From 76db7f4048116a23c82bdd70bb11dd004e347e8e Mon Sep 17 00:00:00 2001
From: Bryan Newbold <bnewbold@robocracy.org>
Date: Tue, 8 Oct 2019 15:56:53 -0700
Subject: new cleanup python tool/framework

---
 python/fatcat_cleanup.py                 |  59 +++++++++++++
 python/fatcat_tools/cleanups/NOTES.txt   |  24 ++++++
 python/fatcat_tools/cleanups/__init__.py |   3 +
 python/fatcat_tools/cleanups/common.py   | 140 +++++++++++++++++++++++++++++++
 python/fatcat_tools/cleanups/files.py    |  74 ++++++++++++++++
 5 files changed, 300 insertions(+)
 create mode 100755 python/fatcat_cleanup.py
 create mode 100644 python/fatcat_tools/cleanups/NOTES.txt
 create mode 100644 python/fatcat_tools/cleanups/__init__.py
 create mode 100644 python/fatcat_tools/cleanups/common.py
 create mode 100644 python/fatcat_tools/cleanups/files.py

(limited to 'python')

diff --git a/python/fatcat_cleanup.py b/python/fatcat_cleanup.py
new file mode 100755
index 00000000..42887299
--- /dev/null
+++ b/python/fatcat_cleanup.py
@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+
+import os, sys, argparse
+from fatcat_tools import authenticated_api
+from fatcat_tools.importers import JsonLinePusher
+from fatcat_tools.cleanups import *
+
+
+def run_files(args):
+    fmi = FileCleaner(args.api,
+        dry_run_mode=args.dry_run,
+        edit_batch_size=args.batch_size,
+        editgroup_description=args.editgroup_description_override)
+    JsonLinePusher(fmi, args.json_file).run()
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--host-url',
+        default="http://localhost:9411/v0",
+        help="connect to this host/port")
+    parser.add_argument('--batch-size',
+        help="size of batch to send",
+        default=50, type=int)
+    parser.add_argument('--editgroup-description-override',
+        help="editgroup description override",
+        default=None, type=str)
+    parser.add_argument('--dry-run',
+        help="dry-run mode (don't actually update)",
+        default=False, type=bool)
+    subparsers = parser.add_subparsers()
+
+    sub_files = subparsers.add_parser('files')
+    sub_files.set_defaults(
+        func=run_files,
+        auth_var="FATCAT_AUTH_WORKER_CLEANUP",
+    )
+    sub_files.add_argument('json_file',
+        help="files JSON file to import from",
+        default=sys.stdin, type=argparse.FileType('r'))
+
+    args = parser.parse_args()
+    if not args.__dict__.get("func"):
+        print("tell me what to do!")
+        sys.exit(-1)
+
+    # allow editgroup description override via env variable (but CLI arg takes
+    # precedence)
+    if not args.editgroup_description_override \
+            and os.environ.get('FATCAT_EDITGROUP_DESCRIPTION'):
+        args.editgroup_description_override = os.environ.get('FATCAT_EDITGROUP_DESCRIPTION')
+
+    args.api = authenticated_api(
+        args.host_url,
+        # token is an optional kwarg (can be empty string, None, etc)
+        token=os.environ.get(args.auth_var))
+    args.func(args)
+
+if __name__ == '__main__':
+    main()
diff --git a/python/fatcat_tools/cleanups/NOTES.txt b/python/fatcat_tools/cleanups/NOTES.txt
new file mode 100644
index 00000000..cdaed6b1
--- /dev/null
+++ b/python/fatcat_tools/cleanups/NOTES.txt
@@ -0,0 +1,24 @@
+
+design is to iterate over JSON list of full entities. perform transforms/fixes.
+if no changes, bail early. if changes, do a request to check that current rev
+of entity is same as processed, to prevent race conditions; if a match, do
+update (in import/merge batch style).
+
+should pre-filter entities piped in. also have a CLI mode to do a single
+entity; check+update code should be distinct from fix code.
