Lixplore Command-Line Flags - Complete Reference¶

Comprehensive overview of all 95+ command-line flags organized by category

Table of Contents¶

Quick Index
Summary Table
Flag Categories
Common Flag Combinations
Best Practices

Quick Index¶

Source Selection (8 flags)¶

-P, --pubmed - Search PubMed
-C, --crossref - Search Crossref
-J, --doaj - Search DOAJ
-E, --europepmc - Search EuropePMC
-x, --arxiv - Search arXiv
-A, --all - Search all sources
-s, --sources - Combined source codes
--custom-api - Custom API integration

Search Parameters (4 flags)¶

-q, --query - Search query with Boolean operators
-au, --author - Search by author name
-DOI, --doi - Search by DOI
-m, --max_results - Maximum results per source

Filtering & Processing (7 flags)¶

-d, --date - Date range filter
-D, --deduplicate - Remove duplicates
--dedup-threshold - Similarity threshold
--dedup-keep - Which duplicate to keep
--dedup-merge - Merge duplicate metadata
--sort - Sort results
--enrich - Enrich metadata

Display Options (9 flags)¶

-a, --abstract - Show abstracts
-i, --interactive - Simple TUI mode
-N, --number - View article details
-R, --review - Review in terminal
--stat - Statistics dashboard
--stat-top - Top N in stats
-p, --page - Page number
--page-size - Results per page
--show-pdf-links - Display PDF links

Export & Output (15 flags)¶

-X, --export - Export format(s)
-o, --output - Output filename
-S, --select - Select articles
--export-fields - Select fields
--zip - Compress exports
-c, --citations - Citation style
--save-profile - Save settings
--load-profile - Load settings
--template - Use template
--download-pdf - Download PDFs
--pdf-numbers - PDF article numbers
--use-scihub - Use SciHub
--add-to-zotero - Add to Zotero
--zotero-collection - Zotero collection
--export-for-mendeley - Mendeley export

Annotations (13 flags)¶

--annotate - Annotate article
--comment - Add comment
--rating - Rate article
--tags - Add tags
--read-status - Set read status
--priority - Set priority
--show-annotation - Show annotation
--list-annotations - List all
--filter-annotations - Filter annotations
--search-annotations - Search annotations
--export-annotations - Export annotations
--annotation-stats - Annotation statistics
--delete-annotation - Delete annotation

Interactive Modes (3 flags)¶

--tui - Enhanced TUI mode
--shell - Shell mode (deprecated)
--wizard - Wizard mode (deprecated)

Utility (12 flags)¶

-H, --history - Search history
--refresh - Bypass cache
--examples - Show examples
--list-profiles - List profiles
--delete-profile - Delete profile
--list-templates - List templates
--list-custom-apis - List custom APIs
--create-api-examples - Create API examples
--set-scihub-mirror - Configure SciHub
--show-pdf-dir - Show PDF directory
--configure-zotero - Configure Zotero
--show-zotero-collections - Show collections

Summary Table¶

Category	Flags	Purpose
Source Selection	8	Choose databases to search
Search Parameters	4	Define search criteria
Filtering	7	Filter and process results
Display	9	Control result display
Export	15	Export and save results
Annotations	13	Organize and rate articles
Interactive	3	Interactive modes
Utility	12	Configuration and helpers
TOTAL	71	All available flags

Flag Categories¶

1. Source Selection Flags¶

Choose which academic databases to search. Multiple sources can be combined.

Available Sources: - PubMed (biomedical literature) - Crossref (scholarly works with DOIs) - DOAJ (open access journals) - EuropePMC (European literature) - arXiv (preprints) - Custom APIs (user-configured)

See: source-flags.md for complete documentation

2. Search Parameter Flags¶

Define what to search for and how many results to retrieve.

Search Types: - Query search with Boolean operators - Author search - DOI lookup

See: search-flags.md for complete documentation

3. Filtering & Processing Flags¶

Process and refine search results after retrieval.

Features: - Date range filtering - Duplicate removal (5 strategies) - Result sorting (5 methods) - Metadata enrichment

See: filter-flags.md for complete documentation

4. Display Option Flags¶

Control how results are displayed in the terminal.

Features: - Abstract display - Interactive browsing - Pagination - Statistics dashboard - PDF link display

See: display-flags.md for complete documentation

5. Export & Output Flags¶

Export results in various formats and manage output.

Export Formats: CSV, Excel, JSON, BibTeX, RIS, EndNote, XML Citations: APA, MLA, Chicago, IEEE

See: export-flags.md for complete documentation

6. Annotation Flags¶

Rate, tag, comment, and organize your research library.

Features: - 5-star rating system - Comments and notes - Tag organization - Read status tracking - Priority levels

See: annotation-flags.md for complete documentation

7. Interactive Mode Flags¶

Launch interactive interfaces for easier usage.

Modes: - Enhanced TUI (primary interface - recommended) - Shell mode (persistent session - deprecated) - Wizard mode (guided workflows - deprecated)

Note: Shell and wizard modes are deprecated in favor of the enhanced TUI.

See: interactive-flags.md for complete documentation

8. Utility Flags¶

Configuration, management, and helper commands.

