Initial commit
This commit is contained in:
Zhongwei Li
185
skills/graphpad-prism-skill/SKILL.md
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skills/graphpad-prism-skill/SKILL.md
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---
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name: graphpad-prism
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description: Expert assistance with GraphPad Prism scientific graphing and statistics software, specializing in Prism scripting for automation, batch processing, and data analysis workflows.
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---
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# GraphPad Prism Scripting Expert
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You are an expert in GraphPad Prism scripting, helping users automate data analysis, create batch processing workflows, and integrate Prism with other scientific software tools.
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## When to Activate This Skill
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This skill should be used when users:
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- Ask about GraphPad Prism scripting or automation
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- Need help with Prism script syntax or commands
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- Want to batch process multiple data files in Prism
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- Need to integrate Prism with Excel, Python, or other tools
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- Ask about Prism file formats (.pzfx, .pzc, .pzm)
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- Want to export or import data programmatically
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- Need guidance on automating graph generation or analysis
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## Core Capabilities
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### 1. Prism Script Commands
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You have complete knowledge of all 71 Prism script commands including:
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- **Navigation**: GoTo command for navigating sheets/sections
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- **Loops**: ForEach, ForEachSheet for batch operations
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- **File Operations**: Open, Close, Save, Import, Export
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- **Data Operations**: Import, InsertData, Copy, Paste, SetInfo
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- **Graph Export**: 10+ formats (PDF, SVG, PNG, JPG, EPS, etc.)
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- **Text Output**: 14 W* commands for writing data to files
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- **Special Commands**: AnalyzeData, Regenerate, Beep, etc.
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Reference the `command_reference.md` file for quick command lookup with syntax.
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### 2. Understanding Limitations
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**Critical**: Prism scripts have important limitations you must communicate:
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- ❌ **No conditional logic** (no if/else statements)
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- ❌ **No variables** (except %N, %F, %S for output)
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- ❌ **Cannot read values** into variables for decisions
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- ❌ **Cannot control analysis** (defined in project file, not script)
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- ✅ Scripts are **purely procedural** - good for batch processing, not logic
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### 3. Workarounds for Reading Data
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When users need to read/query current Prism state, recommend the **PZFX XML approach**:
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**The PZFX Format**:
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- Prism files saved as .pzfx are plain XML
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- Data and info tables are readable/editable XML
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- Analysis results are encrypted (readable but not editable)
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- External programs (Python, R, etc.) can read/modify data
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- Prism auto-updates when file is reopened
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**Workflow**:
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1. Save Prism project as .pzfx
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2. Use external tool (Python/R/etc.) to parse XML
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3. Read data, make decisions, modify if needed
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4. Reopen in Prism - everything updates automatically
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Reference `reference/xml_schemas.md` for XML structure details.
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### 4. Platform-Specific Integration
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**macOS**:
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- AppleScript: Limited to launching scripts only (activate, open file, quit)
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- Automator: Can run scripts via Automator Actions
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- Recommendation: Use PZFX XML for data access, not AppleScript
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**Windows**:
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- Shell command: Launch scripts from batch files
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- OLE/ActiveX: More control, sequential execution
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- Desktop shortcuts: User-friendly script launching
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- Excel VBA integration: MacScript or OLE automation
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Reference the overview_and_running.md summary for detailed integration examples.
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## How to Help Users
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### For Script Writing Tasks:
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1. **Understand the goal**: What are they trying to automate?
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2. **Check feasibility**: Is it possible with Prism's limitations?
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3. **Suggest architecture**:
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- Template-based (recommended): Create Prism file with analysis, script just imports data
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- Script-driven: Script handles file operations, Prism handles analysis
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4. **Provide syntax**: Use exact command syntax from reference files
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5. **Include examples**: Adapt from script_examples.md
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6. **Warn about limitations**: No conditionals, no reading values, etc.
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### For Integration Tasks:
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1. **Identify platform**: macOS or Windows?
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2. **Choose method**:
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- Simple batch: Direct script execution
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- Excel integration: VBA examples in summaries
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- Complex logic: Recommend PZFX + external tool
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3. **Provide complete workflow**: Include synchronization patterns (done.txt polling)
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### For Troubleshooting:
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1. **Check syntax**: Commands are case-insensitive, but syntax matters
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2. **Verify navigation**: Always GoTo before operating on a sheet
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3. **Check file paths**: SetPath or full paths required
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4. **Review limitations**: Often users expect features that don't exist
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## Reference Files
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Access these files for detailed information:
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- `command_reference.md` - Quick command syntax reference (all 71 commands)
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- `reference/overview_and_running.md` - Overview & running scripts
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- `reference/script_examples.md` - 7 script examples
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- `reference/syntax_and_basics.md` - Syntax & basics
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- `reference/data_operations.md` - Data operations
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- `reference/advanced_features.md` - Advanced features
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- `reference/xml_schemas.md` - PZFX file format & XML schemas
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- `reference/reading_current_data.md` - How to query Prism state
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## Common Use Cases
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### Batch Import Multiple Files
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```prism
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SetPath "C:\Data\Experiment1"
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GoTo D
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ForEach *.csv
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GoTo %N
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Import
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Next
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```
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### Monte Carlo Simulation
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```prism
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ForEach 1000
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GoTo R, 1
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Regenerate
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AnalyzeData
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GoTo R, 2
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WCell 5, 3
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Next
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```
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### Export All Graphs
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```prism
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GoTo G
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ForEachSheet
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ExportPDF "%S.pdf"
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Next
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```
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### Template-Based Workflow
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```prism
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Open "template.pzfx"
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GoTo D, 1
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Import "newdata.csv"
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SaveAs "results_%F.pzfx"
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GoTo L, 1
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Print
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```
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## Key Syntax Reminders
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- **Numbering**: Sheets start at 1 (not 0), first data row is 1, X column is 0
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- **Sections**: D (data), I (info), R (results), G (graphs), L (layouts)
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- **Variables**: %N (loop number), %F (filename), %S (sheet name)
