PDF Management Guide¶

Complete guide for PDF downloading, viewing, and organization

Table of Contents¶

PDF Sources
Download Methods
Configuration
Organization
Troubleshooting

PDF Sources¶

Lixplore attempts PDF download in this order:

PubMed Central (PMC) - Open access biomedical articles
arXiv - Preprints (physics, CS, math)
DOI Resolution - Publisher links via Unpaywall
SciHub - Fallback (optional, user-configured)

Source Comparison¶

Source	Coverage	Speed	Reliability	Legal Status
PMC	Biomedical OA	Fast	High	✓ Legal
arXiv	STEM preprints	Fast	High	✓ Legal
Unpaywall	All OA	Medium	High	✓ Legal
SciHub	Paywalled	Slow	Variable	⚠️ Gray area

Download Methods¶

Method 1: Show PDF Links (No Download)¶

Display clickable links without downloading:

lixplore -x -q "neural networks" -m 15 --show-pdf-links

Output:

[1] Deep Learning with Neural Networks
    Open PDF → https://arxiv.org/pdf/2103.12345.pdf

[2] Convolutional Neural Networks for Image Recognition
    Open PDF → https://arxiv.org/pdf/2104.67890.pdf

Best for: - Quick preview - Selective download - Modern terminals (iTerm2, GNOME Terminal, Windows Terminal)

Method 2: Download All PDFs¶

Download PDFs for all search results:

lixplore -J -q "open access research" -m 10 --download-pdf

Process:

Checking for open access PDFs...
[1/10] Downloading: paper1.pdf... ✓
[2/10] Downloading: paper2.pdf... ✓
[3/10] Not available: paper3
[4/10] Downloading: paper4.pdf... ✓
...
Downloaded 7/10 PDFs to ~/Lixplore_PDFs/

Method 3: Download Specific Articles¶

Download PDFs for selected articles only:

lixplore -P -q "cancer" -m 30 --download-pdf --pdf-numbers 1 3 5 7

Best for: - After reviewing abstracts - High-priority articles only - Bandwidth conservation

Method 4: With SciHub Fallback¶

Use SciHub for articles not available via legal sources:

# Setup SciHub mirror (one-time)
lixplore --set-scihub-mirror https://sci-hub.se

# Download with SciHub fallback
lixplore -P -q "research" -m 10 --download-pdf --use-scihub

⚠️ Disclaimer: Use SciHub responsibly. Check your institution's policies.

Configuration¶

Check PDF Directory¶

lixplore --show-pdf-dir

Output:

PDF download directory: /home/user/Lixplore_PDFs/
Total PDFs downloaded: 342

Set SciHub Mirror¶

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

Active Mirrors (as of Dec 2024): - https://sci-hub.se - https://sci-hub.st - https://sci-hub.ru - https://sci-hub.tw

Note: Mirrors change frequently. Check https://sci-hub.now.sh for current list.

Change PDF Directory¶

Edit configuration file:

nano ~/.lixplore/config.json

{
  "pdf_download_dir": "/path/to/custom/directory"
}

Organization¶

Default Organization¶

~/Lixplore_PDFs/
├── paper_title_1.pdf
├── paper_title_2.pdf
├── paper_title_3.pdf
└── ...

Recommended Organization¶

By Topic:

# Create topic folders
mkdir -p ~/Lixplore_PDFs/Machine_Learning
mkdir -p ~/Lixplore_PDFs/Cancer_Research
mkdir -p ~/Lixplore_PDFs/Climate_Change

# Download to specific folder (manual move after download)
lixplore -x -q "machine learning" -m 20 --download-pdf
# Then: mv ~/Lixplore_PDFs/ml*.pdf ~/Lixplore_PDFs/Machine_Learning/

By Date:

# Create monthly folders
mkdir -p ~/Lixplore_PDFs/2024-12
mkdir -p ~/Lixplore_PDFs/2024-11

# Move downloaded PDFs by month
mv ~/Lixplore_PDFs/*.pdf ~/Lixplore_PDFs/2024-12/

By Project:

# Project-based organization
mkdir -p ~/Lixplore_PDFs/PhD_Chapter1
mkdir -p ~/Lixplore_PDFs/PhD_Chapter2
mkdir -p ~/Lixplore_PDFs/Grant_Proposal

# Download and organize
lixplore -P -q "methodology chapter1 topic" -m 15 --download-pdf
# Move to project folder

Complete Workflows¶

Workflow 1: Open Access Literature Review¶

# Step 1: Search open access sources
lixplore -J -q "public health interventions" -m 30 --show-pdf-links

# Step 2: Review abstracts and select
lixplore -J -q "public health interventions" -m 30 -a

# Step 3: Download selected PDFs
lixplore -J -q "public health interventions" -m 30 --download-pdf --pdf-numbers 1 3 5 8 12

# Step 4: Annotate
lixplore --annotate 1 --rating 5 --tags "important,read"

Workflow 2: arXiv Latest Papers¶

# Step 1: Get latest CS papers
lixplore -x -q "deep learning" -d 2024-12-01 2024-12-31 -m 20 --sort newest

# Step 2: Show PDF links (all arXiv papers have PDFs)
lixplore -x -q "deep learning" -d 2024-12-01 2024-12-31 -m 20 --show-pdf-links

