Export & Output Flags¶

Complete documentation for all export and output flags

Table of Contents¶

Export Formats
Selection & Fields
Profiles & Templates
PDF Downloads
Reference Managers

Export Formats¶

`-X, --export`¶

Description: Export results in specified format(s).

Formats: csv, xlsx, json, bibtex, ris, enw, endnote, xml

Syntax:

lixplore -q "QUERY" -X FORMAT [-o FILE]
lixplore -q "QUERY" -X FORMAT1,FORMAT2,FORMAT3  # Multiple

Examples¶

Example 1: CSV Export

lixplore -P -q "cancer" -m 30 -X csv

Example 2: Excel with Custom Name

lixplore -P -q "diabetes" -m 50 -X xlsx -o my_research.xlsx

Example 3: BibTeX for LaTeX

lixplore -C -q "quantum physics" -m 40 -X bibtex -o refs.bib

Example 4: EndNote Tagged

lixplore -P -q "neuroscience" -m 60 -X enw -o brain.enw

Example 5: Multiple Formats

lixplore -A -q "AI" -m 100 -D -X csv,ris,bibtex

Export Locations: - CSV: exports/csv/ - Excel: exports/excel/ - JSON: exports/json/ - BibTeX: exports/bibtex/ - RIS: exports/ris/ - EndNote: exports/endnote_tagged/

`-o, --output`¶

Description: Custom output filename.

Syntax:

lixplore -q "QUERY" -X FORMAT -o FILENAME

Examples¶

Example 1: Named Export

lixplore -P -q "COVID-19" -m 50 -X xlsx -o covid_research.xlsx

Example 2: Multi-Format Base Name

lixplore -A -q "genetics" -m 100 -D -X csv,ris -o genetics_papers
# Creates: genetics_papers.csv, genetics_papers.ris

`--zip`¶

Description: Compress exported files to ZIP format.

Syntax:

lixplore -q "QUERY" -X FORMAT --zip

Examples¶

Example 1: Compressed CSV

lixplore -P -q "cancer" -m 200 -X csv --zip

Example 2: Multi-Format ZIP

lixplore -A -q "research" -m 300 -D -X csv,ris,bibtex --zip

Selection & Fields¶

`-S, --select`¶

Description: Select specific articles to export.

Patterns: numbers (1 3 5), ranges (1-10), keywords (odd, even, first:N, last:N)

Syntax:

lixplore -q "QUERY" -S SELECTION -X FORMAT

Examples¶

Example 1: Specific Numbers

lixplore -P -q "cancer" -m 50 -S 1 3 5 7 -X xlsx

Example 2: Range

lixplore -P -q "diabetes" -m 100 -S 10-20 -X csv

Example 3: Odd Articles

lixplore -P -q "genetics" -m 80 -S odd -X enw

Example 4: Even Articles

lixplore -A -q "AI" -m 100 -D -S even -X bibtex

Example 5: First N

lixplore -A -q "climate" -m 200 -D --sort newest -S first:30 -X xlsx

Example 6: Last N

lixplore -P -q "history" -m 100 --sort oldest -S last:10 -X csv

Example 7: Top Results

lixplore -P -q "COVID-19" -m 100 -S top:25 -X enw

Example 8: Mixed Patterns

lixplore -P -q "research" -m 100 -S 1 3 5-10 odd -X xlsx

`--export-fields`¶

Description: Select specific metadata fields to export.

Fields: title, authors, abstract, journal, year, doi, url, source

Syntax:

lixplore -q "QUERY" -X FORMAT --export-fields FIELD1 FIELD2...

Examples¶

Example 1: Essential Fields Only

lixplore -P -q "cancer" -m 50 -X csv --export-fields title authors year doi

Example 2: Citation Fields

lixplore -C -q "research" -m 30 -X xlsx --export-fields title authors journal year

Example 3: Minimal Export

lixplore -P -q "diabetes" -m 100 -X csv --export-fields title doi

Profiles & Templates¶

`--save-profile`¶

Description: Save current export settings as reusable profile.

Syntax:

lixplore -q "QUERY" -X FORMAT [OPTIONS] --save-profile NAME

Examples¶

Example 1: Save Export Profile

lixplore -P -q "test" -m 10 -X xlsx --export-fields title authors year doi --save-profile my_workflow

Example 2: Complex Profile

lixplore -A -q "test" -m 50 -D --sort newest -X csv,ris --save-profile comprehensive_search

`--load-profile`¶

Description: Load previously saved export profile.

Syntax:

lixplore -q "QUERY" --load-profile NAME

Examples¶

Example 1: Use Saved Profile

lixplore -P -q "new research" --load-profile my_workflow

`--list-profiles`¶

Description: List all saved export profiles.

Syntax:

lixplore --list-profiles

`--delete-profile`¶

Description: Delete saved export profile.

Syntax:

lixplore --delete-profile NAME

`--template`¶

Description: Use predefined export template.

Templates: nature, science, ieee

Syntax:

lixplore -q "QUERY" --template NAME

Examples¶

Example 1: Nature Format

lixplore -P -q "biology" -m 30 --template nature

Example 2: IEEE Format

lixplore -x -q "engineering" -m 40 --template ieee

`--list-templates`¶

Description: List available export templates.

Syntax:

lixplore --list-templates

Citations¶

`-c, --citations`¶

Description: Export as formatted citations.