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- **Comments**: `//` single line or `/* */` multi-line
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- **Data blocks**: `<DATA>...</DATA>` for embedded data
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- **Arguments**: `[required]` `<optional>`
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## Important Notes
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1. **No nested loops**: Only one loop level allowed
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2. **No API**: Must use scripts or PZFX manipulation
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3. **Sequential only**: No parallel processing
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4. **Template recommended**: Store analysis in .pzm template, script imports data
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5. **Cross-platform**: Scripts work on both Mac/Windows but integration differs
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## Response Style
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- Be concise but complete
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- Always show actual syntax, not pseudocode
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- Warn about limitations upfront
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- Suggest workarounds when features don't exist
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- Provide complete, runnable examples
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- Reference partition summaries for complex scenarios
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192
skills/graphpad-prism-skill/command_reference.md
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192
skills/graphpad-prism-skill/command_reference.md
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# GraphPad Prism Script Commands - Quick Reference
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## All Commands
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**AnalyzeData** - Execute analysis
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**ApplyColorScheme** ["scheme name"]
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**Beep** - Play alert sound
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**ClearTable** <row>,<col>,<subcol>
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**Close** - Close current file
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**CloseOutput** - Close output file
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**CloseScriptDialog** - Close script dialog
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**Copy** - Copy entire sheet to clipboard
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**Copy** [#rows] [#columns] [first row] [first col] <first subcol>
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**CreateLayout** [#rows] [#columns] <orientation> <#StartingGraphIndex> <#Graphs>
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**CreateLog** - Create log file
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**DeleteAllDataSets** <CLEAR>
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**DuplicateDataTable** <CLEAR>
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**DuplicateFamily** [prepend_text] <CLEAR>
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**EndTable** - End table definition
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**Exit** - Exit Prism (Windows only)
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**ExportAllPDF** [filename] <mode> <CLEAR>
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**ExportBMP** [filename] <mode><resolution>
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**ExportEMF** [filename] <CLEAR> (Windows only)
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**ExportEPS** [filename] <mode> <CLEAR> <nofonts>
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**ExportJPG** [filename] <mode> <resolution>
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**ExportPDF** [filename] <mode> <CLEAR>
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**ExportPNG** [filename] <resolution><CLEAR>
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**ExportSVG** [filename] <CLEAR>
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**ExportTable** [filename] <ALL>
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**ExportTIF** [filename] <resolution> <mode> <compress or LZW> <CLEAR>
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**ExportWMF** [filename] <CLEAR> (Windows only)
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**ForEach** [# of loops]
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**ForEach** [filespec, i.e. "C:\data\DR*.txt"]
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**ForEachSheet** - Loop over all sheets in current section
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**GoTo** <section: D, I, R, G, or L>, <sheet#>, V<tab#>
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**GoTo** + (next sheet)
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**GoTo** - (previous sheet)
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**Import** <"filename">, <row>, <col>, <subcol>
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**ImportLink** <"filename">, <row>, <col>, <subcol>
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**InsertData** <row>, <col>, <subcol>
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**InsertDataLink** <row>, <col>, <subcol>
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**Next** - End loop iteration
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**NextRow** - Move to next table row
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**Open** ["filename"]
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**OpenOutput** ["filename"] ,<CLEAR>, <"delimiter">
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**Paste** - Paste from clipboard at current position
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**Paste** [first row] [first col] <first subcol>
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**Print** - Print current sheet
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**RecalcAll** - Recalculate all results
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**Regenerate** - Regenerate random numbers (Monte Carlo)
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**Save** <"filename">
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**SendToPP** - Send to PowerPoint (Windows only)
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**SendToWord** - Send to Word (Windows only)
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**SetAxisLimits** [which axis: X, Y, or Y2] <segment #> [Top/Bottom/Interval] [value]
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**SetAxisTitle** [which axis: X, Y, or Y2] ["new title"]
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**SetGraphTitle** ["new title"]
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**SetInfo** ["value"] [rownumber] <position: 0 (name) or 1 (value) or 2 (notes)>
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**SetPath** ["drive and folder path"]
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**SetProjectName** ["new name"]
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**SetScriptDialogTitle** ["dialog title"]
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**SetSheetTitle** [new_name] <K>
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**SetValueToInfo** [infotable #] [inforow#] [datarow] [datacol] <datasubcol>
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**SetYReplicates** [#]
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**Table** Prism [datatable number] <CLEAR>
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**Table** SQL [datasource] <table> <login> <password> <CLEAR>
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**Table** XML [filename]
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**WBlock** [row(s)] [column(s)] <row label> <;>
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**WCell** [row], [col], <subcol> <;&>
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**WCol** [row], <col>, <subcol><;&>
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**WDate** <;&>
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**WRow** [row], <col>, <subcol> <;&>
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**WSheet** <row, col, subcol><;&>
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**WTable** [column title] [row] [col] <subcol>
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**WTable** [column title] [text or %F or %N]
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**WText** <"text"> <;&>
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**WTBlock** [row(s)] [columns to include] <row label> <;>
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**WTCol** [row, col] <, subcolumn><;&>
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**WTitle** - Write sheet title
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**WTRow** [row] <,col, subcol> <;&>
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**WTSheet** <row, col, subcol><;&>
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**WVersion** - Write Prism version
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## Variables
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%N - Loop iteration number
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%F - Filename (without extension)
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%X - File extension
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%S - Sheet name
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%D - Date and time file was last saved
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%P - Prism project filename
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%% - Literal percent sign
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## Syntax Notation
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[required] - Required parameter
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<optional> - Optional parameter
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<;&> - Optional semicolon (continue on same line with tab) or ampersand (continue without tab)
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<;> - Optional semicolon (joins text without delimiter)
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CLEAR - Keyword to clear existing content
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## Section Codes
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D - Data tables
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I - Info tables
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R - Results tables
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G - Graphs
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L - Layouts
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## Column/Row Numbering
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Columns: -1 (Row titles), 0 (X column), 1 (Column A), 2 (Column B)...
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Rows: 0 or -1 (Column titles), 1 (First data row), 2 (Second data row)...
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## Data Block Syntax
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<DATA>
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value1 value2 value3
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value4 value5 value6
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</DATA>
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## Comments
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// Single line comment
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/* Multi-line comment */
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299
skills/graphpad-prism-skill/reference/Prism7XMLSchema.xml
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299
skills/graphpad-prism-skill/reference/Prism7XMLSchema.xml
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<?xml version="1.0"?>
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<Schema name="http://graphpad.com/prism/Prism.htm"
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xmlns:xs="http://www.w3.org/2001/XMLSchema"
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xmlns="urn:schemas-microsoft-com:xml-data"
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xmlns:dt="urn:schemas-microsoft-com:datatypes">
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<description>
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XML Schema for storing data and info tables from GraphPad Prism 7.0.
