Merge pull request #837 from CitrineInformatics/feature/file-ingest

kroenlein · web-flow · commit 19b7c03edf48 · 2023-03-28T16:19:25.000-06:00
Add files ingest method
diff --git a/src/citrine/__version__.py b/src/citrine/__version__.py
@@ -1 +1 @@
-__version__ = '2.9.0'
+__version__ = '2.10.0'
diff --git a/src/citrine/_rest/collection.py b/src/citrine/_rest/collection.py
@@ -36,7 +36,9 @@ def _put_resource_ref(self, subpath: str, uid: Union[UUID, str]):
         ref = ResourceRef(uid)
         return self.session.put_resource(url, ref.dump(), version=self._api_version)
 
-    def _get_path(self, uid: Optional[Union[UUID, str]] = None,
+    def _get_path(self,
+                  uid: Optional[Union[UUID, str]] = None,
+                  *,
                   ignore_dataset: Optional[bool] = False) -> str:
         """Construct a url from __base_path__ and, optionally, id."""
         subpath = format_escaped_url('/{}', uid) if uid else ''
diff --git a/src/citrine/resources/file_link.py b/src/citrine/resources/file_link.py
@@ -5,7 +5,7 @@
 from pathlib import Path
 from enum import Enum
 from logging import getLogger
-from typing import Optional, Tuple, Union, List, Dict
+from typing import Optional, Tuple, Union, List, Dict, Iterable
 from urllib.parse import urlparse, quote
 from uuid import UUID
 
@@ -182,8 +182,8 @@ def __init__(self, project_id: UUID, dataset_id: UUID, session: Session):
 
     def _get_path(self,
                   uid: Optional[Union[UUID, str]] = None,
-                  ignore_dataset: Optional[bool] = False,
                   *,
+                  ignore_dataset: Optional[bool] = False,
                   version: Union[str, UUID] = None,
                   action: str = None) -> str:
         """Build the path for taking an action with a particular file version."""
@@ -248,7 +248,7 @@ def get(self,
             *,
             version: Optional[Union[UUID, str, int]] = None) -> FileLink:
         """
-        Get an element of the collection by its id.
+        Retrieve an on-platform FileLink from its filename or file uuid.
 
         Parameters
         ----------
@@ -359,7 +359,7 @@ def _make_upload_request(self, file_path: Path, dest_name: str):
             aws_session_token, bucket, object_key, & upload_id.
 
         """
-        path = self._get_path() + "/uploads"
+        path = self._get_path(action="uploads")
         mime_type = self._mime_type(file_path)
         file_size = file_path.stat().st_size
         assert isinstance(file_size, int)
@@ -423,7 +423,7 @@ def _search_by_file_name(self,
             All the data needed for a file.
 
         """
-        path = self._get_path() + "/search"
+        path = self._get_path(action="search")
 
         search_json = {
             'fileSearchFilter':
@@ -456,7 +456,7 @@ def _search_by_file_version_id(self,
             All the data needed for a file.
 
         """
-        path = self._get_path() + "/search"
+        path = self._get_path(action="search")
 
         search_json = {
             'fileSearchFilter': {
@@ -495,7 +495,7 @@ def _search_by_dataset_file_id(self,
             All the data needed for a file.
 
         """
-        path = self._get_path() + "/search"
+        path = self._get_path(action="search")
 
         search_json = {
             'fileSearchFilter': {
@@ -644,14 +644,12 @@ def read(self, *, file_link: Union[str, UUID, FileLink]):
 
         if self._is_external_url(file_link.url):  # Pull it from where ever it lives
             final_url = file_link.url
-        elif self._validate_local_url(file_link.url):
+        else:
             # The "/content-link" route returns a pre-signed url to download the file.
             content_link = self._get_path_from_file_link(file_link, action='content-link')
             content_link_response = self.session.get_resource(content_link)
             pre_signed_url = content_link_response['pre_signed_read_link']
             final_url = rewrite_s3_links_locally(pre_signed_url, self.session.s3_endpoint_url)
-        else:  # Unrecognized
-            raise ValueError(f"URL was malformed for a local file resource ({file_link.url}).")
 
         download_response = requests.get(final_url)
         return download_response.content
@@ -690,10 +688,10 @@ def process(self, *, file_link: Union[FileLink, str, UUID],
             A JobSubmissionResponse which can be used to poll for the result.
 
