Utility Flags¶

Complete documentation for utility and configuration flags

Table of Contents¶

History & Cache
Profile Management
Template Management
Custom API Management
PDF Configuration
Reference Manager Configuration
Help & Examples

History & Cache¶

`-H, --history`¶

Description: Show search history.

Syntax:

lixplore -H
lixplore --history

Type: Boolean flag

Storage: ~/.lixplore_history.json

History Includes: - Timestamp - Query string - Sources searched - Result count

Examples¶

Example 1: View History

lixplore --history

Output:

SEARCH HISTORY (15 searches)

[1] 2024-12-28 14:30:15 (2 hours ago)
    Query: machine learning
    Sources: PubMed, Crossref
    Results: 95

[2] 2024-12-27 09:15:42 (1 day ago)
    Query: COVID-19 AND vaccine
    Sources: All sources
    Results: 247

`--refresh`¶

Description: Bypass cache and fetch fresh results.

Syntax:

lixplore [SOURCE] -q "QUERY" --refresh

Type: Boolean flag

Cache Duration: 7 days (default)

Examples¶

Example 1: Fresh Search

lixplore -P -q "breaking news topic" -m 10 --refresh

Example 2: Update Cached Search

lixplore -A -q "COVID-19" -m 50 --refresh -D

Profile Management¶

`--save-profile`¶

Description: Save current export settings as reusable profile.

Syntax:

lixplore [OPTIONS] --save-profile NAME

Storage: ~/.lixplore/profiles/

Examples¶

Example 1: Save Profile

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

`--load-profile`¶

Description: Load previously saved export profile.

Syntax:

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

Examples¶

Example 1: Load Profile

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

`--list-profiles`¶

Description: List all saved export profiles.

Syntax:

lixplore --list-profiles

Examples¶

Example 1: View Profiles

lixplore --list-profiles

Output:

Saved export profiles:
  • quick_export
      Format: xlsx
      Fields: title, authors, year
  • comprehensive
      Format: csv,ris,bibtex
      Citation: apa

`--delete-profile`¶

Description: Delete saved export profile.

Syntax:

lixplore --delete-profile NAME

Examples¶

Example 1: Delete Profile

lixplore --delete-profile old_profile

Template Management¶

`--list-templates`¶

Description: List all available export templates.

Syntax:

lixplore --list-templates

Built-in Templates: nature, science, ieee

Examples¶

Example 1: View Templates

lixplore --list-templates

Output:

Available export templates:
  • nature
      Format: xlsx
      Description: Nature journal format
  • science
      Format: csv
      Description: Science journal format
  • ieee
      Format: bibtex
      Description: IEEE citation format

Custom API Management¶

`--list-custom-apis`¶

Description: List all configured custom API sources.

Syntax:

lixplore --list-custom-apis

Examples¶

Example 1: View Custom APIs

lixplore --list-custom-apis

Output:

Configured custom API sources:
  • springer
      Springer Nature API
      Requires authentication
  • base
      Bielefeld Academic Search Engine

`--create-api-examples`¶

Description: Create example custom API configurations.

Syntax:

lixplore --create-api-examples

Creates: ~/.lixplore/custom_apis.json with templates

Examples¶

Example 1: Setup API Templates

lixplore --create-api-examples

Output:

Created example API configurations in ~/.lixplore/custom_apis.json
Example APIs: Springer, BASE, IEEE (templates only)
Edit the file and add your API keys to enable.

Configuration File:

{
  "springer": {
    "name": "Springer",
    "base_url": "https://api.springernature.com/meta/v2/json",
    "api_key_param": "api_key",
    "query_param": "q",
    "requires_auth": true,
    "api_key": "YOUR_KEY_HERE"
  }
}

PDF Configuration¶

`--set-scihub-mirror`¶

Description: Configure SciHub mirror URL for PDF downloads.

Syntax:

lixplore --set-scihub-mirror URL

Storage: ~/.lixplore/config.json

Examples¶

Example 1: Configure SciHub

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

Example 2: Update Mirror

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

Common Mirrors: - https://sci-hub.se - https://sci-hub.st - https://sci-hub.ru

Disclaimer: Use SciHub responsibly and at your own discretion. Check your institution's policies.

`--show-pdf-dir`¶

Description: Show PDF download directory location and statistics.

Syntax:

lixplore --show-pdf-dir

PDF Directory: ~/Lixplore_PDFs/

Examples¶

Example 1: Check PDF Directory

lixplore --show-pdf-dir

Output:

PDF download directory: /home/user/Lixplore_PDFs/
Total PDFs downloaded: 127

Reference Manager Configuration¶

`--configure-zotero`¶

Description: Configure Zotero API access credentials.

Syntax:

lixplore --configure-zotero API_KEY USER_ID

Storage: ~/.lixplore/zotero_config.json

Setup Process¶

Step 1: Get API Credentials 1. Visit: https://www.zotero.org/settings/keys 2. Create new private key with read/write access 3. Note your User ID (numeric, in settings)

Step 2: Configure Lixplore

lixplore --configure-zotero YOUR_API_KEY YOUR_USER_ID

Examples¶

Example 1: Initial Setup

lixplore --configure-zotero ABC123DEF456GHI789 1234567

Output:

Zotero API configured successfully!
API Key: ABC123...789
User ID: 1234567

Test connection...
✓ Connection successful
✓ Library accessible (142 items)

You can now use:
  --add-to-zotero
  --show-zotero-collections

`--show-zotero-collections`¶

Description: List Zotero collections with their keys.