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Copyright 1992-2016 GraphPad Software, Inc.
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</description>
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<ElementType name="BR" content="empty" model="closed" />
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<ElementType name="br" content="empty" model="closed" />
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<ElementType name="b" />
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<ElementType name="B" />
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<ElementType name="i" />
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<ElementType name="I" />
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<ElementType name="u" />
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<ElementType name="U" />
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<ElementType name="sup" />
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<ElementType name="SUP" />
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<ElementType name="sub" />
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<ElementType name="SUB" />
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<AttributeType name="Selected" dt:type="boolean"/>
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<AttributeType name="Highlighted" dt:type="int"/>
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<ElementType name="Font" model="open">
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<AttributeType name="Face" />
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<AttributeType name="Color" />
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||||
<AttributeType name="Size" dt:type="int" />
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<attribute type="Face" />
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||||
<attribute type="Size" />
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||||
<attribute type="Color" />
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||||
</ElementType>
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||||
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||||
<ElementType name="TextAlign" model="open">
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<AttributeType name="align" dt:type="enumeration" dt:values="Left Center Right" required="yes"/>
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||||
<attribute type="align"/>
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||||
</ElementType>
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||||
|
||||
<AttributeType name="CreatedByProgram" />
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||||
<AttributeType name="CreatedByVersion" />
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||||
<AttributeType name="DateTime" dt:type="dateTime.tz" />
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||||
<AttributeType name="RegisteredTo" />
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||||
<AttributeType name="Login" />
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||||
<AttributeType name="MinVersion" />
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||||
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||||
<ElementType name="OriginalVersion" content="mixed" model="closed">
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||||
<attribute type="CreatedByProgram" />
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||||
<attribute type="CreatedByVersion" />
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||||
<attribute type="DateTime" />
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||||
<attribute type="RegisteredTo" />
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||||
<attribute type="Login" />
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||||
<attribute type="MinVersion" />
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||||
</ElementType>
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||||
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||||
<ElementType name="MostRecentVersion" content="mixed" model="closed">
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||||
<attribute type="CreatedByProgram" />
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||||
<attribute type="CreatedByVersion" />
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||||
<attribute type="DateTime" />
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||||
<attribute type="RegisteredTo" />
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||||
<attribute type="Login" />
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||||
<attribute type="MinVersion" />
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||||
</ElementType>
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||||
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||||
<ElementType name="Created" content="mixed" model="open">
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||||
<element type="OriginalVersion" maxOccurs="1" minOccurs="1"/>
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||||
<element type="MostRecentVersion" maxOccurs="1" minOccurs="0"/>
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||||
</ElementType>
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||||
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||||
<ElementType name="HelpTopic" content="mixed" model="open">
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||||
<AttributeType name="TopicID" dt:type="int"/>
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||||
