fetchpdf 0.1.3__tar.gz → 0.1.5__tar.gz

{fetchpdf-0.1.3/fetchpdf.egg-info → fetchpdf-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fetchpdf
-Version: 0.1.3
+Version: 0.1.5
 Summary: A comprehensive tool to download PDFs from DOIs using multiple sources
 Author-email: Dan Elton <delton17@gmail.com>
 License-Expression: MIT
@@ -56,7 +56,7 @@ A comprehensive Python package to download academic papers (PDFs) from DOIs (or
 - [Supplementary Material](#supplementary-material)
 - [`--pull-everything`: the second layer](#--pull-everything-the-second-layer)
 - [Figure Images](#figure-images)
-- [Institutional access](#institutional-access-via-cookies-ie-using-your-librarys-subscriptions) — papers your library subscribes to (`fetchpdf cookies setup`)
+- [Institutional access](#institutional-access-via-cookies-ie-using-your-librarys-subscriptions) — papers your library subscribes to (`fetchpdf fetchcookies`)
 - [Calling fetchpdf from a script or an agent](#calling-fetchpdf-from-a-script-or-an-agent) — `--json`
 - [API Reference](#api-reference)
 - [Download Sources](#download-sources-in-order-of-priority)
@@ -85,7 +85,7 @@ A comprehensive Python package to download academic papers (PDFs) from DOIs (or
 - 🖨️ **[XML to HTML / PDF](#rendering-the-xml-as-html-or-pdf)**: `--generate-html-from-xml` / `--generate-pdf-from-xml` render a retrieved XML as one self-contained page, figures and tables embedded
 - 🔗 **[Linked Datasets & Code](#linked-datasets-and-code-stem_linked_artifactsjson)**: the same pass discovers each paper's external datasets/software via ScholeXplorer, Europe PMC and DataCite, downloads ownership-confirmed deposits from figshare/Zenodo/OSF/Dryad/Dataverse, and records every link in a sidecar
 - 🤖 **[LLM-assisted retrieval](#--pull-everything-the-second-layer)**: `--pull-everything` adds a second layer — a model reads the paper itself and goes after the SI and datasets the APIs missed
-- 🔐 **[Institutional access](#institutional-access-via-cookies-ie-using-your-librarys-subscriptions)** (opt-in): a one-time `fetchpdf cookies setup` lets fetchpdf download papers your library subscribes to
+- 🔐 **[Institutional access](#institutional-access-via-cookies-ie-using-your-librarys-subscriptions)** (opt-in): a one-time `fetchpdf fetchcookies` lets fetchpdf download papers your library subscribes to
 - 🚀 **Batch Processing**: Process multiple DOIs/PMIDs from CSV files or lists
 - ⚡ **Parallel Execution**: Download multiple papers simultaneously with configurable workers
 
@@ -184,7 +184,7 @@ fetchpdf '10.1002/(SICI)1521-3773(19981116)37:21<2922::AID-ANIE2922>3.0.CO;2-1,
 #   ...but single-quote any list holding ( ) < > ; -- the shell would read them as syntax
 ```
 
-**At a university?** Run `fetchpdf cookies setup` once and fetchpdf will also fetch
+**At a university?** Run `fetchpdf fetchcookies` once and fetchpdf will also fetch
 papers your library subscribes to. See
 [Institutional access](#institutional-access-via-cookies-ie-using-your-librarys-subscriptions).
 
@@ -1005,11 +1005,17 @@ fetchpdf-render ./out --html --pdf --fetch-figures   # XML you already have
 
 **A rendering, not the publisher's PDF**, and never written as `{stem}.pdf`:
 that name means the typeset article to the skip check and the validators. The
-page opens with a banner naming the source file, the DOI, and how many figures
-were embedded. A figure whose image could not be had keeps a visible
+page opens with a banner naming the source file, the fetchpdf version and the
+DOI, plus a note for anything that could not be shown: figures without an image,
+tables published only as an image that is missing, or no reference list. A figure whose image could not be had keeps a visible
 placeholder, so an incomplete rendering looks incomplete. The prose and
-tables come from the same walker as `--to-markdown`, so the two agree;
-references are omitted and formulas stay as text.
+tables come from the same walker as `--to-markdown`, so the two agree, except
+that the page ends with the reference list (with DOI links), which the Markdown
+leaves out. Formulas stay as text. The XML never says how large a figure was
+typeset, so each is given about the same area (a square figure ~10.5 cm across),
+shaped by its aspect ratio and capped at the column width. Under the title come
+the authors, their affiliations and the journal citation (volume, issue, pages).
+Tables always fit the page width in the PDF; very wide ones print smaller.
 
 Only records whose XML was kept are rendered — add `--get-xml-or-html` to keep
 the XML beside the PDF.
@@ -1026,7 +1032,7 @@ library, for the papers that have no open-access copy.
 Browser cookie support is included in the standard fetchpdf installation.
 
