Scientific paper search, enrichment, download, and management
Drift inferred · capture-to-capture
No drift recorded — single capability capture; advisories appear once its surface changes.
transport stdio counts 0 tools · 0 res
· 0 prompts
permission surface via code analysis
no tools enumerated yet for this server.
prompt-surface
shipped agent-instruction files + hidden-content / dangerous-code findings —
quoted from the analyzed source
analyzed commit c7d7dcd · analyzer v17 · 2d ago
skills & prompt files 1
evidence-backed
findings quoted directly from the published source artifact — not inferred
filesystem 91
- fs ywatanabe1989-scitex-scholar-c7d7dcd/scripts/download_neurovista_pdfs.py :29
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_cli_main.py :28
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_mcp/handlers.py :15
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_mcp_server.py :71
from pathlib import Path as _Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_utils/bibtex/_parse_bibtex.py :25
with open(bibtex_path, "r", encoding="utf-8") as f: - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_utils/papers_utils.py :68
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_utils/validation/validate_library_dois.py :17
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/auth/core/BrowserAuthenticator.py :395
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/auth/providers/EZProxyAuthenticator.py :26
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/auth/providers/ShibbolethAuthenticator.py :21
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/auth/session/AuthCacheManager.py :24
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/auth/sso/BaseSSOAutomator.py :181
with open(session_file, "w") as f: - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/browser/ScholarBrowserManager.py :20
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/citation_graph/builder.py :8
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/citation_graph/database.py :11
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/citation_graph/example.py :10
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/_doi_operations.py :4
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/_library_index.py :7
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/_materialize.py :17
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/_project_tree.py :10
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/download_pdf.py :103
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/handlers/bibtex_handler.py :7
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/handlers/doi_handler.py :7
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/handlers/project_handler.py :7
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/open_browser.py :26
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/open_browser_auto.py :20
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/open_browser_monitored.py :17
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/config/ScholarConfig.py :17
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/config/core/_PathManager.py :21
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/config/core/_path_helpers.py :20
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/Papers.py :23
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/Scholar.py :17
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/_mixins/_library_handlers.py :14
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/_mixins/_loaders.py :14
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/_mixins/_pdf_download.py :15
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/_mixins/_project_handlers.py :14
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/_mixins/_savers.py :13
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/_mixins/_services.py :13
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/journal_normalizer.py :36
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/oa_cache.py :17
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/ensure_workspace.py :7
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/gui/_app.py :4
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/impact_factor/jcr/ImpactFactorJCREngine.py :38
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/impact_factor/jcr/build_database.py :37
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/integration/base.py :10
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/integration/zotero/_attachment_resolver.py :14
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/integration/zotero/_diff_handler.py :126
with open(metadata_file) as f: - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/integration/zotero/_export_handler.py :8
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/integration/zotero/_import_handler.py :6
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/integration/zotero/exporter.py :14
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/integration/zotero/local_migrator.py :24
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/integration/zotero/local_reader.py :20
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/integration/zotero/migration_report.py :7
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/jobs/_Job.py :15
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/jobs/_JobManager.py :14
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/jobs/_errors.py :18
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/jobs/_executors.py :252
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/local_dbs/export.py :14
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/mcp_server.py :39
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/metadata_engines/ScholarEngine.py :83
with open(self.cache_file, "r") as f: - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/migration/_connected_papers.py :10
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_download/ScholarPDFDownloader.py :11
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_download/_cli.py :10
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_download/strategies/chrome_pdf_viewer.py :15
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_download/strategies/direct_download.py :15
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_download/strategies/manual_download_fallback.py :14
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_download/strategies/manual_download_utils.py :25
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_download/strategies/open_access_download.py :11
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_download/strategies/response_body.py :16
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_highlight/_blocks.py :8
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_highlight/_cli.py :13
