generic fileset importer class, with test coverage

6 files changed, 169 insertions, 0 deletions

diff --git a/python/fatcat_import.py b/python/fatcat_import.py
index b82e81c7..6f331aaa 100755
--- a/python/fatcat_import.py
+++ b/python/fatcat_import.py
@@ -325,6 +325,14 @@ def run_file_meta(args):
     )
     JsonLinePusher(fmi, args.json_file).run()
 
+def run_fileset(args):
+    fmi = FilesetImporter(
+        args.api,
+        edit_batch_size=100,
+        skip_release_fileset_check=args.skip_release_fileset_check,
+    )
+    JsonLinePusher(fmi, args.json_file).run()
+
 def main():
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -750,6 +758,19 @@ def main():
         help="File with jsonlines from file_meta schema to import from",
         default=sys.stdin, type=argparse.FileType('r'))
 
+    sub_fileset = subparsers.add_parser('fileset',
+        help="generic fileset importer")
+    sub_fileset.set_defaults(
+        func=run_fileset,
+        auth_var="FATCAT_API_AUTH_TOKEN",
+    )
+    sub_fileset.add_argument('json_file',
+        help="File with jsonlines of fileset entities to import",
+        default=sys.stdin, type=argparse.FileType('r'))
+    sub_fileset.add_argument('--skip-release-fileset-check',
+        action='store_true',
+        help="create without checking if releases already have related filesets")
+
     args = parser.parse_args()
     if not args.__dict__.get("func"):
         print("tell me what to do!")
diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py
index 9cb18506..5da669e1 100644
--- a/python/fatcat_tools/importers/__init__.py
+++ b/python/fatcat_tools/importers/__init__.py
@@ -33,3 +33,4 @@ from .file_meta import FileMetaImporter
 from .doaj_article import DoajArticleImporter
 from .dblp_release import DblpReleaseImporter
 from .dblp_container import DblpContainerImporter
+from .fileset_generic import FilesetImporter
diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py
index e936477c..680b4f9c 100644
--- a/python/fatcat_tools/importers/common.py
+++ b/python/fatcat_tools/importers/common.py
@@ -447,6 +447,10 @@ class EntityImporter:
         existing.urls = [u for u in existing.urls if u.url not in redundant_urls]
         return existing
 