 ```bash
-fetchpdf cookies setup
+fetchpdf fetchcookies
 ```
 
 The wizard asks two questions, then opens some tabs:
@@ -1058,7 +1064,7 @@ session exists but the test article was refused: the session lapsed, or your
 library does not take that particular journal. Access is turned on only if at
 least one publisher works.
 
-**Cookies often expire within hours**. You likely will have to rerun `fetchpdf cookies setup` periodically to restore access.
+**Cookies often expire within hours**. You likely will have to rerun `fetchpdf fetchcookies` periodically to restore access.
 
 ### Living with it
 
@@ -1092,7 +1098,7 @@ run. This works the same for a single DOI and for a batch:
 ```
 
 Runs that cannot be asked (pipes, cron, `--json`) print the command instead
-(`fetchpdf cookies setup --publishers wiley,tandf`, or `refresh --publishers ...`).
+(`fetchpdf fetchcookies --publishers wiley,tandf`, or `refresh --publishers ...`).
 `--no-cookies` and `--cookies FILE` turn the offer off. Royal Society papers are
 not offered, because there is no test article to sign in on.
 

{fetchpdf-0.1.3 → fetchpdf-0.1.5}/README.md

@@ -17,7 +17,7 @@ A comprehensive Python package to download academic papers (PDFs) from DOIs (or
 - [Supplementary Material](#supplementary-material)
 - [`--pull-everything`: the second layer](#--pull-everything-the-second-layer)
 - [Figure Images](#figure-images)
-- [Institutional access](#institutional-access-via-cookies-ie-using-your-librarys-subscriptions) — papers your library subscribes to (`fetchpdf cookies setup`)
+- [Institutional access](#institutional-access-via-cookies-ie-using-your-librarys-subscriptions) — papers your library subscribes to (`fetchpdf fetchcookies`)
 - [Calling fetchpdf from a script or an agent](#calling-fetchpdf-from-a-script-or-an-agent) — `--json`
 - [API Reference](#api-reference)
 - [Download Sources](#download-sources-in-order-of-priority)
@@ -46,7 +46,7 @@ A comprehensive Python package to download academic papers (PDFs) from DOIs (or
 - 🖨️ **[XML to HTML / PDF](#rendering-the-xml-as-html-or-pdf)**: `--generate-html-from-xml` / `--generate-pdf-from-xml` render a retrieved XML as one self-contained page, figures and tables embedded
 - 🔗 **[Linked Datasets & Code](#linked-datasets-and-code-stem_linked_artifactsjson)**: the same pass discovers each paper's external datasets/software via ScholeXplorer, Europe PMC and DataCite, downloads ownership-confirmed deposits from figshare/Zenodo/OSF/Dryad/Dataverse, and records every link in a sidecar
 - 🤖 **[LLM-assisted retrieval](#--pull-everything-the-second-layer)**: `--pull-everything` adds a second layer — a model reads the paper itself and goes after the SI and datasets the APIs missed
-- 🔐 **[Institutional access](#institutional-access-via-cookies-ie-using-your-librarys-subscriptions)** (opt-in): a one-time `fetchpdf cookies setup` lets fetchpdf download papers your library subscribes to
+- 🔐 **[Institutional access](#institutional-access-via-cookies-ie-using-your-librarys-subscriptions)** (opt-in): a one-time `fetchpdf fetchcookies` lets fetchpdf download papers your library subscribes to
 - 🚀 **Batch Processing**: Process multiple DOIs/PMIDs from CSV files or lists
 - ⚡ **Parallel Execution**: Download multiple papers simultaneously with configurable workers
 