+
+releases
+- extra.subtitle => subtitle
+- has pmid, type is journal-article, title like "Retraction:" => type is retraction
+- similar to above, title like "Retracted:" => status is retracted
+- longtail release year is bogus (like > 2030?) => remove release year
+
+files
+- URL has ://archive.org/ link with rel=repository => rel=archive
+- URL has ://web.archive.org/web/None/ link => delete URL
+- URL has short wayback date ("2017") and another url with that as prefix => delete URL
+- mimetype is bogus like (???) => clean mimetype
+
+container
+- extra.issnp = "NA" => delete key
+    => in general, issne or issnp not valid ISSNs -> delete key
diff --git a/python/fatcat_tools/cleanups/__init__.py b/python/fatcat_tools/cleanups/__init__.py
new file mode 100644
index 00000000..587c7b9b
--- /dev/null
+++ b/python/fatcat_tools/cleanups/__init__.py
@@ -0,0 +1,3 @@
+
+from .common import EntityCleaner
+from .files import FileCleaner
diff --git a/python/fatcat_tools/cleanups/common.py b/python/fatcat_tools/cleanups/common.py
new file mode 100644
index 00000000..ad2ff858
--- /dev/null
+++ b/python/fatcat_tools/cleanups/common.py
@@ -0,0 +1,140 @@
+
+import json
+import copy
+import subprocess
+from collections import Counter
+
+from fatcat_openapi_client import ApiClient, Editgroup
+from fatcat_openapi_client.rest import ApiException
+from fatcat_tools.transforms import entity_from_dict, entity_to_dict
+
+
+class EntityCleaner:
+    """
+    API for individual jobs:
+
+        # record iterators sees
+        push_record(record)
+        finish()
+
+        # provided helpers
+        self.api
+        self.get_editgroup_id()
+        counts({'lines', 'skip', 'merged', 'updated'})
+
+        # implemented per-task
+        try_merge(idents, primary=None) -> int (entities updated)
+
+    This class is pretty similar to EntityImporter, but isn't subclassed.
+    """
+
+    def __init__(self, api, entity_type, **kwargs):
+
+        eg_extra = kwargs.get('editgroup_extra', dict())
+        eg_extra['git_rev'] = eg_extra.get('git_rev',
+            subprocess.check_output(["git", "describe", "--always"]).strip()).decode('utf-8')
+        eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.EntityCleaner')
+
+        self.api = api
+        self.entity_type = entity_type
+        self.dry_run_mode = kwargs.get('dry_run_mode', True)
+        self.edit_batch_size = kwargs.get('edit_batch_size', 50)
+        self.editgroup_description = kwargs.get('editgroup_description')
+        self.editgroup_extra = eg_extra
+        self.reset()
+        self.ac = ApiClient()
+
+        if self.dry_run_mode:
+            print("Running in dry-run mode!")
+
+    def reset(self):
+        self.counts = Counter({'lines': 0, 'cleaned': 0, 'updated': 0})
+        self._edit_count = 0
+        self._editgroup_id = None
+        self._entity_queue = []
+        self._idents_inflight = []
+
+    def push_record(self, record):
+        """
+        Intended to be called by "pusher" class (which could be pulling from
+        JSON file, Kafka, whatever).
+
+        Input is expected to be an entity in JSON-like dict form.
+
+        Returns nothing.
+        """
+        self.counts['lines'] += 1
+        if (not record):
+            self.counts['skip-null'] += 1
+            return
+
+        entity = entity_from_dict(record, self.entity_type, api_client=self.ac)
+
+        if entity.state != 'active':
+            self.counts['skip-inactive'] += 1
+            return
+
+        cleaned = self.clean_entity(copy.deepcopy(entity))
+        if entity == cleaned:
+            self.counts['skip-clean'] += 1
+            return
+        else:
+            self.counts['cleaned'] += 1
+
+        if self.dry_run_mode:
+            entity_dict = entity_to_dict(entity, api_client=self.ac)
+            print(json.dumps(entity_dict))
+            return
+
+        if entity.ident in self._idents_inflight:
+            raise ValueError("Entity already part of in-process update: {}".format(entity.ident))
+
+        updated = self.try_update(cleaned)
+        if updated:
+            self.counts['updated'] += updated
+            self._edit_count += updated
+            self._idents.inflight.append(entity.ident)
+
+        if self._edit_count >= self.edit_batch_size:
+            self.api.accept_editgroup(self._editgroup_id)
+            self._editgroup_id = None
+            self._edit_count = 0
+            self._idents_inflight = []
+        return
+
+    def clean_entity(self, entity):
+        """
+        Mutates entity in-place and returns it
+        """
+        # implementations should fill this in
+        raise NotImplementedError
+
+    def try_update(self, entity):
+        """
+        Returns edit count (number of entities updated).
