+                        toggleButtonEl.setAttribute("is-open", "false");
+                        toggleButtonEl.textContent = "Show details";
+                    } else {
+                        toggleButtonEl.setAttribute("is-open", "true");
+                        toggleButtonEl.textContent = "Hide details";
+                    }
+                });
+            }
+        });
+    };
+
+    // If the `<endpoint-search-widget>` custom HTML element is available, add it to the DOM.
+    // Note: That custom HTML element gets defined within the `custom-elements.js` script.
+    // Docs: https://developer.mozilla.org/en-US/docs/Web/API/Web_components/Using_custom_elements#using_a_custom_element
+    if (customElements.get("endpoint-search-widget")) {
+        console.debug("Setting up endpoint search widget");
+        const endpointSearchWidgetEl = document.createElement("endpoint-search-widget");
+        bodyEl.querySelector(".scheme-container").after(endpointSearchWidgetEl); // put it below the "Authorize" section
+    }
+});

nmdc_runtime/api/swagger_ui/assets/style.css

@@ -0,0 +1,155 @@
+.nmdc-info {
+    padding: 1em;
+    background-color: #448aff1a;
+    border: .075rem solid #448aff;
+    border-radius: 4px;
+}
+.nmdc-info-token code {
+    font-size: x-small;
+}
+.nmdc-success {
+    color: green;
+}
+.nmdc-error {
+    color: red;
+}
+
+/**
+ * Style the NMDC logo we add to the top of the Swagger UI page via JavaScript.
+ *
+ * Notes:
+ * - We set the background size larger than the element size, and then offset
+ *   the background a small amount, so that we do not display the thin border
+ *   that is baked into this SVG image.
+ * - On wide screens, we set the heading group (which contains the logo, and a
+ *   wrapper element—introduced via JavaScript—containing the normal API title
+ *   and link to the OpenAPI schema) to use `display: flex`, so that the logo
+ *   appears next to that wrapper element. On narrow screens, we allow them
+ *   to stack like they normally would.
+ */
+@media screen and (min-width: 768px) {
+    .nmdc-heading-group {
+        display: flex;
+    }
+}
+.nmdc-heading-group .nmdc-logo {
+    width: 64px;
+    height: 64px;
+    margin-right: 16px;
+    background-image: url("/static/NMDC_logo.svg");
+    background-repeat: no-repeat;
+    background-size: 68px 68px;
+    background-position: -2px -2px;
+    border-radius: 4px;
+}
+
+/** 
+ * Hides the following text from the Swagger UI modal login form:
+ *
+ * > Scopes are used to grant an application different levels of
+ * > access to data on behalf of the end user. Each API may declare
+ * > one or more scopes.
+ * > 
+ * > API requires the following scopes. Select which ones you want
+ * > to grant to Swagger UI.
+ *
+ * TODO: Check whether this text can be hidden via standard
+ *       Swagger UI configuration, rather than custom CSS.
+ */
+.auth-wrapper .modal-ux-content .auth-container .scope-def {
+    display: none;
+}
+
+/** 
+ * Hides the following text from the Swagger UI modal login form:
+ *
+ * > Scopes are used to grant an application different levels of
+ * > access to data on behalf of the end user. Each API may declare
+ * > one or more scopes.
+ * > 
+ * > API requires the following scopes. Select which ones you want
+ * > to grant to Swagger UI.
+ *
+ * TODO: Check whether this text can be hidden via standard
+ *       Swagger UI configuration, rather than custom CSS.
+ */
+.auth-wrapper .modal-ux-content .auth-container .scope-def {
+    display: none;
+}
+
+/**
+ * Style the ORCID Login widget we inject via JavaScript into the
+ * Swagger UI modal login form.
+ */
+.auth-container.nmdc-orcid-login {
+    padding-bottom: 20px;
+    font-size: 14px;
+ }
+.auth-container.nmdc-orcid-login .nmdc-orcid-login-icon-link {
+    display: flex;
+    align-items: center;
+    gap: 0.5em;
+}
+.auth-container.nmdc-orcid-login .nmdc-orcid-login-icon-link > a {
+    color: #4990e2;
+    text-decoration: none;
+}
+.auth-container.nmdc-orcid-login .nmdc-orcid-login-icon-link > a:hover {
+    color: #1f69c0;
+}
+
+/**
+ * In the tag description, hide the details portion (i.e. the portion the user
+ * can toggle the visibility of), and color the hyperlinks the same as in
+ * the overall introductory text at the top of the Swagger UI page.
+ */
+.tag-description-details.hidden {
+    display: none;
+}
+ .tag-description-details a {
+    color: #4990e2;
+}
+.tag-description-details a:hover {
+    color: #1f69c0;
+}
+
+/*****************************************************************************
+ * Customize Swagger UI's default elements.
+ *****************************************************************************/
+
+ /* Standardize the line height of the description in the top section of the page. */
+.swagger-ui .information-container .info__description {
+    line-height: 1em;
+}
+/* Slightly deemphasize the version numbers in the description. */
+.swagger-ui .information-container .info__description code {
+    font-weight: normal;
+}
+
+/* Remove the box shadow from the top section of the page. */
+.swagger-ui .scheme-container {
+    box-shadow: none;
+}
+/* Draw a border around each section. */
+.swagger-ui div.opblock-tag-section {
+    border: 1px solid rgba(59,65,81,.3);
+    border-radius: 4px;
+    padding-top: 15px;
+    padding-left: 15px;
+    padding-right: 15px;
+    margin-bottom: 15px;
+}
+/* Stack the elements of each section header vertically. */
+.swagger-ui .opblock-tag {
+    flex-direction: column;
+    align-items: stretch;
+    border-bottom: none;
+}
+.swagger-ui .opblock-tag:hover {
+    background-color: transparent;
+}
+/* Remove the left margin from the description and chevron icon rows. */
+.swagger-ui .opblock-tag > small,
+.swagger-ui .opblock-tag > button {
+    padding-left: 0;
+}