@@ -145,7 +145,7 @@ fetchpdf '10.1002/(SICI)1521-3773(19981116)37:21<2922::AID-ANIE2922>3.0.CO;2-1,
 #   ...but single-quote any list holding ( ) < > ; -- the shell would read them as syntax
 ```
 
-**At a university?** Run `fetchpdf cookies setup` once and fetchpdf will also fetch
+**At a university?** Run `fetchpdf fetchcookies` once and fetchpdf will also fetch
 papers your library subscribes to. See
 [Institutional access](#institutional-access-via-cookies-ie-using-your-librarys-subscriptions).
 
@@ -966,11 +966,17 @@ fetchpdf-render ./out --html --pdf --fetch-figures   # XML you already have
 
 **A rendering, not the publisher's PDF**, and never written as `{stem}.pdf`:
 that name means the typeset article to the skip check and the validators. The
-page opens with a banner naming the source file, the DOI, and how many figures
-were embedded. A figure whose image could not be had keeps a visible
+page opens with a banner naming the source file, the fetchpdf version and the
+DOI, plus a note for anything that could not be shown: figures without an image,
+tables published only as an image that is missing, or no reference list. A figure whose image could not be had keeps a visible
 placeholder, so an incomplete rendering looks incomplete. The prose and
-tables come from the same walker as `--to-markdown`, so the two agree;
-references are omitted and formulas stay as text.
+tables come from the same walker as `--to-markdown`, so the two agree, except
+that the page ends with the reference list (with DOI links), which the Markdown
+leaves out. Formulas stay as text. The XML never says how large a figure was
+typeset, so each is given about the same area (a square figure ~10.5 cm across),
+shaped by its aspect ratio and capped at the column width. Under the title come
+the authors, their affiliations and the journal citation (volume, issue, pages).
+Tables always fit the page width in the PDF; very wide ones print smaller.
 
 Only records whose XML was kept are rendered — add `--get-xml-or-html` to keep
 the XML beside the PDF.
@@ -987,7 +993,7 @@ library, for the papers that have no open-access copy.
 Browser cookie support is included in the standard fetchpdf installation.
 
 ```bash
-fetchpdf cookies setup
+fetchpdf fetchcookies
 ```
 
 The wizard asks two questions, then opens some tabs:
@@ -1019,7 +1025,7 @@ session exists but the test article was refused: the session lapsed, or your
 library does not take that particular journal. Access is turned on only if at
 least one publisher works.
 
-**Cookies often expire within hours**. You likely will have to rerun `fetchpdf cookies setup` periodically to restore access.
+**Cookies often expire within hours**. You likely will have to rerun `fetchpdf fetchcookies` periodically to restore access.
 
 ### Living with it
 
@@ -1053,7 +1059,7 @@ run. This works the same for a single DOI and for a batch:
 ```
 
 Runs that cannot be asked (pipes, cron, `--json`) print the command instead
-(`fetchpdf cookies setup --publishers wiley,tandf`, or `refresh --publishers ...`).
+(`fetchpdf fetchcookies --publishers wiley,tandf`, or `refresh --publishers ...`).
 `--no-cookies` and `--cookies FILE` turn the offer off. Royal Society papers are
 not offered, because there is no test article to sign in on.
 

{fetchpdf-0.1.3 → fetchpdf-0.1.5}/fetchpdf/__init__.py

@@ -15,7 +15,7 @@ from .fetch_metadata_from_doi import fetch_metadata_from_doi
 # behavioural difference, it is the same object.
 fetch_pdf_from_doi = fetch_pdf
 
-__version__ = "0.1.3"
+__version__ = "0.1.5"
 __all__ = [
     "fetch_pdf",
     "fetch_pdf_from_doi",  # deprecated alias for fetch_pdf

{fetchpdf-0.1.3 → fetchpdf-0.1.5}/fetchpdf/fetchpdf.py

@@ -2721,10 +2721,6 @@ def try_pmid_direct_pdf_fallback(pmid: str, save_path: str, verbose=False, allow
                 if verbose:
                     print(f"✅ PMID native PMCID route success for PMID {pmid}")
                 return True
-        if allow_xml:
-            xml_got = try_pmc_xml_fallback(pmcid, save_path, verbose=verbose, doi=f"pmid:{pmid}")
-            if xml_got:
-                return xml_got
 