         """
-        file_link = self._resolve_file_link(file_link)
-        if not self._validate_local_url(file_link.url):
+        if self._is_external_url(file_link.url):
             raise ValueError(f"Only on-platform resources can be processed. "
                              f"Passed URL {file_link.url}.")
+        file_link = self._resolve_file_link(file_link)
 
         params = {"processing_type": processing_type.value}
         response = self.session.put_resource(
@@ -797,6 +795,38 @@ def file_processing_result(self, *,
 
         return results
 
+    def ingest(self, files: Iterable[FileLink]):
+        """
+        [ALPHA] Ingest a set of CSVs and/or Excel Workbooks formatted per the gemd-ingest protocol.
+
+        Parameters
+        ----------
+        files: List[FileLink]
+            A list of files, already on platform, from which GEMD objects should be built
+
+        """
+        targets = [self._resolve_file_link(f) for f in files]
+        if any(self._is_external_url(f.url) for f in targets):
+            externals = [f.url for f in targets if self._is_external_url(f.url)]
+            raise ValueError(f"All files must be on-platform to load them.  "
+                             f"The following are not: {externals}")
+
+        file_infos = [
+            {"dataset_file_id": str(f.uid),
+             "file_version_uuid": str(f.version)
+             }
+            for f in targets]
+        req = {
+            "project_id": str(self.project_id),
+            "dataset_id": str(self.dataset_id),
+            "files": file_infos
+        }
+        base_url = format_escaped_url("/projects/{}/ingestions", self.project_id)
+        create_ingestion_resp = self.session.post_resource(path=base_url, json=req)
+        ingestion_id = create_ingestion_resp["ingestion_id"]
+        job_url = base_url + format_escaped_url("/{}/gemd-objects", ingestion_id)
+        return self.session.post_resource(path=job_url, json={})
+
     def delete(self, file_link: FileLink):
         """
         Delete the file associated with a given FileLink from the database.
@@ -817,8 +847,25 @@ def delete(self, file_link: FileLink):
 
     def _resolve_file_link(self, identifier: Union[str, UUID, FileLink]) -> FileLink:
         """Generate the FileLink object referenced by the passed argument."""
-        if isinstance(identifier, FileLink):  # Passthrough for convenience
-            return identifier
+        if isinstance(identifier, GEMDFileLink):
+            if isinstance(identifier, FileLink) and identifier.uid is not None:
+                # Passthrough since it's as full as it can get
+                return identifier
+            if self._is_external_url(identifier.url):
+                # Up-convert type with existing info
+                return FileLink(filename=identifier.filename, url=identifier.url)
+            # Resolve on-platform uid and possibly up-convert
+            file_id, version_id = self._get_ids_from_url(identifier.url)
+            if file_id is None:
+                raise ValueError(f"URL was malformed for local resources; "
+                                 f"passed URL {identifier.url}")
+            platform_link = self.get(uid=file_id, version=version_id)
+            if platform_link.filename != identifier.filename:
+                raise ValueError(
+                    f"Name mismatch between link ({identifier.filename}) "
+                    f"and platform ({platform_link.filename})"
+                )
+            return platform_link
         elif isinstance(identifier, str) and self._is_external_url(identifier):
             # Assume it's an absolute URL
             filename = urlparse(identifier).path.split('/')[-1]
@@ -848,10 +895,3 @@ def _is_external_url(self, url: str):
             return False
 