+
+        If >= 1, does not need to update self.counts. If no entities updated,
+        do need to update counts internally.
+        """
+        # implementations should fill this in
+        raise NotImplementedError
+
+    def finish(self):
+        if self._edit_count > 0:
+            self.api.accept_editgroup(self._editgroup_id)
+            self._editgroup_id = None
+            self._edit_count = 0
+            self._idents_inflight = []
+
+        return self.counts
+
+    def get_editgroup_id(self):
+
+        if not self._editgroup_id:
+            eg = self.api.create_editgroup(
+                Editgroup(
+                    description=self.editgroup_description,
+                    extra=self.editgroup_extra))
+            self._editgroup_id = eg.editgroup_id
+
+        return self._editgroup_id
diff --git a/python/fatcat_tools/cleanups/files.py b/python/fatcat_tools/cleanups/files.py
new file mode 100644
index 00000000..c2733ba0
--- /dev/null
+++ b/python/fatcat_tools/cleanups/files.py
@@ -0,0 +1,74 @@
+
+from fatcat_openapi_client.rest import ApiException
+from fatcat_openapi_client.models import FileEntity
+from fatcat_tools.transforms import entity_to_dict, entity_from_json
+
+from .common import EntityCleaner
+
+
+class FileCleaner(EntityCleaner):
+    """
+    File fixups!
+    """
+
+    def __init__(self, api, **kwargs):
+
+        eg_desc = kwargs.pop('editgroup_description',
+            "Automated cleanup of file entities (eg, remove bad URLs)")
+        eg_extra = kwargs.pop('editgroup_extra', dict())
+        eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.FileCleaner')
+        super().__init__(api,
+            entity_type=FileEntity,
+            editgroup_description=eg_desc,
+            editgroup_extra=eg_extra,
+            **kwargs)
+
+    def clean_entity(self, entity):
+        """
+        TODO: mimetype is bogus like (???) => clean mimetype
+        """
+
+        # URL has ://web.archive.org/web/None/ link => delete URL
+        entity.urls = [u for u in entity.urls if not '://web.archive.org/web/None/' in u.url]
+
+        # URL has ://archive.org/ link with rel=repository => rel=archive
+        for u in entity.urls:
+            if '://archive.org/' in u.url and u.rel == 'repository':
+                u.rel = 'archive'
+
+        # URL has short wayback date ("2017") and another url with that as prefix => delete URL
+        stub_wayback_urls = []
+        full_wayback_urls = []
+        for u in entity.urls:
+            if '://web.archive.org/web/' in u.url:
+                if len(u.url.split('/')[4]) <= 8:
+                    stub_wayback_urls.append(u.url)
+                else:
+                    full_wayback_urls.append('/'.join(u.url.split('/')[5:]))
+        for stub in stub_wayback_urls:
+            target = '/'.join(stub.split('/')[5:])
+            if target in full_wayback_urls:
+                entity.urls = [u for u in entity.urls if u.url != stub]
+
+        return entity
+
+    def try_update(self, entity):
+
+        try:
+            existing = self.api.get_file(entity.ident)
+        except ApiException as err:
+            if err.status != 404:
+                raise err
+            self.counts['skip-not-found'] += 1
+            return 0
+
+        if existing.state != 'active':
+            self.counts['skip-existing-inactive'] += 1
+            return 0
+        if existing.revision != entity.revision:
+            self.counts['skip-revision'] += 1
+            return 0
+
+        self.update_file(self.get_editgroup_id(), entity.ident, entity)
+        return 1
+
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