     # Europe PMC record full-text URLs.
     try:
@@ -2797,6 +2793,12 @@ def try_pmid_direct_pdf_fallback(pmid: str, save_path: str, verbose=False, allow
         if verbose:
             print(f"  PMID native PubMed provider lookup failed for {pmid}: {str(e)[:100]}")
 
+    # XML only after every PDF route above has failed.
+    if allow_xml and pmcid:
+        xml_got = try_pmc_xml_fallback(pmcid, save_path, verbose=verbose, doi=f"pmid:{pmid}")
+        if xml_got:
+            return xml_got
+
     return False
 
 
@@ -4024,7 +4026,7 @@ def _try_institutional(save_path, resolved, cookies_file=None, verbose=False,
                        _source_out=None):
     """The institutional-access route. Returns the saved path, or None.
 
-    Off unless the user opted in -- `fetchpdf cookies setup`, or --cookies FILE --
+    Off unless the user opted in -- `fetchpdf fetchcookies`, or --cookies FILE --
     and silent for a publisher the route does not cover, so a run over APA or
     Elsevier DOIs carries no extra noise.
     """
@@ -4372,6 +4374,12 @@ def _fetch_pdf_chain(doi,
     # Defer Elsevier XML fallback until all PDF-oriented fallbacks have failed.
     elsevier_crossref_message = None
     _pmid_cache = [None]  # Cached from PMC idconv when available; used for DOI->PMID fallback
+    # XML copies found mid-chain (PMC, eLife, Crossref text-mining links) are
+    # queued here, not returned: an open PDF later in the chain beats them.
+    # PLOS ONE 10.1371/journal.pone.0000308 came back as XML because Europe
+    # PMC's ?pdf=render 403'd and the PMC step took the JATS, while PLOS
+    # itself serves the PDF. Each entry is (source, callable -> path or None).
+    deferred_xml = []
 
     # Skip if PDF or XML already exists
     xml_path = os.path.splitext(save_path)[0] + ".xml"
@@ -5055,12 +5063,9 @@ def _fetch_pdf_chain(doi,
                     # pdf=render 404s for OA records Europe PMC holds only as
                     # JATS (eLife 34573, PLOS Currents). The XML is the paper.
                     if allow_xml_fallback:
-                        xml_got = try_pmc_xml_fallback(
+                        deferred_xml.append(("pmc", lambda pmcid=pmcid: try_pmc_xml_fallback(
                             pmcid, save_path, verbose=verbose, doi=doi
-                        )
-                        if xml_got:
-                            _record_source(_source_out, "pmc")
-                            return xml_got
+                        )))
                         # Europe PMC serves fullTextXML only for records inside
                         # its OA subset. NIH author manuscripts are not in it --
                         # free to read on the PMC website, not redistributable --
@@ -5075,26 +5080,17 @@ def _fetch_pdf_chain(doi,
                         # A non-OA record's efetch reply is a well-formed
                         # <article> with no <body> and the refusal in an XML
                         # comment; _looks_like_jats_fulltext already rejects it.
-                        xml_got = try_pmc_efetch_xml_fallback(
+                        deferred_xml.append(("pmc_efetch", lambda pmcid=pmcid: try_pmc_efetch_xml_fallback(
                             pmcid, save_path, verbose=verbose, doi=doi
-                        )
-                        if xml_got:
-                            _record_source(_source_out, "pmc_efetch")
-                            return xml_got
+                        )))
     except Exception as e:
         if verbose: print(f"Error with PMC: {e}")
         pass
 
     # ---------------- eLife CDN / API XML (HTML site 406s) ----------------
     if allow_xml_fallback and _elife_article_id(doi):
-        try:
-            xml_got = try_elife_xml_fallback(doi, save_path, verbose=verbose)
-            if xml_got:
-                _record_source(_source_out, "elife")
-                return xml_got
-        except Exception as e:
-            if verbose:
-                print(f"Error with eLife XML: {e}")
+        deferred_xml.append(("elife", lambda: try_elife_xml_fallback(
+            doi, save_path, verbose=verbose)))
 