<AttributeType name="TopicName" />
|
||||
<attribute type="TopicID" required = "no" />
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||||
<attribute type="TopicName" required = "no" />
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||||
</ElementType>
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||||
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||||
<ElementType name="DefGraphButton" model="open">
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||||
<AttributeType name="ButtonID" dt:type="int"/>
|
||||
<attribute type="ButtonID" required = "no" />
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||||
</ElementType>
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||||
|
||||
<AttributeType name="ID" dt:type="id" />
|
||||
|
||||
<ElementType name="WebLink" content = "mixed" model="closed">
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||||
<AttributeType name="ToolTip"/>
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||||
<AttributeType name="URL"/>
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||||
<AttributeType name="Flags" dt:type="int"/>
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||||
<attribute type="ToolTip" required="no"/>
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||||
<attribute type="URL" required = "yes"/>
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||||
<attribute type="Flags" default = "0" required="no"/>
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||||
</ElementType>
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||||
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||||
<ElementType name="FloatingNote" content="mixed" model="open">
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||||
<AttributeType name="Auto" dt:type="boolean"/>
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||||
<AttributeType name="Color" dt:type="enumeration" dt:values="Yellow Red Blue Green Purple Orange Gray" />
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||||
<AttributeType name="Left" dt:type="int" />
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||||
<AttributeType name="Top" dt:type="int" />
|
||||
<AttributeType name="Width" dt:type="int" />
|
||||
<AttributeType name="Height" dt:type="int" />
|
||||
<AttributeType name="ScrWidth" dt:type="int" />
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||||
<AttributeType name="ScrHeight" dt:type="int" />
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||||
<AttributeType name="ScrDPI" dt:type="int" />
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||||
<attribute type="ID" required="no" />
|
||||
<attribute type="Auto" required="no" />
|
||||
<attribute type="Left" />
|
||||
<attribute type="Top" />
|
||||
<attribute type="Width" />
|
||||
<attribute type="Height" />
|
||||
<attribute type="Color" />
|
||||
<attribute type="ScrWidth" />
|
||||
<attribute type="ScrHeight" />
|
||||
<attribute type="ScrDPI" />
|
||||
<element type="WebLink" minOccurs="0" maxOccurs="*" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="Ref" content="empty" model="closed">
|
||||
<AttributeType name="ID" dt:type="idref" />
|
||||
<attribute type="ID" />
|
||||
<attribute type="Selected" />
|
||||
</ElementType>
|
||||
|
||||
<AttributeType name="FileName" />
|
||||
|
||||
<ElementType name="InfoSequence" content="eltOnly" model="closed">
|
||||
<attribute type="Selected" />
|
||||
<element type="Ref" maxOccurs="*" minOccurs="0"/>
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="TableSequence" content="eltOnly" model="closed">
|
||||
<attribute type="Selected" />
|
||||
<element type="Ref" maxOccurs="*" minOccurs="0" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="Title" content="mixed" model="open" />
|
||||
<ElementType name="Name" content="mixed" model="open" />
|
||||
<ElementType name="Value" content="mixed" model="open" />
|
||||
<ElementType name="Notes" content="mixed" model="open" />
|
||||
|
||||
<ElementType name="Constant" content="eltOnly" model="closed">
|
||||
<element type="Name" maxOccurs="1" minOccurs="1" />
|
||||
<element type="Value" maxOccurs="1" minOccurs="0" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="Info" content="eltOnly" model="closed" order="many">
|
||||
<attribute type="ID" />
|
||||
<attribute type="Icon" />
|
||||
<attribute type="Highlighted" />
|
||||
<element type="Title" maxOccurs="1" minOccurs="0" />
|
||||
<element type="Notes" maxOccurs="1" minOccurs="0" />
|
||||
<element type="Constant" maxOccurs="*" minOccurs="0" />
|
||||
<element type="FloatingNote" maxOccurs="*" minOccurs="0" />
|
||||
</ElementType>
|
||||
|
||||
<AttributeType name="Version" />
|
||||
<AttributeType name="Width" />
|
||||
<AttributeType name="Decimals" />
|
||||
<AttributeType name="Subcolumns" />
|
||||
<AttributeType name="XFormat" dt:type="enumeration" dt:values="none text numbers error series date startenddate time" />
|
||||
<AttributeType name="YFormat" dt:type="enumeration" dt:values="replicates SD SE CV SDN SEN CVN low-high text upper-lower-limits" />
|
||||
<AttributeType name="Replicates" dt:type="int" />
|
||||
<AttributeType name="StartAt" />
|
||||
<AttributeType name="Interval" />
|
||||
<AttributeType name="Icon" />
|
||||
<AttributeType name="TableType" dt:type="enumeration" dt:values="Result Legacy XY OneWay TwoWay Contingency Survival PartsOfWhole" required="no"/>
|
||||
<AttributeType name="EVFormat" dt:type="enumeration" dt:values="Number AsteriskAfterNumber Blank" required="no"/>
|
||||
<AttributeType name="OwnSet" dt:type="int" />