Styles: apa, mla, chicago, ieee

Syntax:

lixplore -q "QUERY" -c STYLE

Examples¶

Example 1: APA Style

lixplore -P -q "psychology" -m 20 -c apa

Example 2: MLA Style

lixplore -P -q "literature" -m 15 -c mla

Example 3: Chicago Style

lixplore -C -q "history" -m 25 -c chicago

Example 4: IEEE Style

lixplore -x -q "engineering" -m 30 -c ieee

PDF Downloads¶

`--download-pdf`¶

Description: Download full-text PDFs for search results.

Sources: PMC, arXiv, DOI resolution, SciHub (optional)

Syntax:

lixplore -q "QUERY" --download-pdf [--use-scihub]

Examples¶

Example 1: Download All PDFs

lixplore -x -q "machine learning" -m 10 --download-pdf

Example 2: Specific Articles

lixplore -J -q "open access" -m 20 --download-pdf --pdf-numbers 1 3 5

Example 3: With SciHub Fallback

lixplore -P -q "cancer" -m 15 --download-pdf --use-scihub

PDF Directory: ~/Lixplore_PDFs/

`--pdf-numbers`¶

Description: Download PDFs only for specific article numbers.

Syntax:

lixplore -q "QUERY" --download-pdf --pdf-numbers N1 N2 N3...

Examples¶

Example 1: Selected PDFs

lixplore -P -q "genetics" -m 30 --download-pdf --pdf-numbers 1 5 10 15

`--use-scihub`¶

Description: Use SciHub as fallback for PDF downloads.

Syntax:

lixplore -q "QUERY" --download-pdf --use-scihub

Setup Required:

lixplore --set-scihub-mirror https://sci-hub.se

`--set-scihub-mirror`¶

Description: Configure SciHub mirror URL.

Syntax:

lixplore --set-scihub-mirror URL

Example¶

lixplore --set-scihub-mirror https://sci-hub.se

`--show-pdf-dir`¶

Description: Show PDF download directory location.

Syntax:

lixplore --show-pdf-dir

Reference Managers¶

`--add-to-zotero`¶

Description: Add search results to Zotero library.

Prerequisites: Zotero API configuration

Syntax:

lixplore -q "QUERY" --add-to-zotero [--zotero-collection KEY]

Examples¶

Example 1: Add to Library

lixplore -P -q "genetics" -m 20 --add-to-zotero

Example 2: Add to Collection

lixplore -P -q "cancer" -m 30 --add-to-zotero --zotero-collection ABC123DEF

`--configure-zotero`¶

Description: Configure Zotero API access.

Syntax:

lixplore --configure-zotero API_KEY USER_ID

Setup¶

Step 1: Get API Key - Visit: https://www.zotero.org/settings/keys - Create new private key

Step 2: Configure

lixplore --configure-zotero YOUR_API_KEY YOUR_USER_ID

`--show-zotero-collections`¶

Description: List Zotero collections with their keys.

Syntax:

lixplore --show-zotero-collections

`--export-for-mendeley`¶

Description: Export results as RIS for Mendeley import.

Syntax:

lixplore -q "QUERY" --export-for-mendeley

Example¶

lixplore -P -q "biology" -m 50 --export-for-mendeley

Import to Mendeley: 1. Open Mendeley Desktop 2. File → Import → RIS file 3. Select exported file

Best Practices¶

1. Enrich Before Export¶

lixplore -A -q "research" -m 100 -D --enrich -X bibtex

2. Use Selection for Large Sets¶

lixplore -P -q "cancer" -m 500 --sort newest -S first:50 -X xlsx

3. Multi-Format for Flexibility¶

lixplore -A -q "genetics" -m 100 -D -X csv,ris,bibtex

4. Save Profiles for Repeated Workflows¶

# Save once
lixplore -P -q "test" -X xlsx --export-fields title authors year --save-profile quick_export

# Reuse many times
lixplore -P -q "different query" --load-profile quick_export

5. Organize with Output Names¶

lixplore -P -q "COVID-19" -m 100 --sort newest -S first:30 -X xlsx -o covid_latest_30.xlsx

Last Updated: 2024-12-28

Export & Output Flags¶

Table of Contents¶

Export Formats¶

-X, --export¶

Examples¶

-o, --output¶

Examples¶

--zip¶

Examples¶

Selection & Fields¶

-S, --select¶

Examples¶

--export-fields¶

Examples¶

Profiles & Templates¶

--save-profile¶

Examples¶

--load-profile¶

Examples¶

--list-profiles¶

--delete-profile¶

--template¶

Examples¶

--list-templates¶

Citations¶

-c, --citations¶

Examples¶

PDF Downloads¶

--download-pdf¶

Examples¶

--pdf-numbers¶

Examples¶

--use-scihub¶

--set-scihub-mirror¶

Example¶

--show-pdf-dir¶

Reference Managers¶

--add-to-zotero¶

Examples¶

--configure-zotero¶

Setup¶

--show-zotero-collections¶

--export-for-mendeley¶

Example¶

Best Practices¶

1. Enrich Before Export¶

2. Use Selection for Large Sets¶

3. Multi-Format for Flexibility¶

4. Save Profiles for Repeated Workflows¶

5. Organize with Output Names¶

`-X, --export`¶

`-o, --output`¶

`--zip`¶

`-S, --select`¶

`--export-fields`¶

`--save-profile`¶

`--load-profile`¶

`--list-profiles`¶

`--delete-profile`¶

`--template`¶

`--list-templates`¶

`-c, --citations`¶

`--download-pdf`¶

`--pdf-numbers`¶

`--use-scihub`¶

`--set-scihub-mirror`¶

`--show-pdf-dir`¶

`--add-to-zotero`¶

`--configure-zotero`¶

`--show-zotero-collections`¶

`--export-for-mendeley`¶