     # ---------------- eScholarship via PubMed LinkOut ----------------
     # UC and other universities deposit in eScholarship; PubMed abstract lists these
@@ -5131,7 +5127,7 @@ def _fetch_pdf_chain(doi,
     # tail (Crossref landing pages, CORE, DOAJ, DataCite, PMID, Elsevier) that
     # rarely finds what a subscription serves in a second or two. Grey sources
     # (fetchpdf_grey) still run after the whole walk. A no-op unless the user
-    # ran `fetchpdf cookies setup` or passed --cookies, and for publishers it does
+    # ran `fetchpdf fetchcookies` or passed --cookies, and for publishers it does
     # not cover. Once per record: not on related-DOI re-entries.
     if _top_level and not (xml_only or xml_html_only):
         institutional_path = _try_institutional(
@@ -5165,12 +5161,9 @@ def _fetch_pdf_chain(doi,
             # is the CDN JATS file the HTML site 406s would have pointed at.
             if allow_xml_fallback:
                 for xml_url in _crossref_tdm_xml_urls(m):
-                    xml_got = _try_save_jats_xml(
+                    deferred_xml.append(("crossref", lambda xml_url=xml_url: _try_save_jats_xml(
                         xml_url, save_path, verbose=verbose, doi=doi
-                    )
-                    if xml_got:
-                        _record_source(_source_out, "crossref")
-                        return xml_got
+                    )))
             # Landing page fallback
             landing = m.get("URL")
             if try_download(landing, save_path, verbose):
@@ -5199,13 +5192,14 @@ def _fetch_pdf_chain(doi,
                 elsevier_crossref_message = m
             # A published paper's PsyArXiv/bioRxiv copy is a Crossref relation,
             # not Unpaywall's "best" location. Re-enter the chain on that DOI;
-            # _visited stops a cycle.
+            # _visited stops a cycle. PDF only: the related chain returning its
+            # XML here would beat every PDF source still ahead of this one.
             for related in _crossref_related_dois(m, doi):
                 if verbose:
                     print(f"  Trying Crossref related DOI: {related}")
                 related_path = fetch_pdf(
                     related, save_path, email, verbose, delay=0,
-                    allow_xml_fallback=allow_xml_fallback,
+                    allow_xml_fallback=False,
                     use_playwright=use_playwright,
                     _source_out=_source_out, _visited=_visited,
                 )
@@ -5496,12 +5490,19 @@ def _fetch_pdf_chain(doi,
         if pmid:
             pmid_str = str(pmid).strip()
             pmid_got = try_pmid_direct_pdf_fallback(
-                pmid_str, save_path, verbose, allow_xml=allow_xml_fallback
+                pmid_str, save_path, verbose, allow_xml=False
             )
             if pmid_got:
                 _record_source(_source_out, "pmid_direct")
                 return pmid_got if isinstance(pmid_got, str) else save_path
-
+            # The PMID route's own PMC XML, unless the PMC step above already
+            # queued XML for this record. Re-running the route repeats its PDF
+            # attempts before the XML, but only once every PDF source has failed.
+            if allow_xml_fallback and not any(
+                source in ("pmc", "pmc_efetch") for source, _ in deferred_xml
+            ):
+                deferred_xml.append(("pmid_direct", lambda: try_pmid_direct_pdf_fallback(
+                    pmid_str, save_path, verbose, allow_xml=True)))
 
     # ---------------- Google Scholar via SerpApi ---------------------------
     # Preserve search credits until the ordinary PDF sources are exhausted.
@@ -5530,6 +5531,20 @@ def _fetch_pdf_chain(doi,
             if verbose:
                 print(f"Error with deferred Elsevier fallback: {e}")
 
+    # ---------------- Deferred XML (every PDF source has failed) -----------
+    # Last of all, after SerpApi too: XML is the last-ditch format, so a PDF
+    # from any source -- even one that spends a search credit -- comes first.
+    for xml_source, attempt in deferred_xml:
+        try:
+            xml_got = attempt()
+        except Exception as e:
+            if verbose:
+                print(f"Error with deferred {xml_source} XML: {e}")
+            continue
+        if xml_got:
+            _record_source(_source_out, xml_source)
+            return xml_got if isinstance(xml_got, str) else save_path
+
 
