feat: record spike progress before revert

Makefile

@@ -1,6 +1,7 @@
 init:
 	pip install --upgrade pip-tools pip setuptools
 	pip install --editable .
+	pip install --editable nmdc_runtime_client/
 	pip install --upgrade -r requirements/main.txt  -r requirements/dev.txt
 
 update-deps:
@@ -74,9 +75,12 @@ dagster-deploy-spin:
 	rancher kubectl rollout restart deployment/dagit-readonly --namespace=nmdc-runtime-dev
 	rancher kubectl rollout restart deployment/dagster-daemon --namespace=nmdc-runtime-dev
 
-publish:
+publish-all:
 	invoke publish
 
+publish-client:
+	cd nmdc_runtime_client && invoke publish
+
 docs-dev:
 	mkdocs serve -a localhost:8080
 

nmdc_runtime_client/nmdc_runtime/client/lib.py

@@ -0,0 +1,14 @@
+from datetime import timedelta, datetime, timezone
+
+
+def now(as_str=False):
+    dt = datetime.now(timezone.utc)
+    return dt.isoformat() if as_str else dt
+
+
+def expiry_dt_from_now(days=0, hours=0, minutes=0, seconds=0):
+    return now() + timedelta(days=days, hours=hours, minutes=minutes, seconds=seconds)
+
+
+def has_passed(dt):
+    return now() > dt

nmdc_runtime_client/nmdc_runtime/client/main.py

@@ -1,4 +1,134 @@
+from datetime import timedelta
+
 import click
+import requests
+from nmdc_runtime.
+from nmdc_runtime.client.lib import expiry_dt_from_now, has_passed
+from pydash import merge
+
+
+class RuntimeApiSiteClient:
+    def __init__(self, base_url: str, site_id: str, client_id: str, client_secret: str):
+        self.base_url = base_url
+        self.site_id = site_id
+        self.client_id = client_id
+        self.client_secret = client_secret
+        self.headers = {}
+        self.token_response = None
+        self.refresh_token_after = None
+        self.get_token()
+
+    def request(self, method, url_path, params_or_json_data=None):
+        self.ensure_token()
+        kwargs = {"url": self.base_url + url_path, "headers": self.headers}
+        if method.upper() == "GET":
+            kwargs["params"] = params_or_json_data
+        else:
+            kwargs["json"] = params_or_json_data
+        return requests.request(method, **kwargs)
+
+    def get_token(self):
+        rv = requests.post(
+            self.base_url + "/token",
+            data={
+                "grant_type": "client_credentials",
+                "client_id": self.client_id,
+                "client_secret": self.client_secret,
+            },
+        )
+        self.token_response = rv.json()
+        if "access_token" not in self.token_response:
+            raise Exception(f"Getting token failed: {self.token_response}")
+
+        self.headers["Authorization"] = f'Bearer {self.token_response["access_token"]}'
+        self.refresh_token_after = expiry_dt_from_now(
+            **self.token_response["expires"]
+        ) - timedelta(seconds=5)
+
+    def ensure_token(self):
+        if has_passed(self.refresh_token_after):
+            self.get_token()
+
+    def put_object_in_site(self, object_in):
+        return self.request("POST", f"/sites/{self.site_id}:putObject", object_in)
+
+    def get_site_object_link(self, access_method):
+        return self.request(
+            "POST", f"/sites/{self.site_id}:getObjectLink", access_method
+        )
+
+    def get_operation(self, op_id):
+        return self.request("GET", f"/operations/{op_id}")
+
+    def operation_is_done(self, op_id):
+        op = self.get_operation(op_id).json()
+        return op.get("done") is True
+
+    def update_operation(self, op_id, op_patch):
+        return self.request("PATCH", f"/operations/{op_id}", op_patch)
+
+    def list_operations(self, req):
+        rv = self.request("GET", "/operations", req)
+        lor = ListOperationsResponse(**rv.json())
+        resources_so_far = lor.resources
+        if not lor.next_page_token:
+            return resources_so_far
+        else:
+            resources_rest = self.list_operations(
+                merge(req, {"page_token": lor.next_page_token})
+            )
+            return resources_so_far + resources_rest
+
+    def create_object(self, drs_object_in: DrsObjectIn):
+        DrsObjectIn(**drs_object_in)  # validate before network request
+        return self.request("POST", "/objects", drs_object_in)
+
+    def create_object_from_op(self, op_doc):
+        return self.request("POST", "/objects", op_doc["result"])
+
+    def ensure_object_tag(self, object_id, tag_id):
+        object_type_ids = [
+            t["id"] for t in self.request("GET", f"/objects/{object_id}/types").json()
+        ]
+        if tag_id not in object_type_ids:
+            return self.request(
+                "PUT", f"/objects/{object_id}/types", object_type_ids + [tag_id]
+            )
+
+    def get_object_info(self, object_id):
+        return self.request("GET", f"/objects/{object_id}")
+
+    def get_object_access(self, object_id, access_id):
+        return self.request("GET", f"/objects/{object_id}/access/{access_id}")
+
+    def get_object_bytes(self, object_id) -> requests.Response:
+        obj = DrsObject(**self.get_object_info(object_id).json())
+        method = obj.access_methods[0]
+        if method.access_url is None:
+            access = AccessURL(
+                **self.get_object_access(object_id, method.access_id).json()
+            )
+            if access.url.startswith(
+                os.getenv("API_HOST_EXTERNAL")
+            ) and self.base_url == os.getenv("API_HOST"):
+                access.url = access.url.replace(
+                    os.getenv("API_HOST_EXTERNAL"), os.getenv("API_HOST")
+                )
+        else:
+            access = AccessURL(url=method.access_url.url)
+        return requests.get(access.url)
+
+    def list_jobs(self, list_request=None):
+        if list_request is None:
+            params = {}
+        else:
+            if "filter" in list_request and isinstance(list_request["filter"], dict):
+                list_request["filter"] = json.dumps(list_request["filter"])
+            params = ListRequest(**list_request)
+        return self.request("GET", "/jobs", params)
+
+    def claim_job(self, job_id):
+        return self.request("POST", f"/jobs/{job_id}:claim")
 
 
 @click.command()

nmdc_runtime_client/setup.py

@@ -13,8 +13,7 @@
     name="nmdc_runtime_client",
     url="https://github.com/microbiomedata/nmdc-runtime",
     packages=["nmdc_runtime.client"],
-    use_scm_version=True,
-    setup_requires=["setuptools_scm"],
+    version="0.1.0",
     author="Donny Winston",
     author_email="[email protected]",
     description="Client for the NMDC Runtime",

nmdc_runtime_client/tasks.py

@@ -0,0 +1,8 @@
+from invoke import task
+
+
+@task
+def publish(c):
+    c.run("rm dist/*.*", warn=True)
+    c.run("python setup.py sdist bdist_wheel")
+    c.run("twine upload dist/*")

tasks.py

@@ -18,7 +18,5 @@ def publish(c):
     run(["git", "push"])
     run(["git", "push", "--tags"])
     c.run("rm dist/*.*", warn=True)
-    # c.run("python setup.py sdist bdist_wheel")
-    # c.run("twine upload dist/*")
-    c.run("cd nmdc_runtime_client && python setup.py sdist bdist_wheel")
+    c.run("python setup.py sdist bdist_wheel")
     c.run("twine upload dist/*")