         return urlparse(self._get_path()).netloc != parsed.netloc
-
-    def _validate_local_url(self, url):
-        """Verify link is well formed."""
-        if self._is_external_url(url):
-            return False
-
-        return self._get_ids_from_url(url)[1] is not None  # Implies file_id is None, too
diff --git a/tests/resources/test_file_link.py b/tests/resources/test_file_link.py
@@ -352,8 +352,10 @@ def test_file_download(collection: FileCollection, session, tmpdir):
     """
     # Given
     filename = 'diagram.pdf'
-    url = f"projects/{collection.project_id}/datasets/{collection.dataset_id}/files/{uuid4()}/versions/{uuid4()}"
-    file = FileLink.build(FileLinkDataFactory(url=url, filename=filename))
+    file_uid = str(uuid4())
+    version_uid = str(uuid4())
+    url = f"projects/{collection.project_id}/datasets/{collection.dataset_id}/files/{file_uid}/versions/{version_uid}"
+    file = FileLink.build(FileLinkDataFactory(url=url, filename=filename, id=file_uid, version=version_uid))
     pre_signed_url = "http://files.citrine.io/secret-codes/jiifema987pjfsda"  # arbitrary
     session.set_response({
         'pre_signed_read_link': pre_signed_url,
@@ -403,8 +405,10 @@ def test_read(collection: FileCollection, session):
     """
     # Given
     filename = 'diagram.pdf'
-    url = f"projects/{collection.project_id}/datasets/{collection.dataset_id}/files/{uuid4()}/versions/{uuid4()}"
-    file = FileLink.build(FileLinkDataFactory(url=url, filename=filename))
+    file_uid = str(uuid4())
+    version_uid = str(uuid4())
+    url = f"projects/{collection.project_id}/datasets/{collection.dataset_id}/files/{file_uid}/versions/{version_uid}"
+    file = FileLink.build(FileLinkDataFactory(url=url, filename=filename, id=file_uid, version=version_uid))
     pre_signed_url = "http://files.citrine.io/secret-codes/jiifema987pjfsda"  # arbitrary
     session.set_response({
         'pre_signed_read_link': pre_signed_url,
@@ -499,8 +503,8 @@ def test_process_file(collection: FileCollection, session):
     """Test processing an existing file."""
 
     file_id, version_id = str(uuid4()), str(uuid4())
-    full_url = 'www.citrine.io/develop/files/{}/versions/{}'.format(file_id, version_id)
-    file_link = collection.build(FileLinkDataFactory(url=full_url))
+    full_url = collection._get_path(uid=file_id, version=version_id)
+    file_link = collection.build(FileLinkDataFactory(url=full_url, id=file_id, version=version_id))
 
     job_id_resp = {
         'job_id': str(uuid4())
@@ -548,8 +552,8 @@ def test_process_file_no_waiting(collection: FileCollection, session):
     """Test processing an existing file without waiting on the result."""
 
     file_id, version_id = str(uuid4()), str(uuid4())
-    full_url = 'www.citrine.io/develop/files/{}/versions/{}'.format(file_id, version_id)
-    file_link = collection.build(FileLinkDataFactory(url=full_url))
+    full_url = collection._get_path(uid=file_id, version=version_id)
+    file_link = collection.build(FileLinkDataFactory(url=full_url, id=file_id, version=version_id))
 
     job_id_resp = {
         'job_id': str(uuid4())
@@ -566,11 +570,9 @@ def test_process_file_no_waiting(collection: FileCollection, session):
 
 def test_process_file_exceptions(collection: FileCollection, session):
     """Test processing an existing file without waiting on the result."""
-
-    file_id, version_id = str(uuid4()), str(uuid4())
-    full_url = 'https://www.citrine.io/develop/files/{}/versions/{}'.format(file_id, version_id)
+    full_url = f'http://www.files.com/file.path'
     file_link = collection.build(FileLinkDataFactory(url=full_url))
-
+    collection._get_path()
     # First does a PUT on the /processed endpoint
     # then does a GET on the job executions endpoint
     with pytest.raises(ValueError, match="on-platform resources"):
@@ -580,6 +582,22 @@ def test_process_file_exceptions(collection: FileCollection, session):
                                wait_for_response=False)
 