|
||||
|
||||
<AttributeType name="Excluded" dt:type="boolean"/>
|
||||
<AttributeType name="Scientific" dt:type="boolean"/>
|
||||
|
||||
<ElementType name="d" content="mixed" model="open">
|
||||
<attribute type="Excluded" default="0" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="Subcolumn" content="eltOnly" model="closed">
|
||||
<element type="Title" maxOccurs="1" minOccurs="0" />
|
||||
<element type="d" maxOccurs="*" minOccurs="0" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="SubColumnTitles" content="eltOnly" model="closed">
|
||||
<attribute type="OwnSet" />
|
||||
<element type="Subcolumn" maxOccurs="*" minOccurs="0" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="RowTitlesColumn" content="eltOnly" model="closed">
|
||||
<attribute type="Width" />
|
||||
<element type="Subcolumn" maxOccurs="1" minOccurs="0" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="XColumn" content="eltOnly" model="closed">
|
||||
<attribute type="Width" />
|
||||
<attribute type="Decimals" />
|
||||
<attribute type="Subcolumns" />
|
||||
<attribute type="Scientific" />
|
||||
<element type="Title" maxOccurs="1" minOccurs="0" />
|
||||
<element type="Subcolumn" maxOccurs="*" minOccurs="0" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="XAdvancedColumn" content="eltOnly" model="closed">
|
||||
<attribute type="Version" />
|
||||
<attribute type="Width" />
|
||||
<attribute type="Decimals" />
|
||||
<attribute type="Subcolumns" />
|
||||
<attribute type="Scientific" />
|
||||
<element type="Title" maxOccurs="1" minOccurs="0" />
|
||||
<element type="Subcolumn" maxOccurs="*" minOccurs="0" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="YColumn" content="eltOnly" model="closed">
|
||||
<attribute type="Width" />
|
||||
<attribute type="Decimals" />
|
||||
<attribute type="Subcolumns" />
|
||||
<attribute type="Scientific" />
|
||||
<element type="Title" maxOccurs="1" minOccurs="0" />
|
||||
<element type="Subcolumn" maxOccurs="*" minOccurs="0" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="Table" content="eltOnly" model="closed" order="many">
|
||||
<attribute type="ID" />
|
||||
<attribute type="XFormat" />
|
||||
<attribute type="YFormat" />
|
||||
<attribute type="Replicates" />
|
||||
<attribute type="StartAt" />
|
||||
<attribute type="Interval" />
|
||||
<attribute type="Icon" />
|
||||
<attribute type="Highlighted" />
|
||||
<attribute type="TableType" />
|
||||
<attribute type="EVFormat" />
|
||||
<element type="Title" maxOccurs="1" minOccurs="0" />
|
||||
<element type="Info" maxOccurs="*" minOccurs="0" />
|
||||
<element type="SubColumnTitles" maxOccurs="1" minOccurs="0" />
|
||||
<element type="RowTitlesColumn" maxOccurs="1" minOccurs="0" />
|
||||
<element type="XColumn" maxOccurs="1" minOccurs="0" />
|
||||
<element type="XAdvancedColumn" maxOccurs="1" minOccurs="0" />
|
||||
<element type="YColumn" maxOccurs="*" minOccurs="0" />
|
||||
<element type="FloatingNote" maxOccurs="*" minOccurs="0" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="HugeTable" content="eltOnly" model="closed" order="many">
|
||||
<attribute type="ID" />
|
||||
<attribute type="XFormat" />
|
||||
<attribute type="YFormat" />
|
||||
<attribute type="Replicates" />
|
||||
<attribute type="StartAt" />
|
||||
<attribute type="Interval" />
|
||||
<attribute type="Icon" />
|
||||
<attribute type="Highlighted" />
|
||||
<attribute type="TableType" />
|
||||
<attribute type="EVFormat" />
|
||||
<element type="Title" maxOccurs="1" minOccurs="0" />
|
||||
<element type="Info" maxOccurs="*" minOccurs="0" />
|
||||
<element type="SubColumnTitles" maxOccurs="1" minOccurs="0" />
|
||||
<element type="RowTitlesColumn" maxOccurs="1" minOccurs="0" />
|
||||
<element type="XColumn" maxOccurs="1" minOccurs="0" />
|
||||
<element type="XAdvancedColumn" maxOccurs="1" minOccurs="0" />
|
||||
<element type="YColumn" maxOccurs="*" minOccurs="0" />
|
||||
<element type="FloatingNote" maxOccurs="*" minOccurs="0" />
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="Script" content="textOnly" model="closed">
|
||||
<AttributeType name="RunOnFileOpen" dt:type="enumeration" dt:values="0 no false 1 yes true"/>
|
||||
<AttributeType name="RunOnFileClose" dt:type="enumeration" dt:values="0 no false 1 yes true"/>
|
||||
<AttributeType name="Name"/>
|
||||
<attribute type="Name" required="yes"/>
|
||||
<attribute type="RunOnFileOpen" required="no" default="no"/>
|
||||
<attribute type="RunOnFileClose" required="no" default="no"/>
|
||||
</ElementType>
|
||||
|
||||
<ElementType name="TemplateDescription" content="textOnly" />
|
||||
|
||||
<ElementType name="Template" content="textOnly" dt:type="bin.base64">
|
||||
<attribute type="FileName" />
|
||||
</ElementType>
|
||||
|
||||
<AttributeType name="CreatedByPrismVersion" />
|
||||
<AttributeType name="LowestVersionThatCanOpen" />
|
||||
<AttributeType name="PrismXMLVersion" />
|
||||
|
||||
<ElementType name="GraphPadPrismFile" content="eltOnly" model="closed" order="many">
|
||||
<attribute type="CreatedByPrismVersion" required="no" />
|
||||
<attribute type="LowestVersionThatCanOpen" required="no" />
|
||||
<attribute type="PrismXMLVersion" required="yes" />
|
||||
|
||||
<element type="Created" maxOccurs="1" minOccurs="0" />
|
||||
<element type="HelpTopic" maxOccurs="1" minOccurs="0" />
|
||||
<element type="DefGraphButton" maxOccurs="1" minOccurs="0" />
|
||||
<element type="InfoSequence" maxOccurs="1" minOccurs="0" />
|
||||
<element type="TableSequence" maxOccurs="1" minOccurs="0" />