nmdc_runtime/api/swagger_ui/swagger_ui.py

@@ -0,0 +1,34 @@
+"""Constants related to configuring Swagger UI."""
+
+# Reference: https://swagger.io/docs/open-source-tools/swagger-ui/usage/configuration/#parameters
+base_swagger_ui_parameters: dict = {
+    "withCredentials": True,
+    # Collapse the "Schemas" section by default.
+    # Note: `-1` would omit the section entirely.
+    "defaultModelsExpandDepth": 0,
+    # Display the response times of the requests performed via "Try it out".
+    # Note: In my local testing, the response times reported by this
+    #       are about 50-100ms longer than the response times reported
+    #       by Chrome DevTools. That is the case whether the actual
+    #       response time is short (e.g. 100ms) or long (e.g. 60s);
+    #       i.e. not proportional to the actual response time.
+    "displayRequestDuration": True,
+    # Expand all tag sections (i.e. groups of endpoints) by default.
+    # Note: `"list"` expands them, and `"none"` collapses them.
+    "docExpansion": "list",
+    # Make it so a logged-in user remains logged in even after reloading
+    # the web page (or leaving the web page and revisiting it later).
+    "persistAuthorization": True,
+    # Specify the Swagger UI plugins we want to use (see note below).
+    #
+    # Note: FastAPI's `get_swagger_ui_html` function always serializes
+    #       the value of this property as a _string_, while the Swagger UI
+    #       JavaScript code requires it to be an _array_. To work around that,
+    #       we just add a placeholder string here; then, after we pass this
+    #       dictionary to FastAPI's `get_swagger_ui_html` function and get the
+    #       returned HTML for the web page, we replace this placeholder string
+    #       (within the returned HTML) with the JavaScript array we wanted
+    #       the "plugins" property to contain all along.
+    #
+    "plugins": r"{{ NMDC_SWAGGER_UI_PARAMETERS_PLUGINS_PLACEHOLDER }}",
+}

nmdc_runtime/config.py

@@ -43,15 +43,14 @@ def is_env_var_true(name: str, default: str = "false") -> bool:
     return os.environ.get(name, default).lower() in lowercase_true_strings
 
 
-# The name of the schema class representing the database. We don't bother to
-# make this customizable via the environment, as we expect it to never change.
-DATABASE_CLASS_NAME: str = "Database"
-
-# Feature flag that can be used to enable/disable the `/nmdcschema/related_ids`
-# endpoint and the tests that target it.
-IS_RELATED_IDS_ENDPOINT_ENABLED: bool = is_env_var_true(
-    "IS_RELATED_IDS_ENDPOINT_ENABLED", default="true"
+# Feature flag to enable/disable the `/nmdcschema/linked_instances` endpoint and the tests that target it.
+IS_LINKED_INSTANCES_ENDPOINT_ENABLED: bool = is_env_var_true(
+    "IS_LINKED_INSTANCES_ENDPOINT_ENABLED", default="true"
 )
 
