Pubmed Downloader
PubMed paper downloader implementation.
PubmedDownloader
Bases: BasePaperDownloader
PubMed-specific implementation of paper downloader.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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__init__(config)
Initialize PubMed downloader with configuration.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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_add_service_identifier(entry, identifier)
Add PMID and PubMed-specific fields to entry.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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_fetch_pdf_url_with_fallbacks(pmcid)
Fetch PDF URL from OA API with comprehensive fallback strategies.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
pmcid
|
str
|
PMC ID (e.g., 'PMC1234567') |
required |
Returns:
Type | Description |
---|---|
str
|
PDF URL string (empty if all strategies fail) |
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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_get_paper_identifier_info(paper)
Get PubMed-specific identifier info for paper summary.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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_try_direct_pmc_url(pmcid)
Try direct PMC PDF URL pattern.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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_try_europe_pmc(pmcid)
Try Europe PMC service for PDF.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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_try_oa_api(pmcid)
Try to get PDF URL from official OA API.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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_try_pmc_page_scraping(pmcid)
Try scraping PMC page for PDF meta tag.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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construct_pdf_url(metadata, identifier)
Construct PDF URL using multiple fallback strategies.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
metadata
|
dict[str, Any]
|
JSON response from ID converter |
required |
identifier
|
str
|
PMID |
required |
Returns:
Type | Description |
---|---|
str
|
PDF URL string (empty if no PDF available) |
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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extract_paper_metadata(metadata, identifier, pdf_result)
Extract structured metadata from PubMed ID converter response.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
metadata
|
dict[str, Any]
|
JSON response from ID converter |
required |
identifier
|
str
|
PMID |
required |
pdf_result
|
tuple[str, str] | None
|
Tuple of (temp_file_path, filename) if PDF downloaded |
required |
Returns:
Type | Description |
---|---|
dict[str, Any]
|
Standardized paper metadata dictionary |
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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fetch_metadata(identifier)
Fetch paper metadata from PubMed ID Converter API.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
identifier
|
str
|
PMID (e.g., '12345678') |
required |
Returns:
Type | Description |
---|---|
dict[str, Any]
|
JSON response from PMC ID Converter API |
Raises:
Type | Description |
---|---|
RequestException
|
If API call fails |
RuntimeError
|
If no records found in response |
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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get_default_filename(identifier)
Generate default filename for PubMed paper.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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get_identifier_name()
Return identifier display name.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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get_service_name()
Return service name.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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get_snippet(abstract)
Override to handle PubMed-specific abstract placeholder.
Source code in aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py
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