 def _append_missing_si_to_report(output_dir, si_statuses, run_timestamp, lock,
                                  drafts_by_doi=None, figure_statuses=None):
@@ -5809,6 +5824,14 @@ def _prune_empty_record_dir(record_dir):
     """
     if not record_dir:
         return
+    # The resolution cache is written beside the artifact, so a record that got
+    # nothing still holds one; alone, it is not something the record wrote.
+    from .retrieval.cache import CACHE_FILENAME
+    try:
+        if os.listdir(record_dir) == [CACHE_FILENAME]:
+            os.unlink(os.path.join(record_dir, CACHE_FILENAME))
+    except OSError:
+        pass
     try:
         os.rmdir(record_dir)
     except OSError:
@@ -6423,7 +6446,11 @@ def _batch_fetch_pdfs_inner(dois, output_dir, email=None, verbose=False, delay=0
         # path, or a record with four supplementary PDFs would report "pdf 5" and
         # corrupt the format composition tally.
         _pull_si(display_id, raw_identifier, canonical_doi, save_path)
-        _pull_figures(display_id, raw_identifier, canonical_doi, save_path)
+        # Unlike the supplements, figures belong to an article we have: with no
+        # artifact there is nothing for them to illustrate, and the pass would
+        # leave an empty `_figures/` and manifest in a record that failed.
+        if success:
+            _pull_figures(display_id, raw_identifier, canonical_doi, save_path)
         _render_xml(display_id, save_path)
         _pull_images(result or save_path, display_id)
 
@@ -7000,7 +7027,7 @@ def _ask_yes(question: str) -> bool:
 
 
 def _import_cookies(cfg, publishers) -> bool:
-    """Run `fetchpdf cookies setup` (no config yet) or `refresh` in-process,
+    """Run `fetchpdf fetchcookies` (no config yet) or `refresh` in-process,
     for *publishers* only -- the ones the failed papers are at.
 
     True when the retry is worth making: setup succeeded, or refresh found a
@@ -7064,7 +7091,7 @@ def _offer_cookie_import(failed, retry):
     if cfg is None:
         print(f"🔐 {n} failed {noun} ({where}) may be available through your "
               f"library's subscriptions, by importing your browser's cookies.")
-        command = f"fetchpdf cookies setup --publishers {','.join(publishers)}"
+        command = f"fetchpdf fetchcookies --publishers {','.join(publishers)}"
     else:
         print(f"🔐 {n} failed {noun} ({where}) are at publishers your library access "
               f"covers. If your library sign-in there has lapsed, signing in again may get them.")
@@ -7319,6 +7346,9 @@ def main(argv=None):
     if argv and argv[0] == "cookies":
         from .get_cookies import main as cookies_main
         return cookies_main(argv[1:])
+    if argv and argv[0] == "fetchcookies":
+        from .get_cookies import main as cookies_main
+        return cookies_main(["setup"] + argv[1:])
 
     pre = argparse.ArgumentParser(add_help=False)
     pre.add_argument("--json", action="store_true")
@@ -7410,7 +7440,7 @@ def _main(argv=None, json_out=None):
         description="Download PDFs from DOIs using multiple fallback sources.",
         epilog=(
             "Institutional access:\n"
-            "  fetchpdf cookies setup    # sign in through your library\n"
+            "  fetchpdf fetchcookies    # sign in through your library\n"
             "  fetchpdf cookies --help   # all cookie commands\n\n"
             "Examples:\n"
             "  fetchpdf papers.csv -o ./pdfs                      # batch from CSV\n"
@@ -7824,7 +7854,7 @@ def _main(argv=None, json_out=None):
         metavar="FILE",
         default=None,
         help="Institutional access from this cookie file instead of the one "
-             "`fetchpdf cookies setup` configured. Without it, access is used only "
+             "`fetchpdf fetchcookies` configured. Without it, access is used only "
              "if setup has been run. Covers publishers whose PDF URL follows "
              "from the DOI (Wiley, T&F, SAGE, Springer, Royal Society, Hogrefe, "
              "INFORMS); tried after the fast open-access lookups. Only cookies "
@@ -7890,7 +7920,7 @@ def _main(argv=None, json_out=None):
     if args.cookies_only:
         if args.no_cookies or not _institutional.active_cookies_file():
             print("❌ --cookies-only: institutional access is not set up. Run "
-                  "`fetchpdf cookies setup` (or pass --cookies FILE).")
+                  "`fetchpdf fetchcookies` (or pass --cookies FILE).")
             return 2
         _institutional.set_cookies_only(True)
         # "Alone" includes the grey last resorts an installed fetchpdf_grey adds.
@@ -8295,7 +8325,9 @@ def _main(argv=None, json_out=None):
             except Exception as e:
                 print(f"\n📎 supplementary pass failed: {str(e)[:200]}")
 