 # Feature flag that can be used to enable/disable the `/scalar` endpoint.
 IS_SCALAR_ENABLED: bool = is_env_var_true("IS_SCALAR_ENABLED", default="true")
+
+# Feature flag that can be used to enable/disable performance profiling,
+# which can be activated via the `?profile=true` URL query parameter.
+IS_PROFILING_ENABLED: bool = is_env_var_true("IS_PROFILING_ENABLED", default="false")

nmdc_runtime/minter/adapters/repository.py

@@ -2,9 +2,8 @@ import abc
 import re
 from typing import Union
 
-from fastapi import HTTPException
 from pymongo import ReturnDocument
-from toolz import merge, dissoc
+from toolz import merge
 from pymongo.database import Database as MongoDatabase
 
 
@@ -137,6 +136,10 @@ class MongoIDStore(abc.ABC):
         self.db = mdb
 
     def mint(self, req_mint: MintingRequest) -> list[Identifier]:
+        """
+        TODO: Document this method.
+        """
+
         if not self.db["minter.services"].find_one({"id": req_mint.service.id}):
             raise MinterError(f"Unknown service {req_mint.service.id}")
         if not self.db["minter.requesters"].find_one({"id": req_mint.requester.id}):
@@ -191,6 +194,10 @@ class MongoIDStore(abc.ABC):
         return collected
 
     def bind(self, req_bind: BindingRequest) -> Identifier:
+        """Associate the specified arbitrary metadata with the specified ID.
+
+        TODO: Do not allow users to bind identifiers minted by _other_ users.
+        """
         id_stored = self.resolve(req_bind)
         if id_stored is None:
             raise MinterError(f"ID {req_bind.id_name} is unknown")
@@ -208,15 +215,28 @@ class MongoIDStore(abc.ABC):
                 )
 
     def resolve(self, req_res: ResolutionRequest) -> Union[Identifier, None]:
+        """Get the metadata that is bound to the specified identifier."""
         match re.match(r"nmdc:([^-]+)-([^-]+)-.*", req_res.id_name).groups():
             case (_, _):
                 doc = self.db["minter.id_records"].find_one({"id": req_res.id_name})
                 # TODO if draft ID, check requester
+                #
+                #      Note: The above "TODO" comment is about checking whether the user that wants to
+                #            resolve the identifier, is the same user that minted the identifier. If
+                #            it isn't, then... what? (i.e. allow resolution, or deny resolution)?
+                #
                 return Identifier(**doc) if doc else None
             case _:
                 raise MinterError("Invalid ID name")
 
     def delete(self, req_del: DeleteRequest):
+        """Delete an identifier that is still in the draft state.
+
+        Note: You can mint (draft) as many IDs as you want. As long as you don't bind them
+              (i.e. as long as they are still in the draft state), you can still delete them.
+
+        TODO: Do not allow users to delete identifiers minted by _other_ users.
+        """
         id_stored = self.resolve(req_del)
         if id_stored is None:
             raise MinterError(f"ID {req_del.id_name} is unknown")

nmdc_runtime/minter/config.py

@@ -23,9 +23,11 @@ def typecodes() -> List[dict]:
           that class _today_; regardless of what it may have used in the past.
 
     >>> typecode_descriptors = typecodes()
+
     # Test #1: We get the typecode we expect, for a class whose pattern contains only one typecode.
     >>> any((td["name"] == "sty" and td["schema_class"] == "nmdc:Study") for td in typecode_descriptors)
     True
+
     # Tests #2 and #3: We get only the typecode we expect, for a class whose pattern contains multiple typecodes.
     >>> any((td["name"] == "dgms" and td["schema_class"] == "nmdc:MassSpectrometry") for td in typecode_descriptors)
     True

nmdc_runtime/minter/domain/model.py

@@ -1,9 +1,11 @@
 from enum import Enum
+import re
 from typing import Optional
 
+from base32_lib import base32
 from pydantic import BaseModel, PositiveInt
 
-from nmdc_runtime.minter.config import schema_classes
+from nmdc_runtime.minter.config import schema_classes, typecodes
 
 
 class Entity(BaseModel):
@@ -20,9 +22,29 @@ class ValueObject(BaseModel):
 