+    @staticmethod
+    def generic_fileset_cleanups(existing):
+        return existing
+
     def match_existing_release_fuzzy(self, release: ReleaseEntity) -> Optional[Tuple[str, str, ReleaseEntity]]:
         """
         This helper function uses fuzzycat (and elasticsearch) to look for
diff --git a/python/fatcat_tools/importers/fileset_generic.py b/python/fatcat_tools/importers/fileset_generic.py
new file mode 100644
index 00000000..f0ad5460
--- /dev/null
+++ b/python/fatcat_tools/importers/fileset_generic.py
@@ -0,0 +1,83 @@
+
+import fatcat_openapi_client
+
+from fatcat_tools import entity_from_dict
+from .common import EntityImporter
+
+
+class FilesetImporter(EntityImporter):
+    """
+    General purpose importer for fileset entities. Simply fileset schema JSON
+    and inserts.
+
+    By default requires release_ids to be non-empty, and will check each
+    release_id to see if a fileset is already associated; if so, skips the
+    import. This behavior may change in the future, and can be disabled.
+
+    Currently only creates (insert), no updates.
+    """
+
+    def __init__(self, api, **kwargs):
+
+        eg_desc = kwargs.pop('editgroup_description', None) or "Generic Fileset entity import"
+        eg_extra = kwargs.pop('editgroup_extra', dict())
+        eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.FilesetImporter')
+        kwargs['do_updates'] = bool(kwargs.get("do_updates", False))
+        self.skip_release_fileset_check = bool(kwargs.get("skip_release_fileset_check", False))
+        super().__init__(api,
+            editgroup_description=eg_desc,
+            editgroup_extra=eg_extra,
+            **kwargs)
+
+        # bezerk mode doesn't make sense for this importer
+        assert self.bezerk_mode == False
+
+    def want(self, row):
+        if not row.get('release_ids'):
+            self.counts['skip-no-release-ids'] += 1
+            return False
+        if not row.get('urls'):
+            self.counts['skip-no-urls'] += 1
+            return False
+        if not row.get('manifest'):
+            self.counts['skip-no-files'] += 1
+            return False
+
+        for f in row.get('manifest'):
+            for k in ('sha1', 'md5'):
+                if not f.get(k):
+                    self.counts['skip-missing-file-field'] += 1
+                    return False
+        return True
+
+    def parse_record(self, row):
+
+        fse = entity_from_dict(
+            row,
+            fatcat_openapi_client.FilesetEntity,
+            api_client=self.api.api_client,
+        )
+        fse = self.generic_fileset_cleanups(fse)
+        return fse
+
+    def try_update(self, fse):
+
+        if not self.skip_release_fileset_check:
+            for release_id in fse.release_ids:
+                # don't catch 404, that would be an error
+                release = self.api.get_release(release_id, expand='filesets', hide='abstracts,refs')
+                assert release.state == 'active'
+                if release.filesets:
+                    self.counts['exists'] += 1
+                    self.counts['exists-via-release-filesets'] += 1
+                    return False
+
+        # do the insert
+        return True
+
+    def insert_batch(self, batch):
+        self.api.create_fileset_auto_batch(fatcat_openapi_client.FilesetAutoBatch(
+            editgroup=fatcat_openapi_client.Editgroup(
+                description=self.editgroup_description,
+                extra=self.editgroup_extra),
+            entity_list=batch))
diff --git a/python/tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json b/python/tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json
new file mode 100644
index 00000000..6ba9d573
--- /dev/null
+++ b/python/tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json
@@ -0,0 +1 @@
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diff --git a/python/tests/import_fileset_generic.py b/python/tests/import_fileset_generic.py
new file mode 100644
index 00000000..44310304
--- /dev/null
+++ b/python/tests/import_fileset_generic.py
@@ -0,0 +1,59 @@
+
+import json
+import pytest
+
+from fatcat_tools.importers import FilesetImporter, JsonLinePusher
+from fixtures import *
+
+
+@pytest.fixture(scope="function")
+def fileset_importer(api):
+    yield FilesetImporter(api)
+
+# TODO: use API to check that entities actually created...
+def test_fileset_importer_basic(fileset_importer):
+    with open('tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json', 'r') as f:
+        JsonLinePusher(fileset_importer, f).run()
+
+def test_fileset_importer(fileset_importer):
+    last_index = fileset_importer.api.get_changelog(limit=1)[0].index
+    with open('tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json', 'r') as f:
+        fileset_importer.bezerk_mode = True
+        counts = JsonLinePusher(fileset_importer, f).run()
+    assert counts['insert'] == 1
+    assert counts['exists'] == 0
+    assert counts['skip'] == 0
+
+    # fetch most recent editgroup
+    change = fileset_importer.api.get_changelog_entry(index=last_index+1)
+    eg = change.editgroup
+    assert eg.description
+    assert "generic fileset" in eg.description.lower()
+    assert eg.extra['git_rev']
+    assert "fatcat_tools.FilesetImporter" in eg.extra['agent']
+
+    # re-insert; should skip
+    with open('tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json', 'r') as f:
+        fileset_importer.reset()
+        fileset_importer.bezerk_mode = False
+        counts = JsonLinePusher(fileset_importer, f).run()
+    assert counts['insert'] == 0
+    assert counts['exists'] == 1
+    assert counts['skip'] == 0
+
+def test_fileset_dict_parse(fileset_importer):
+    with open('tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json', 'r') as f:
+        raw = json.loads(f.readline())
+        fs = fileset_importer.parse_record(raw)
+
+        assert fs.manifest[0].sha1 == "cc9bd558ca79b30b2966714da7ef4129537fde0c"
+        assert fs.manifest[0].md5 == "742c40404c9a4dbbd77c0985201c639f"
+        assert fs.manifest[0].sha256 == "3a7c07ad17ce3638d5a1dd21f995a496e430b952eef00270ad741d506984370f"
+        assert fs.manifest[0].size == 640500
+        assert fs.manifest[0].path == "070111_LatA_100nM.txt"
+        assert fs.manifest[0].extra['mimetype'] == "text/plain"
+        assert len(fs.urls) == 3
+        for u in fs.urls:
+            if u.rel == "repo":
+                assert u.url == "https://merritt.cdlib.org/d/ark%3A%2Fb5068%2Fd1rp49/1/"
+        assert len(fs.release_ids) == 1