Syntax:

lixplore --show-zotero-collections

Requires: Zotero API configuration

Examples¶

Example 1: List Collections

lixplore --show-zotero-collections

Output:

Zotero Collections:

[1] My Library (root)
    Key: N/A (use without --zotero-collection)

[2] PhD Research
    Key: ABC123DEF
    Items: 45

[3] Literature Review
    Key: GHI789JKL
    Items: 127

[4] Methodology Papers
    Key: MNO456PQR
    Items: 23

Use collection key with:
  lixplore -P -q "query" --add-to-zotero --zotero-collection ABC123DEF

Help & Examples¶

`--examples`¶

Description: Show quick examples (tldr-style) and exit.

Syntax:

lixplore --examples

Type: Boolean flag

Examples¶

Example 1: View Examples

lixplore --examples

Output:

LIXPLORE - Quick Examples

BASIC SEARCH
  Search PubMed:
    $ lixplore -P -q "cancer treatment" -m 10

MULTI-SOURCE SEARCH
  Search all sources with deduplication:
    $ lixplore -A -q "COVID-19" -m 50 -D

EXPORT
  Export to Excel:
    $ lixplore -P -q "diabetes" -m 20 -X xlsx

[... more examples ...]

Configuration Files¶

File Locations¶

~/.lixplore/
├── config.json              # General configuration
├── profiles/                # Saved export profiles
│   ├── quick_export.json
│   └── comprehensive.json
├── custom_apis.json         # Custom API configurations
├── zotero_config.json       # Zotero credentials
└── templates/               # Custom export templates
    └── custom_template.json

~/.lixplore_cache.json       # Search results cache
~/.lixplore_history.json     # Search history
~/.lixplore_annotations.json # Article annotations

Manual Configuration¶

Edit Configuration:

# Main config
nano ~/.lixplore/config.json

# Custom APIs
nano ~/.lixplore/custom_apis.json

# Zotero
nano ~/.lixplore/zotero_config.json

Clear Cache:

rm ~/.lixplore_cache.json

Clear History:

rm ~/.lixplore_history.json

Backup Annotations:

cp ~/.lixplore_annotations.json ~/backup/annotations_backup.json

Best Practices¶

1. Regular Profile Management¶

# Save commonly used workflows
lixplore -P -q "test" -X xlsx --export-fields title authors year --save-profile standard_export

# List profiles periodically
lixplore --list-profiles

# Clean up unused profiles
lixplore --delete-profile old_profile

2. API Key Security¶

DO: - Store API keys in configuration files - Use environment variables for sensitive keys - Restrict file permissions: chmod 600 ~/.lixplore/zotero_config.json

DON'T: - Share configuration files publicly - Commit API keys to version control - Use shared credentials

3. Cache Management¶

# Use cache for speed (default)
lixplore -P -q "query" -m 20

# Bypass cache when needed
lixplore -P -q "latest news" -m 10 --refresh

# Review from cache
lixplore -R 1 2 3  # Uses cached results

4. History Tracking¶

# Review recent searches
lixplore --history

# Reproduce previous search
# Copy query from history and re-run
lixplore -P -q "exact query from history" -m 50

Troubleshooting¶

Problem: Zotero connection fails¶

Solution: Verify credentials

# Reconfigure
lixplore --configure-zotero NEW_API_KEY NEW_USER_ID

# Test connection
lixplore --show-zotero-collections

Problem: Custom API not working¶

Solution: Check configuration

# List configured APIs
lixplore --list-custom-apis

# Recreate examples
lixplore --create-api-examples

# Edit and verify
nano ~/.lixplore/custom_apis.json

Problem: Cache issues¶

Solution: Clear and refresh

# Remove cache
rm ~/.lixplore_cache.json

# Force fresh search
lixplore -P -q "query" -m 20 --refresh

Problem: Profile not loading¶

Solution: List and verify

# List profiles
lixplore --list-profiles

# Check profile exists
ls ~/.lixplore/profiles/

# Delete and recreate
lixplore --delete-profile problematic_profile
lixplore -P -q "test" -X xlsx --save-profile new_profile

Last Updated: 2024-12-28

Utility Flags¶

Table of Contents¶

History & Cache¶

-H, --history¶

Examples¶

--refresh¶

Examples¶

Profile Management¶

--save-profile¶

Examples¶

--load-profile¶

Examples¶

--list-profiles¶

Examples¶

--delete-profile¶

Examples¶

Template Management¶

--list-templates¶

Examples¶

Custom API Management¶

--list-custom-apis¶

Examples¶

--create-api-examples¶

Examples¶

PDF Configuration¶

--set-scihub-mirror¶

Examples¶

--show-pdf-dir¶

Examples¶

Reference Manager Configuration¶

--configure-zotero¶

Setup Process¶

Examples¶

--show-zotero-collections¶

Examples¶

Help & Examples¶

--examples¶

Examples¶

Configuration Files¶

File Locations¶

Manual Configuration¶

Best Practices¶

1. Regular Profile Management¶

2. API Key Security¶

3. Cache Management¶

4. History Tracking¶

Troubleshooting¶

Problem: Zotero connection fails¶

Problem: Custom API not working¶

Problem: Cache issues¶

Problem: Profile not loading¶

`-H, --history`¶

`--refresh`¶

`--save-profile`¶

`--load-profile`¶

`--list-profiles`¶

`--delete-profile`¶

`--list-templates`¶

`--list-custom-apis`¶

`--create-api-examples`¶

`--set-scihub-mirror`¶

`--show-pdf-dir`¶

`--configure-zotero`¶

`--show-zotero-collections`¶

`--examples`¶