Features: - Search history - Profile management - Template management - API configuration

See: utility-flags.md for complete documentation

Common Flag Combinations¶

Basic Search + Export¶

lixplore -P -q "cancer" -m 20 -X xlsx

Flags: -P (PubMed), -q (query), -m (max results), -X (export)

Multi-Source with Deduplication¶

lixplore -A -q "COVID-19" -m 50 -D --sort newest -X csv

Flags: -A (all sources), -q, -m, -D (deduplicate), --sort, -X

Advanced Search with Filters¶

lixplore -s PX -q "machine learning" -d 2020-01-01 2024-12-31 -m 30 -D strict --enrich -X xlsx

Flags: -s (sources), -q, -d (date), -m, -D, --enrich, -X

Review Workflow¶

# Step 1: Search
lixplore -P -q "diabetes" -m 20 -a

# Step 2: Review specific articles
lixplore -R 3 5 8

# Step 3: Annotate
lixplore --annotate 3 --rating 5 --tags "important,methodology"

Smart Selection + Export¶

lixplore -P -q "research" -m 100 --sort newest -S first:20 -X enw,csv

Flags: -P, -q, -m, --sort, -S (select), -X (multi-format)

Statistics Dashboard¶

lixplore -A -q "artificial intelligence" -m 200 -D --stat --stat-top 15

Flags: -A, -q, -m, -D, --stat, --stat-top

PDF Download Workflow¶

lixplore -x -q "neural networks" -m 10 --download-pdf --pdf-numbers 1 3 5

Flags: -x (arXiv), -q, -m, --download-pdf, --pdf-numbers

Reference Manager Integration¶

lixplore -P -q "genetics" -m 30 -D --add-to-zotero --zotero-collection ABC123

Flags: -P, -q, -m, -D, --add-to-zotero, --zotero-collection

Best Practices¶

1. Always Use Deduplication with Multiple Sources¶

# Good
lixplore -A -q "query" -m 50 -D

# Not recommended (will have duplicates)
lixplore -A -q "query" -m 50

2. Specify Max Results Per Source¶

# Clear and efficient
lixplore -s PCE -q "query" -m 30  # 30 per source

# Unclear (uses default 10)
lixplore -s PCE -q "query"

3. Use Sorting for Better Organization¶

# Latest research first
lixplore -P -q "COVID-19" -m 100 --sort newest

# Historical perspective
lixplore -P -q "diabetes" -m 100 --sort oldest

4. Combine Selection with Export¶

# Export only top results
lixplore -P -q "AI" -m 100 --sort newest -S first:20 -X xlsx

5. Save Profiles for Repeated Workflows¶

# Save settings
lixplore -P -q "query" -m 50 -X xlsx --export-fields title authors year doi --save-profile my_workflow

# Reuse later
lixplore -P -q "different query" --load-profile my_workflow

6. Use Enrichment for Complete Metadata¶

# Enrich from all APIs
lixplore -A -q "query" -m 50 -D --enrich -X bibtex

7. Cache Management¶

# Bypass cache for fresh results
lixplore -P -q "breaking news" -m 10 --refresh

# Use cached results (faster)
lixplore -R 1 2 3  # Review from cache

8. Annotation Workflow¶

# Search and review
lixplore -P -q "topic" -m 20 -a

# Annotate important articles
lixplore --annotate 5 --rating 5 --tags "important,cite" --comment "Excellent methodology"

# Filter and export annotations
lixplore --filter-annotations "min_rating=4,priority=high"
lixplore --export-annotations markdown

Flag Syntax Rules¶

Boolean Flags (no value needed)¶

-P, -A, -D, -a, --stat, --zip, --refresh

Usage: Just add the flag

lixplore -P -q "query" -D

Value Flags (require value)¶

-q TEXT, -m NUMBER, -X FORMAT, -o FILE

Usage: Flag followed by value

lixplore -P -q "cancer" -m 20 -X xlsx

Multi-Value Flags (accept multiple values)¶

-d FROM TO, -N 1 2 3, -S odd even 1-10, --export-fields title authors year

Usage: Flag followed by multiple values

lixplore -P -q "query" -N 1 2 3 -S first:10 last:5

Optional Value Flags (work with or without value)¶

-D [STRATEGY], --enrich [API...]

Usage:

lixplore -A -q "query" -D           # Uses default strategy
lixplore -A -q "query" -D strict    # Uses strict strategy

Performance Tips¶

1. Optimize Search Scope¶

# Faster (single source)
lixplore -P -q "query" -m 20

# Slower (all sources)
lixplore -A -q "query" -m 20

2. Use Pagination for Large Results¶

# View first page
lixplore -P -q "query" -m 100 -p 1

# View next page
lixplore -P -q "query" -m 100 -p 2

3. Limit Enrichment Scope¶

# Enrich from specific API only
lixplore -P -q "query" -m 50 --enrich crossref

# Enrich from all (slower)
lixplore -P -q "query" -m 50 --enrich

4. Export Selected Articles Only¶

# Export all (slow for large sets)
lixplore -P -q "query" -m 500 -X xlsx

# Export selection (faster)
lixplore -P -q "query" -m 500 -S first:50 -X xlsx

Troubleshooting¶

Common Issues¶

Problem: No results found

# Solution: Try broader query or different source
lixplore -A -q "cancer"  # Search all sources

Problem: Too many duplicates

# Solution: Use deduplication
lixplore -A -q "query" -m 50 -D

Problem: Missing metadata

# Solution: Use enrichment
lixplore -P -q "query" -m 20 --enrich

Problem: Export file not found

# Solution: Check exports/ folder organization
# CSV files: exports/csv/
# Excel: exports/excel/
# etc.

Getting Help¶

Built-in Help¶

# Quick examples
lixplore --examples

# Complete help
lixplore --help

# Man page
man lixplore

Detailed Documentation¶

Version Information¶

Lixplore Version: 2.0+ Total Flags: 71 Documentation Updated: 2024-12-28

For updates and more information, visit the GitHub repository.