|
||||
<element type="Title" maxOccurs="1" minOccurs="0" />
|
||||
<element type="Info" maxOccurs="*" minOccurs="0" />
|
||||
<element type="Table" maxOccurs="*" minOccurs="0" />
|
||||
<element type="HugeTable" maxOccurs="*" minOccurs="0" />
|
||||
<element type="Script" maxOccurs="*" minOccurs="0" />
|
||||
<element type="TemplateDescription" maxOccurs="1" minOccurs="0" />
|
||||
<element type="Template" maxOccurs="1" minOccurs="0" />
|
||||
|
||||
</ElementType>
|
||||
|
||||
</Schema>
|
||||
419
skills/graphpad-prism-skill/reference/Prism7XMLStyleSheet.xml
Normal file
419
skills/graphpad-prism-skill/reference/Prism7XMLStyleSheet.xml
Normal file
@@ -0,0 +1,419 @@
|
||||
<?xml version="1.0" encoding="UTF-8" ?>
|
||||
<?xml-stylesheet type="text/xsl" href="#"?>
|
||||
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:dt="urn:schemas-microsoft-com:datatypes" xmlns:ps="http://graphpad.com/prism/Prism.htm" version="1.0">
|
||||
|
||||
<!--
|
||||
XML style sheet template for formatting data and info tables from GraphPad Prism 7.0.
|
||||
Copyright 1992-2016 GraphPad Software, Inc.
|
||||
-->
|
||||
|
||||
<xsl:output method="html" version="4.0" omit-xml-declaration = "yes"/>
|
||||
|
||||
|
||||
<GraphPadPrismFile xmlns="http://graphpad.com/prism/Prism.htm" PrismXMLVersion="5.0" />
|
||||
|
||||
|
||||
<xsl:template match="ps:Info">
|
||||
<a><xsl:attribute name="name"><xsl:value-of select="@ID"/></xsl:attribute></a>
|
||||
|
||||
<table border="0">
|
||||
<tr><td><xsl:apply-templates select="ps:Title"/> </td><td width="20"></td><td><b>Notes</b></td></tr>
|
||||
<tr><td valign="top">
|
||||
<table BORDER="1" CELLSPACING="0">
|
||||
<tr><th>Constant</th><th>Name</th></tr>
|
||||
<xsl:for-each select="ps:Constant">
|
||||
<tr>
|
||||
<td><xsl:apply-templates select="ps:Name"/> </td>
|
||||
<td><xsl:apply-templates select="ps:Value"/> </td>
|
||||
</tr>
|
||||
</xsl:for-each>
|
||||
</table>
|
||||
</td>
|
||||
<td width="20"> </td>
|
||||
<td valign="top">
|
||||
<xsl:apply-templates select="ps:Notes"/>
|
||||
</td></tr>
|
||||
</table>
|
||||
</xsl:template>
|
||||
|
||||
|
||||
<xsl:template match="ps:GraphPadPrismFile">
|
||||
<HTML>
|
||||
<BODY>
|
||||
|
||||
<xsl:variable name="Chars" select="'ABCDEFGHIJKLMNOPQRSTUVWXYZ'"/>
|
||||
<font color="#999999">
|
||||
|
||||
<p align="center">This file can be opened by <a href="http://www.graphpad.com">GraphPad</a> Prism (version
|
||||
<xsl:value-of select="@PrismXMLVersion"/> or later). </p></font><hr />
|
||||
This file contains <xsl:value-of select="count(ps:Table|ps:HugeTable)"/> data tables and
|
||||
<xsl:value-of select="count(ps:Info)+count(ps:Table|ps:HugeTable/ps:Info)"/> info tables:
|
||||
|
||||
<dir>
|
||||
<xsl:for-each select="ps:Info">
|
||||
<li>
|
||||
<a>
|
||||
<xsl:attribute name="href">#<xsl:value-of select="@ID"/></xsl:attribute>
|
||||
<xsl:apply-templates select="ps:Title"/>
|
||||
</a>
|
||||
</li>
|
||||
</xsl:for-each>
|
||||
<xsl:for-each select="ps:Table|ps:HugeTable">
|
||||
<li>
|
||||
<a>
|
||||
<xsl:attribute name="href">#<xsl:value-of select="@ID"/></xsl:attribute>
|
||||
<xsl:apply-templates select="ps:Title"/>
|
||||
</a>
|
||||
<dir>
|
||||
<xsl:for-each select="ps:Info">
|
||||
<li>
|
||||
<a>
|
||||
<xsl:attribute name="href">#<xsl:value-of select="@ID"/></xsl:attribute>
|
||||
<xsl:apply-templates select="ps:Title"/>
|
||||
</a>
|
||||
</li>
|
||||
</xsl:for-each>
|
||||
</dir>
|
||||
</li>
|
||||
</xsl:for-each>
|
||||
</dir>
|
||||
<hr/>
|
||||
|
||||
|
||||
<xsl:apply-templates select="ps:Info"/>
|
||||
|
||||
<br/>
|
||||
<hr/>
|
||||
<br/>
|
||||
|
||||
|
||||
<xsl:for-each select="ps:Table|ps:HugeTable">
|
||||
<xsl:apply-templates select="ps:Title"/>
|
||||
<a><xsl:attribute name="name"><xsl:value-of select="@ID"/></xsl:attribute></a>
|
||||
<xsl:variable name="width" select="100 div count (*/ps:Subcolumn)"/>
|
||||
|
||||
<xsl:variable name="xFormat" select="./@XFormat"/>
|
||||
<xsl:variable name="yFormat" select="./@YFormat"/>
|
||||
<xsl:variable name="nRepl" select = "./@replicates"/>
|
||||
<xsl:variable name="isXAdvancedColumn" select="boolean(($xFormat='date' or $xFormat='time' or $xFormat='startenddate') and count(ps:XAdvancedColumn) > 0)"/>
|
||||
<xsl:variable name="isXAdvancedSubcol" select="boolean(($xFormat='startenddate') or count(ps:XAdvancedColumn/ps:Subcolumn/ps:Title) > 0)"/>
|
||||
<xsl:variable name="isXSubcol" select="boolean(($xFormat='error' or count(ps:XColumn/ps:Subcolumn/ps:Title) > 0) and not ($isXAdvancedColumn))"/>
|
||||
<xsl:variable name="isYSubcol" select = "boolean(($yFormat='replicates'and ./@Replicates>1) or
|
||||
($yFormat!='text'and $yFormat!='replicates') or
|
||||
count(ps:YColumn/ps:Subcolumn/ps:Title)>0)"/>
|
||||
<xsl:variable name="isYSubColNameCustom" select="boolean($isYSubcol and count(ps:SubColumnTitles)>0)"/>
|
||||
<TABLE BORDER="1" CELLSPACING="0">
|
||||
<TR>
|
||||
<xsl:for-each select="ps:RowTitlesColumn">
|
||||
<TD align="center">
|
||||
<xsl:attribute name = "rowspan">
|
||||
<xsl:if test="$isXSubcol or $isXAdvancedSubcol or $isYSubcol">2</xsl:if>
|
||||
</xsl:attribute><BR/>
|
||||
</TD>
|
||||
</xsl:for-each>
|
||||
<xsl:if test="not ($isXAdvancedColumn)">
|
||||
<xsl:for-each select="ps:XColumn">
|
||||
<TD align="center">
|
||||
<xsl:attribute name = "rowspan">
|
||||
<xsl:if test="$isYSubcol and not($isXSubcol)">2</xsl:if>
|
||||
</xsl:attribute>
|
||||
<xsl:attribute name="colspan"><xsl:value-of select="./@Subcolumns"/></xsl:attribute>
|
||||
 
|
||||
<xsl:apply-templates select="ps:Title"/>
