Refactor initial configuration ingestion

extract/extract.py

@@ -8,10 +8,12 @@ import Levenshtein
 from pubs.plugins import PapersPlugin
 from pubs.events import DocAddEvent, NoteEvent
 
-from pubs import repo
+from pubs import repo, pretty
 from pubs.utils import resolve_citekey_list
 from pubs.content import check_file, read_text_file, write_file
+from pubs.query import get_paper_filter
 
+CONFIRMATION_PAPER_THRESHOLD=5
 
 class ExtractPlugin(PapersPlugin):
     """Extract annotations from any pdf document.
@@ -36,32 +38,18 @@ class ExtractPlugin(PapersPlugin):
         self.pubsdir = os.path.expanduser(conf["main"]["pubsdir"])
         self.broker = self.repository.databroker
 
-        # TODO implement custom annotation formatting, akin to main config citekey format
+        settings = conf["plugins"].get("extract", {})
-        # e.g. `> [{page}] {annotation}`
+        self.on_import = settings.get("on_import", False)
-        # or `:: {annotation} :: {page} ::`
+        self.minimum_similarity = float(settings.get("minimum_similarity", 0.75))
-        # and so on
+        self.formatting = settings.get(
-        self.on_import = conf["plugins"].get("extract", {}).get("on_import", False)
-        self.minimum_similarity = float(
-            conf["plugins"].get("extract", {}).get("minimum_similarity", 0.75)
-        )
-        self.formatting = (
-            conf["plugins"]
-            .get("extract", {})
-            .get(
             "formatting",
             "{newline}{quote_begin}> {quote} {quote_end}[{page}]{note_begin}{newline}Note: {note}{note_end}",
         )
-        )
 
-    def update_parser(self, subparsers, conf):
+    def update_parser(self, subparsers, _):
         """Allow the usage of the pubs extract subcommand"""
         # TODO option for ignoring missing documents or erroring.
         extract_parser = subparsers.add_parser(self.name, help=self.description)
-        extract_parser.add_argument(
-            "citekeys",
-            nargs=argparse.REMAINDER,
-            help="citekey(s) of the documents to extract from",
-        )
         extract_parser.add_argument(
             "-w",
             "--write",
@@ -76,29 +64,58 @@ class ExtractPlugin(PapersPlugin):
             action="store_true",
             default=False,
         )
+        extract_parser.add_argument(
+            "-q",
+            "--query",
+            help="Query library instead of providing individual citekeys. For query help see pubs list command.",
+            action="store_true",
+            default=None,
+            dest="is_query",
+        )
+        extract_parser.add_argument(
+            "-i",
+            "--ignore-case",
+            action="store_false",
+            default=None,
+            dest="case_sensitive",
+            help="When using query mode, perform case insensitive search.",
+        )
+        extract_parser.add_argument(
+            "-I",
+            "--force-case",
+            action="store_true",
+            dest="case_sensitive",
+            help="When using query mode, perform case sensitive search.",
+        )
+        extract_parser.add_argument(
+            "--strict",
+            action="store_true",
+            default=False,
+            help="Force strict unicode comparison of query.",
+        )
+        extract_parser.add_argument(
+            "query",
+            nargs=argparse.REMAINDER,
+            help="Citekey(s)/query for the documents to extract from.",
+        )
         extract_parser.set_defaults(func=self.command)
 
     def command(self, conf, args):
         """Run the annotation extraction command."""
-        citekeys = resolve_citekey_list(
+        papers = self._gather_papers(conf, args)
-            self.repository, conf, args.citekeys, ui=self.ui, exit_on_fail=True
+        all_annotations = self.extract(papers)
-        )
-        if not citekeys:
-            return
-        all_annotations = self.extract(citekeys)
         if args.write:
             self._to_notes(all_annotations, self.note_extension, args.edit)
         else:
             self._to_stdout(all_annotations)
         self.repository.close()
 
-    def extract(self, citekeys):
+    def extract(self, papers):
         """Extracts annotations from citekeys.
 
         Returns all annotations belonging to the papers that
         are described by the citekeys passed in.
         """
-        papers = self._gather_papers(citekeys)
         papers_annotated = []
         for paper in papers:
             file = self._get_file(paper)
@@ -108,15 +125,44 @@ class ExtractPlugin(PapersPlugin):
                 self.ui.error(f"Document {file} is broken: {e}")
         return papers_annotated
 
-    def _gather_papers(self, citekeys):
+    def _gather_papers(self, conf, args):
         """Get all papers for citekeys.
 
         Returns all Paper objects described by the citekeys
         passed in.
         """
         papers = []
-        for key in citekeys:
+        if not args.is_query:
+            keys = resolve_citekey_list(
+                self.repository, conf, args.query, ui=self.ui, exit_on_fail=True
+            )
+            if not keys:
+                return []
+            for key in keys:
                 papers.append(self.repository.pull_paper(key))
+        else:
+            papers = list(
+                filter(
+                    get_paper_filter(
+                        args.query,
+                        case_sensitive=args.case_sensitive,
+                        strict=args.strict,
+                    ),
+                    self.repository.all_papers(),
+                )
+            )
+        if len(papers) > CONFIRMATION_PAPER_THRESHOLD:
+            self.ui.message(
+                "\n".join(
+                    pretty.paper_oneliner(
+                        p, citekey_only=False, max_authors=conf["main"]["max_authors"]
+                    )
+                    for p in papers
+                )
+            )
+            self.ui.input_yn(
+                question=f"Extract annotations for these papers?", default="y"
+            )
         return papers
 
     def _get_file(self, paper):
@@ -207,9 +253,9 @@ class ExtractPlugin(PapersPlugin):
             paper = contents[0]
             annotations = contents[1]
             if annotations:
-                output += f"------ {paper.citekey} ------\n\n"
+                output += f"------ {paper.citekey} ------\n"
                 for annot in annotations:
-                    output += f"{annot}\n\n"
+                    output += f"{annot}\n"
                 output += "\n"
         print(output)