-        if args.pull_figures:
+        # Only for a record that was retrieved: figures with no article to go
+        # with them are an empty `_figures/` and manifest in a failed record.
+        if args.pull_figures and result:
             # A separate call above fetch_pdf, for the same reason the
             # supplementary pass is one: the tiered engine re-enters the chain
             # at T5 with a temporary save_path, and a flag threaded through
@@ -8337,6 +8369,8 @@ def _main(argv=None, json_out=None):
                         print(f"\n🖨️  render: {outcome['error']}")
                 except Exception as e:
                     print(f"\n🖨️  render failed: {str(e)[:200]}")
+            elif not result:
+                print("\n🖨️  no XML could be retrieved for this record, so nothing to render")
             else:
                 print("\n🖨️  no .xml was kept for this record, so nothing to render "
                       "(add --get-xml-or-html)")
@@ -8391,7 +8425,8 @@ def _main(argv=None, json_out=None):
             return 0
         else:
             _prune_empty_record_dir(made_record_dir)
-            print(f"\n❌ Failed to download PDF for {args.doi}")
+            wanted = "XML" if args.xml_only else ("XML or HTML" if args.xml_html_only else "PDF")
+            print(f"\n❌ Failed to download {wanted} for {args.doi}")
             _emit_json(json_out, args.doi, resolved_identifier, None,
                        JSON_STATUS_FAILED, identity=identity,
                        reasons=reasons or ["no source produced a usable artifact"],

{fetchpdf-0.1.3 → fetchpdf-0.1.5}/fetchpdf/get_cookies.py

@@ -1,12 +1,12 @@
 """fetchpdf cookies: set up institutional access for fetchpdf, once.
 
-    fetchpdf cookies setup        # one-time wizard
+    fetchpdf fetchcookies        # one-time wizard
     fetchpdf cookies check        # which publishers your sessions currently open
     fetchpdf cookies refresh      # re-open sign-in tabs for the ones that lapsed
     fetchpdf cookies disable      # stop using institutional access
 
 Institutional access lets fetchpdf download a paper your library subscribes to
-when no open-access copy exists. It is OFF until you run ``fetchpdf cookies setup``.
+when no open-access copy exists. It is OFF until you run ``fetchpdf fetchcookies``.
 
 How it works. Each publisher keeps your library sign-in as a cookie on its own
 site (wiley.com, tandfonline.com, ...). The wizard opens one subscription
@@ -378,7 +378,7 @@ def cmd_setup(args) -> int:
         import browser_cookie3  # noqa: F401
     except ImportError:
         print("  A required dependency is missing: browser_cookie3.\n"
-              "  Run pip install 'browser_cookie3>=0.19', then run fetchpdf cookies setup again.")
+              "  Run pip install 'browser_cookie3>=0.19', then run fetchpdf fetchcookies again.")
         return 2
 
     # 1. Library
@@ -443,7 +443,7 @@ def cmd_setup(args) -> int:
 
     if not any(st == "ok" for st in status.values()):
         print("  No publisher served a PDF, so institutional access is NOT turned on.\n"
-              "  Check you can open a PDF in your browser, then run fetchpdf cookies setup again.")
+              "  Check you can open a PDF in your browser, then run fetchpdf fetchcookies again.")
         return 1
 
     cfg["publishers"] = status
@@ -463,7 +463,7 @@ def cmd_setup(args) -> int:
 def _require_config() -> Optional[dict]:
     cfg = inst.load_access_config()
     if not cfg:
-        print("Institutional access is not set up. Run:  fetchpdf cookies setup")
+        print("Institutional access is not set up. Run:  fetchpdf fetchcookies")
     return cfg
 
 
@@ -516,7 +516,7 @@ def cmd_disable(args) -> int:
         return 0
     cfg["enabled"] = False
     _write_private_json(ACCESS_CONFIG, cfg)
-    print(f"Institutional access is OFF. Turn it back on with: fetchpdf cookies setup")
+    print(f"Institutional access is OFF. Turn it back on with: fetchpdf fetchcookies")
     return 0