|
||||
<xsl:if test="count(ps:Title)=0 or ps:Title=''">X-Title</xsl:if>
|
||||
 
|
||||
</TD>
|
||||
</xsl:for-each>
|
||||
</xsl:if>
|
||||
<xsl:if test="$isXAdvancedColumn">
|
||||
<xsl:for-each select="ps:XAdvancedColumn">
|
||||
<TD align="center">
|
||||
<xsl:attribute name = "rowspan">
|
||||
<xsl:if test="$isYSubcol and not($isXAdvancedSubcol)">2</xsl:if>
|
||||
</xsl:attribute>
|
||||
<xsl:attribute name="colspan"><xsl:value-of select="./@Subcolumns"/></xsl:attribute>
|
||||
 
|
||||
<xsl:apply-templates select="ps:Title"/>
|
||||
<xsl:if test="count(ps:Title)=0 or ps:Title=''">X-Title</xsl:if>
|
||||
 
|
||||
</TD>
|
||||
</xsl:for-each>
|
||||
</xsl:if>
|
||||
<xsl:for-each select="ps:YColumn">
|
||||
<xsl:variable name='DefColName2' select="(position()-1) mod 26"/>
|
||||
<xsl:variable name='DefColName1' select="(position()-1-$DefColName2) div 26"/>
|
||||
<TD align="center">
|
||||
<xsl:attribute name="colspan"><xsl:value-of select="./@Subcolumns"/></xsl:attribute>
|
||||
<xsl:attribute name = "rowspan">
|
||||
<xsl:if test="($isXSubcol or $isXAdvancedSubcol) and not($isYSubcol)">2</xsl:if>
|
||||
</xsl:attribute>
|
||||
 
|
||||
<xsl:apply-templates select="ps:Title"/>
|
||||
<xsl:if test="count(ps:Title)=0 or ps:Title=''">
|
||||
<xsl:value-of select="'Data Set-'"/>
|
||||
<xsl:if test="$DefColName1 > 0">
|
||||
<xsl:value-of select="substring($Chars,$DefColName1,1)"/>
|
||||
</xsl:if>
|
||||
<xsl:value-of select="substring($Chars,$DefColName2+1,1)"/>
|
||||
</xsl:if>
|
||||
 
|
||||
</TD>
|
||||
</xsl:for-each>
|
||||
</TR>
|
||||
<xsl:if test="$isXSubcol or $isXAdvancedSubcol or $isYSubcol">
|
||||
<TR>
|
||||
<xsl:if test = "$isXSubcol">
|
||||
<xsl:for-each select="ps:XColumn">
|
||||
<xsl:for-each select="ps:Subcolumn">
|
||||
<TD align="center">
|
||||
 
|
||||
<xsl:apply-templates select="ps:Title"/>
|
||||
<xsl:if test="count(ps:Title)=0 or ps:Title=''">
|
||||
<xsl:choose>
|
||||
<xsl:when test="position()=1"><B>X</B></xsl:when>
|
||||
<xsl:when test="position()=2"><B>Err.Bar</B></xsl:when>
|
||||
</xsl:choose>
|
||||
</xsl:if>
|
||||
 
|
||||
</TD>
|
||||
</xsl:for-each>
|
||||
</xsl:for-each>
|
||||
</xsl:if>
|
||||
<xsl:if test = "$isXAdvancedSubcol">
|
||||
<xsl:for-each select="ps:XAdvancedColumn">
|
||||
<xsl:for-each select="ps:Subcolumn">
|
||||
<TD align="center">
|
||||
 
|
||||
<xsl:apply-templates select="ps:Title"/>
|
||||
<xsl:if test="count(ps:Title)=0 or ps:Title=''">
|
||||
<xsl:choose>
|
||||
<xsl:when test="position()=1"><B>Starting Date</B></xsl:when>
|
||||
<xsl:when test="position()=2"><B>Ending Date</B></xsl:when>
|
||||
</xsl:choose>
|
||||
</xsl:if>
|
||||
 
|
||||
</TD>
|
||||
</xsl:for-each>
|
||||
</xsl:for-each>
|
||||
</xsl:if>
|
||||
<xsl:if test = "$isYSubcol">
|
||||
<xsl:for-each select="ps:YColumn">
|
||||
<xsl:variable name='DefColName2' select="(position()-1) mod 26"/>
|
||||
<xsl:variable name='DefColName1' select="(position()-1-$DefColName2) div 26"/>
|
||||
<xsl:variable name="YColumnNdx" select="position()"/>
|
||||
<xsl:for-each select="ps:Subcolumn">
|
||||
<TD align="center">
|
||||
 
|
||||
<xsl:apply-templates select="ps:Title"/>
|
||||
<xsl:if test="count(ps:Title)=0 or ps:Title=''">
|
||||
<xsl:if test="$yFormat='replicates' or $yFormat='text'">
|
||||
<B>
|
||||
<xsl:if test="$DefColName1 > 0">
|
||||
<xsl:value-of select="substring($Chars,$DefColName1,1)"/>
|
||||
</xsl:if>
|
||||
<xsl:choose>
|
||||
<xsl:when test="$isYSubColNameCustom">
|
||||
<xsl:variable name="subColCustomNamePos" select="position()"/>
|
||||
<xsl:for-each select="../../ps:SubColumnTitles/ps:Subcolumn">
|
||||
<xsl:if test="position()=$subColCustomNamePos">
|
||||
<xsl:choose>
|
||||
<xsl:when test="../../ps:SubColumnTitles/@OwnSet='1'">
|
||||
<xsl:variable name="DItemsCount" select="count(./ps:d)"/>
|
||||
<xsl:choose>
|
||||
<xsl:when test="$DItemsCount<$YColumnNdx or ./ps:d[$YColumnNdx]=''">
|
||||
<xsl:value-of select="substring($Chars,$DefColName2+1,1)"/>:Y<xsl:value-of select="position()"/>
|
||||
</xsl:when>
|
||||
<xsl:otherwise>
|
||||
<xsl:apply-templates select="./ps:d[$YColumnNdx]"/>
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
</xsl:when>
|
||||
<xsl:when test="../../ps:SubColumnTitles/@OwnSet='0'">
|
||||
<xsl:variable name="DItemsCount" select="count(./ps:d)"/>
|
||||
<xsl:choose>
|
||||
<xsl:when test="$DItemsCount<1 or ./ps:d[1]=''">
|
||||
<xsl:value-of select="substring($Chars,$DefColName2+1,1)"/>:Y<xsl:value-of select="position()"/>
|
||||
</xsl:when>
|
||||
<xsl:otherwise>
|
||||
<xsl:apply-templates select="./ps:d[1]"/>
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
</xsl:when>
|
||||
<xsl:otherwise>
|
||||
<xsl:apply-templates select="ps:d"/>
|
||||
<xsl:if test="ps:d=''">
|
||||
<xsl:value-of select="substring($Chars,$DefColName2+1,1)"/>:Y<xsl:value-of select="position()"/>
|
||||
</xsl:if>
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
</xsl:if>
|
||||
</xsl:for-each>
|
||||
</xsl:when>
|
||||
<xsl:otherwise>
|
||||
<xsl:value-of select="substring($Chars,$DefColName2+1,1)"/>:Y<xsl:value-of select="position()"/>
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
</B>
|
||||
</xsl:if>
|
||||
<xsl:if test="$yFormat!='replicates' and $yFormat!='text'">
|
||||
<xsl:if test = "not($yFormat='replicates' or $yFormat='text')">
|
||||
<xsl:if test = "position()=1"><B>Mean</B></xsl:if>
|
||||
<xsl:if test = "position()!=1"> <xsl:choose>
|
||||
<xsl:when test="$yFormat='SD'">
|
||||
<B>SD</B>
|
||||
</xsl:when>
|
||||
<xsl:when test="$yFormat='SE'">
|
||||