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_highlight/highlighter.py :18
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pipelines/ScholarPipelineBibTeX.py :31
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pipelines/_single_steps.py :9
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/BibTeXHandler.py :13
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/PaperIO.py :44
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/ScholarLibrary.py :14
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_BibTeXValidator.py :12
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_DeduplicationManager.py :6
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_LibraryCacheManager.py :17
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_LibraryManager.py :27
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_library_audit.py :18
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_library_dedupe.py :27
import shutil - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_library_index.py :41
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_mixins/_bibtex_handlers.py :12
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_mixins/_library_operations.py :14
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_mixins/_paper_saving.py :144
with open(master_metadata_file) as file_: - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_mixins/_resolution.py :38
with open(metadata_file) as file_: - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_mixins/_storage_helpers.py :38
with open(metadata_file) as f: - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_mixins/_symlink_handlers.py :13
from pathlib import Path - fs ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_project_reconcile.py :20
from pathlib import Path
shell / exec 5
- shell ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_cli_main.py :1613
import subprocess - shell ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_mcp/job_handlers.py :15
import subprocess - shell ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_utils/cleanup/_cleanup_scholar_processes.py :29
import subprocess - shell ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/browser/ScholarBrowserManager.py :17
import subprocess - shell ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/handlers/project_handler.py :22
import subprocess
network 26
- net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_utils/validation/DOIValidator.py :23
import requests - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/auth/gateway/_OpenURLResolver.py :17
from urllib.parse import quote - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/auth/providers/EZProxyAuthenticator.py :28
from urllib.parse import quote, urlparse - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/auth/providers/ShibbolethAuthenticator.py :23
from urllib.parse import urlparse - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/browser/utils/wait_redirects.py :27
from urllib.parse import urlparse - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/cli/_url_utils.py :9
from urllib.parse import urlparse - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/journal_normalizer.py :39
import aiohttp - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/oa_cache.py :20
import aiohttp - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/core/open_access.py :22
import aiohttp - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/metadata_engines/individual/ArXivEngine.py :19
import requests - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/metadata_engines/individual/SemanticScholarEngine.py :17
import requests - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/metadata_engines/individual/URLDOIEngine.py :20
import requests - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/metadata_engines/individual/_BaseDOIEngine.py :30
import requests - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/metadata_engines/individual/_s2_batch.py :13
import requests - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/metadata_engines/utils/_PubMedConverter.py :30
import aiohttp - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_download/strategies/manual_download_utils.py :78
from urllib.parse import urlparse - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/pdf_download/strategies/open_access_download.py :14
import aiohttp - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/search_engines/individual/ArXivSearchEngine.py :18
from urllib.parse import quote - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/url_finder/strategies/find_pdf_urls_by_navigation.py :22
from urllib.parse import urljoin - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/url_finder/translators/_individual/acm_digital_library.py :26
from urllib.parse import quote - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/url_finder/translators/_individual/austlii_and_nzlii.py :9
from urllib.parse import urlparse - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/url_finder/translators/_individual/crossref_rest.py :23
from urllib.parse import quote - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/url_finder/translators/_individual/jstor.py :19
import urllib.parse - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/url_finder/translators/_individual/orcid.py :22
import httpx - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/url_finder/translators/_individual/pubmed.py :19
import httpx - net ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/url_finder/translators/_individual/springer.py :13
from urllib.parse import quote
secrets 1
- secrets ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/auth/providers/ShibbolethAuthenticator.py :434
self.password = os.environ.get("SCITEX_SCHOLAR_SHIBBOLETH_PASSWORD")
database 6
- db ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/citation_graph/database.py :9
import sqlite3 - db ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/impact_factor/ImpactFactorEngine.py :69
import sqlite3 - db ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/impact_factor/jcr/ImpactFactorJCREngine.py :48
from sqlalchemy import Column, Float, String, func - db ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/integration/zotero/_attachment_resolver.py :12
import sqlite3 - db ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/integration/zotero/local_reader.py :19
import sqlite3 - db ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/storage/_library_index.py :39
import sqlite3
tool registrations 2
- scholar_skills_list ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_mcp_server.py :61
- scholar_skills_get ywatanabe1989-scitex-scholar-c7d7dcd/src/scitex_scholar/_mcp_server.py :80
declared dependencies 2
- click@>=8.0
- mcp@*