# Step 3: Download all
lixplore -x -q "deep learning" -d 2024-12-01 2024-12-31 -m 20 --download-pdf

# Step 4: Organize
mv ~/Lixplore_PDFs/*.pdf ~/Papers/DeepLearning/Dec2024/

Workflow 3: Multi-Source with Selective Download¶

# Step 1: Comprehensive search
lixplore -A -q "cancer immunotherapy" -m 100 -D --sort newest

# Step 2: Review with abstracts
lixplore -A -q "cancer immunotherapy" -m 100 -D --sort newest -a

# Step 3: Annotate high-priority
lixplore --annotate 2 --priority high --tags "must-read"
lixplore --annotate 5 --priority high --tags "must-read"
lixplore --annotate 8 --priority high --tags "must-read"

# Step 4: Download PDFs for high-priority only
lixplore -A -q "cancer immunotherapy" -m 100 -D --download-pdf --pdf-numbers 2 5 8

# Step 5: Try SciHub for unavailable
lixplore -A -q "cancer immunotherapy" -m 100 -D --download-pdf --pdf-numbers 2 5 8 --use-scihub

Workflow 4: Systematic PDF Collection¶

# Comprehensive PDF collection for lit review
lixplore -s JX -q "machine learning healthcare" \
  -m 50 \
  -D \
  --sort newest \
  --download-pdf \
  -X xlsx \
  -o ml_healthcare_refs.xlsx

# Result: PDFs + Excel spreadsheet with metadata

PDF Naming¶

Default Naming Convention¶

ArticleTitle_FirstAuthor_Year.pdf

Examples:

Deep_Learning_LeCun_2015.pdf
CRISPR_Gene_Editing_Doudna_2012.pdf

Handle Long Titles¶

Long titles are truncated:

Very_Long_Article_Title_About_Machine_Learning_Applications_In_Healthcare_Smith_2024.pdf
↓
Very_Long_Article_Title_About_Mach..._Smith_2024.pdf

Handle Special Characters¶

Special characters removed:

"Machine Learning: A New Approach" → Machine_Learning_A_New_Approach.pdf

Integration with Reference Managers¶

Export PDFs + Metadata to Zotero¶

# Step 1: Download PDFs
lixplore -P -q "research" -m 20 --download-pdf

# Step 2: Export to Zotero with file attachments
lixplore -P -q "research" -m 20 --add-to-zotero

# Step 3: Manually attach PDFs in Zotero (if needed)

Export for Mendeley with PDF Paths¶

# Export RIS with PDF locations
lixplore -P -q "research" -m 20 --download-pdf --export-for-mendeley

Best Practices¶

1. Start with Open Access Sources¶

# DOAJ + arXiv = maximum PDF availability
lixplore -s JX -q "query" -m 30 --download-pdf

2. Use PDF Links for Preview¶

# Check availability first
lixplore -J -q "query" -m 20 --show-pdf-links

# Then download selected
lixplore -J -q "query" -m 20 --download-pdf --pdf-numbers 1 3 5

3. Organize Immediately¶

# Create organization system before mass download
mkdir -p ~/Papers/{Topic1,Topic2,Topic3}

# Download per topic
lixplore -P -q "topic1" -m 20 --download-pdf
mv ~/Lixplore_PDFs/*.pdf ~/Papers/Topic1/

4. Backup PDFs¶

# Regular backups
rsync -av ~/Lixplore_PDFs/ ~/Backups/PDFs/

# Cloud sync (Dropbox, Google Drive, etc.)
ln -s ~/Lixplore_PDFs ~/Dropbox/Research/PDFs

5. SciHub as Last Resort¶

# Try legal sources first
lixplore -P -q "research" -m 10 --download-pdf

# If many failed, then try SciHub
lixplore -P -q "research" -m 10 --download-pdf --use-scihub

Troubleshooting¶

Problem: No PDFs downloaded¶

Solution 1: Check source

# Use open access sources
lixplore -J -q "query" -m 10 --download-pdf  # DOAJ
lixplore -x -q "query" -m 10 --download-pdf  # arXiv

Solution 2: Try SciHub

lixplore --set-scihub-mirror https://sci-hub.se
lixplore -P -q "query" -m 10 --download-pdf --use-scihub

Problem: PDF download fails¶

Check internet connection:

ping arxiv.org
ping www.ncbi.nlm.nih.gov

Check PDF directory permissions:

ls -ld ~/Lixplore_PDFs/
chmod 755 ~/Lixplore_PDFs/

Problem: SciHub mirror not working¶

Update mirror:

# Try different mirrors
lixplore --set-scihub-mirror https://sci-hub.st
lixplore --set-scihub-mirror https://sci-hub.ru

Problem: PDF links not clickable¶

Requirements: - Modern terminal emulator - iTerm2 (macOS) - GNOME Terminal (Linux) - Windows Terminal (Windows)

Alternative:

# Copy URL manually
lixplore -J -q "query" -m 10 --show-pdf-links
# Copy-paste URL to browser

PDF Statistics¶

Check Download Stats¶

lixplore --show-pdf-dir

Count PDFs by Topic¶

# Count PDFs in organized folders
ls ~/Papers/MachineLearning/*.pdf | wc -l
ls ~/Papers/Genetics/*.pdf | wc -l

Find Duplicate PDFs¶

# Find files with same size
find ~/Lixplore_PDFs -type f -exec ls -l {} \; | sort -k5 -n | uniq -D -w 50

Last Updated: 2024-12-28