 
 class Status(str, Enum):
+    """Status of an identifier.
+
+    Note: These state values were chosen in an attempt to mirror those that DataCite uses for DOIs,
+          which are (currently) "Draft", "Registered", and "Findable" (we use "Indexed" instead).
+          Reference: https://support.datacite.org/docs/doi-states
+    """
+
     draft = "draft"
+    """
+    Draft; i.e., the identifier is reserved for potential use. The identifier can still be deleted.
+    """
+
     registered = "registered"
+    """
+    Registered; i.e., the identifier is in use, but the resource it identifies is not publicly accessible
+    (yet, or anymore). The identifier cannot be deleted.
+    """
+
     indexed = "indexed"
+    """
+    Indexed; i.e., the resource identified by the identifier is publicly accessible (i.e. in the
+    production database). The identifier cannot be deleted.
+    """
 
 
 class MintingRequest(ValueObject):
@@ -71,3 +93,35 @@ class Identifier(Entity):
 class Typecode(Entity):
     schema_class: str
     name: str
+
+
+id_prefix_pattern = rf"(?P<prefix>nmdc)"
+id_typecode_pattern = rf"(?P<typecode>[a-z]{{1,6}})"
+id_shoulder_pattern = rf"(?P<shoulder>[0-9][a-z]{{0,6}}[0-9])"
+id_blade_pattern = rf"(?P<blade>[A-Za-z0-9]+)"
+id_version_pattern = rf"(?P<version>(\.[A-Za-z0-9]+)*)"
+id_locus_pattern = rf"(?P<locus>_[A-Za-z0-9_\.-]+)?"
+id_pattern = (
+    rf"^{id_prefix_pattern}:{id_typecode_pattern}-{id_shoulder_pattern}-"
+    rf"{id_blade_pattern}{id_version_pattern}{id_locus_pattern}$"
+)
+ID_TYPECODE_VALUES = [t["name"] for t in typecodes()]
+id_typecode_pattern_strict = rf"(?P<typecode_strict>({'|'.join(ID_TYPECODE_VALUES)}))"
+id_blade_pattern_strict = rf"(?P<blade_strict>[{base32.ENCODING_CHARS}]+)"
+id_pattern_strict = (
+    rf"^{id_prefix_pattern}:{id_typecode_pattern_strict}-{id_shoulder_pattern}-"
+    rf"{id_blade_pattern_strict}{id_version_pattern}{id_locus_pattern}$"
+)
+id_pattern_strict_compiled = re.compile(id_pattern_strict)
+
+
+def check_valid_ids(ids: list[str]):
+    for id_ in ids:
+        if not re.match(id_pattern, id_):
+            raise ValueError(
+                (
+                    f"Invalid ID format for given ID: '{id_}'.\n\nAn ID must match the pattern: '{id_pattern}'.\n\n"
+                    "See: <https://microbiomedata.github.io/nmdc-schema/identifiers/#ids-minted-for-use-within-nmdc>"
+                )
+            )
+    return ids

nmdc_runtime/minter/entrypoints/fastapi_app.py

@@ -8,7 +8,7 @@ from nmdc_runtime.api.core.util import raise404_if_none
 from nmdc_runtime.api.db.mongo import get_mongo_db
 from nmdc_runtime.api.models.site import get_current_client_site, Site
 from nmdc_runtime.minter.adapters.repository import MongoIDStore, MinterError
-from nmdc_runtime.minter.config import minting_service_id, schema_classes
+from nmdc_runtime.minter.config import minting_service_id
 from nmdc_runtime.minter.domain.model import (
     Identifier,
     AuthenticatedMintingRequest,

nmdc_runtime/mongo_util.py

@@ -1,7 +1,6 @@
-from pymongo import MongoClient
 from pymongo.database import Database
 from pymongo.collection import Collection
-from typing import Any, Mapping, Optional, Type, Callable
+from typing import Any, Optional
 from pymongo.client_session import ClientSession
 import inspect
 

nmdc_runtime/site/backup/nmdcdb_mongodump.py

@@ -6,7 +6,7 @@ $ nmdcdb-mongodump
 
 import os
 import subprocess
-from datetime import datetime, timezone
+from datetime import datetime
 from pathlib import Path
 from zoneinfo import ZoneInfo
 

nmdc_runtime/site/backup/nmdcdb_mongoexport.py

@@ -16,9 +16,7 @@ from toolz import assoc
 
 from nmdc_runtime.api.core.util import pick
 from nmdc_runtime.api.db.mongo import get_mongo_db
-from nmdc_runtime.site.repository import run_config_frozen__normal_env
-from nmdc_runtime.site.resources import get_mongo
-from nmdc_runtime.util import nmdc_jsonschema, schema_collection_names_with_id_field
+from nmdc_runtime.util import schema_collection_names_with_id_field
 
 
 def collection_stats(mdb: MongoDatabase):