 
+def test_ingest(collection: FileCollection, session):
+    """Test the on-platform ingest route."""
+    good_file1 = collection.build({"filename": "good.csv", "id": str(uuid4()), "version": str(uuid4())})
+    good_file2 = collection.build({"filename": "also.csv", "id": str(uuid4()), "version": str(uuid4())})
+    bad_file = FileLink(filename="bad.csv", url="http://files.com/input.csv")
+
+    job_id_resp = {
+        'ingestion_id': str(uuid4())
+    }
+    session.set_responses(job_id_resp, job_id_resp)
+    collection.ingest([good_file1, good_file2])
+
+    with pytest.raises(ValueError, match=bad_file.url):
+        collection.ingest([good_file1, bad_file])
+
+
 def test_resolve_file_link(collection: FileCollection, session):
     # The actual response contains more fields, but these are the only ones we use.
     raw_files = [
@@ -626,17 +644,27 @@ def test_resolve_file_link(collection: FileCollection, session):
     session.set_response({
         'files': [raw_files[1]]
     })
-    assert collection._resolve_file_link(UUID(raw_files[1]['id'])) == file1, "UUID didn't resolve"
+
+    unresolved = FileLink(filename=file1.filename, url=file1.url)
+    assert collection._resolve_file_link(unresolved) == file1, "FileLink didn't resolve"
     assert session.num_calls == 1
 
+    unresolved.filename = "Wrong.file"
+    with pytest.raises(ValueError):
+        collection._resolve_file_link(unresolved)
+    assert session.num_calls == 2
+
+    assert collection._resolve_file_link(UUID(raw_files[1]['id'])) == file1, "UUID didn't resolve"
+    assert session.num_calls == 3
+
     session.set_response({
         'files': [raw_files[1]]
     })
     assert collection._resolve_file_link(raw_files[1]['id']) == file1, "String UUID didn't resolve"
-    assert session.num_calls == 2
+    assert session.num_calls == 4
 
     assert collection._resolve_file_link(raw_files[1]['version']) == file1, "Version UUID didn't resolve"
-    assert session.num_calls == 3
+    assert session.num_calls == 5
 
     abs_link = "https://wwww.website.web/web.pdf"
     assert collection._resolve_file_link(abs_link).filename == "web.pdf"
@@ -646,36 +674,17 @@ def test_resolve_file_link(collection: FileCollection, session):
         'files': [raw_files[1]]
     })
     assert collection._resolve_file_link(file1.url) == file1, "Relative path didn't resolve"
-    assert session.num_calls == 4
+    assert session.num_calls == 6
 
     session.set_response({
         'files': [raw_files[1]]
     })
     assert collection._resolve_file_link(file1.filename) == file1, "Filename didn't resolve"
-    assert session.num_calls == 5
+    assert session.num_calls == 7
 
     with pytest.raises(TypeError):
         collection._resolve_file_link(12345)
-    assert session.num_calls == 5
-
-
-def test_validate_filelink_url(collection: FileCollection):
-    good = [
-        f"projects/{uuid4()}/datasets/{uuid4()}/files/{uuid4()}/versions/{uuid4()}",
-        f"/files/{uuid4()}/versions/{uuid4()}"
-    ]
-    bad = [
-        f"/projects/{uuid4()}/datasets/{uuid4()}/files/{uuid4()}/versions/{uuid4()}/action",
-        f"/projects/{uuid4()}/datasets/{uuid4()}/{uuid4()}/versions/{uuid4()}",
-        f"projects/{uuid4()}/datasets/{uuid4()}/files/{uuid4()}/versions/{uuid4()}?query=param",
-        f"projects/{uuid4()}/datasets/{uuid4()}/files/{uuid4()}/versions/{uuid4()}?#fragment",
-        "http://customer.com/data-lake/files/123/versions/456",
-        "/files/uuid4/versions/uuid4",
-    ]
-    for x in good:
-        assert collection._validate_local_url(x)
-    for x in bad:
-        assert not collection._validate_local_url(x)
+    assert session.num_calls == 7
 
 
 def test_get_ids_from_url(collection: FileCollection):

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-__version__ = '2.9.0'`
	`1`	`+__version__ = '2.10.0'`