<B>SEM</B>
|
||||
</xsl:when>
|
||||
<xsl:when test="$yFormat='CV'">
|
||||
<B>%CV</B>
|
||||
</xsl:when>
|
||||
<xsl:when test="$yFormat='SDN'">
|
||||
<xsl:if test="position()=2"><B>SD</B></xsl:if>
|
||||
<xsl:if test="position()=3"><B>N</B></xsl:if>
|
||||
</xsl:when>
|
||||
<xsl:when test="$yFormat='SEN'">
|
||||
<xsl:if test="position()=2"><B>SEM</B></xsl:if>
|
||||
<xsl:if test="position()=3"><B>N</B></xsl:if>
|
||||
</xsl:when>
|
||||
<xsl:when test="$yFormat='CVN'">
|
||||
<xsl:if test="position()=2"><B>%CV</B></xsl:if>
|
||||
<xsl:if test="position()=3"><B>N</B></xsl:if>
|
||||
</xsl:when>
|
||||
<xsl:when test="$yFormat='low-high'">
|
||||
<xsl:if test="position()=2"><B>+Error</B></xsl:if>
|
||||
<xsl:if test="position()=3"><B>-Error</B></xsl:if>
|
||||
</xsl:when>
|
||||
<xsl:when test="$yFormat='upper-lower-limits'">
|
||||
<xsl:if test="position()=2"><B>UpperLimit</B></xsl:if>
|
||||
<xsl:if test="position()=3"><B>LowerLimit</B></xsl:if>
|
||||
</xsl:when>
|
||||
</xsl:choose>
|
||||
</xsl:if>
|
||||
</xsl:if>
|
||||
</xsl:if>
|
||||
</xsl:if>
|
||||
 
|
||||
</TD>
|
||||
</xsl:for-each>
|
||||
</xsl:for-each>
|
||||
</xsl:if>
|
||||
</TR>
|
||||
</xsl:if>
|
||||
<TR>
|
||||
<xsl:for-each select="ps:RowTitlesColumn/ps:Subcolumn">
|
||||
<td valign="top" nowrap="1">
|
||||
<xsl:attribute name="width"><xsl:value-of select="$width"/>%</xsl:attribute>
|
||||
<xsl:apply-templates select="ps:d"/>
|
||||
<xsl:if test="count(ps:d)=0"><br/></xsl:if>
|
||||
</td>
|
||||
</xsl:for-each>
|
||||
<xsl:if test="not($isXAdvancedColumn)">
|
||||
<xsl:for-each select="ps:XColumn/ps:Subcolumn">
|
||||
<td valign="top" nowrap="1">
|
||||
<xsl:attribute name="width"><xsl:value-of select="$width"/>%</xsl:attribute>
|
||||
<xsl:apply-templates select="ps:d"/>
|
||||
<xsl:if test="count(ps:d)=0"><br/></xsl:if>
|
||||
</td>
|
||||
</xsl:for-each>
|
||||
</xsl:if>
|
||||
<xsl:if test="$isXAdvancedColumn">
|
||||
<xsl:for-each select="ps:XAdvancedColumn/ps:Subcolumn">
|
||||
<td valign="top" nowrap="1">
|
||||
<xsl:attribute name="width"><xsl:value-of select="$width"/>%</xsl:attribute>
|
||||
<xsl:apply-templates select="ps:d"/>
|
||||
<xsl:if test="count(ps:d)=0"><br/></xsl:if>
|
||||
</td>
|
||||
</xsl:for-each>
|
||||
</xsl:if>
|
||||
<xsl:for-each select="ps:YColumn/ps:Subcolumn">
|
||||
<td valign="top" nowrap="1">
|
||||
<xsl:attribute name="width"><xsl:value-of select="$width"/>%</xsl:attribute>
|
||||
<xsl:apply-templates select="ps:d"/>
|
||||
<xsl:if test="count(ps:d)=0"><br/></xsl:if>
|
||||
</td>
|
||||
</xsl:for-each>
|
||||
</TR>
|
||||
</TABLE>
|
||||
<br />
|
||||
<xsl:apply-templates select="ps:Info"/>
|
||||
<br/>
|
||||
<hr/>
|
||||
<br/>
|
||||
</xsl:for-each>
|
||||
|
||||
</BODY>
|
||||
</HTML>
|
||||
</xsl:template>
|
||||
|
||||
|
||||
<!--<xsl:template match="ps:d">
|
||||
<xsl:choose>
|
||||
<xsl:when test="@Excluded and string-length(text())" >
|
||||
<font color="#0000ee">
|
||||
<xsl:apply-templates select="node()"/>*
|
||||
</font>
|
||||
</xsl:when>
|
||||
<xsl:otherwise>
|
||||
<xsl:apply-templates select="node()"/>
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
<xsl:if test="position()!=last()"><br/></xsl:if>
|
||||
</xsl:template>-->
|
||||
|
||||
<xsl:template match="ps:d">
|
||||
<xsl:choose>
|
||||
<xsl:when test="@Excluded and string-length(text())">
|
||||
<xsl:choose>
|
||||
<xsl:when test="../../../@EVFormat='AsteriskAfterNumber'">
|
||||
<font color="#0000ee">
|
||||
<xsl:apply-templates select="node()"/>*
|
||||
</font>
|
||||
</xsl:when>
|
||||
<xsl:when test="../../../@EVFormat='Blank'">
|
||||
</xsl:when>
|
||||
<xsl:otherwise>
|
||||
<xsl:apply-templates select="node()"/>
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
</xsl:when>
|
||||
<xsl:otherwise>
|
||||
<xsl:apply-templates select="node()"/>
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
<xsl:if test="position()!=last()"><br/></xsl:if>
|
||||
</xsl:template>
|
||||
|
||||
|
||||
<xsl:template match="ps:Title">
|
||||
<b><xsl:apply-templates select="node()"/></b>
|
||||
</xsl:template>
|
||||
|
||||
|
||||
<xsl:template match="node()">
|
||||
<xsl:copy>
|
||||
<xsl:apply-templates select="node()"/>
|
||||
</xsl:copy>
|
||||
</xsl:template>
|
||||
|
||||
|
||||
<xsl:template match="ps:Font">
|
||||
<font>
|
||||
<xsl:if test="@Size">
|
||||
<xsl:attribute name="STYLE">font-size:<xsl:value-of select="@Size"/>pt</xsl:attribute>
|
||||
</xsl:if>
|
||||
<xsl:copy-of select="@*"/>
|
||||
<xsl:apply-templates select="node()"/>
|
||||
</font>
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template match="/">
|
||||
<HTML>
|
||||
<BODY>
|
||||
<xsl:apply-templates select="//ps:GraphPadPrismFile"/>
|
||||
</BODY>
|
||||
</HTML>
|
||||
|
||||
</xsl:template>
|
||||
|
||||
</xsl:stylesheet>
|
||||
205
skills/graphpad-prism-skill/reference/advanced_features.md
Normal file
205
skills/graphpad-prism-skill/reference/advanced_features.md
Normal file
@@ -0,0 +1,205 @@
|
||||
# GraphPad Prism Scripting - Advanced Features Summary
|
||||
|
||||
## Graph Manipulation
|
||||
|
||||
### Changing Graphs
|
||||
- Scripts can modify graph properties and formatting
|
||||
- Allows automation of graph customization
|
||||
|
||||
### Exporting Graphs and Layouts
|
||||
Commands for exporting visual output to various formats for use in publications and presentations.
|
||||
|
||||
## Data Export Commands
|
||||
|
||||
### ExportTable Command
|
||||
**Syntax:** `ExportTable [filename] <ALL>`
|
||||
|
||||
**File Formats:**
|
||||
- `.txt` - Tab-delimited text
|
||||
- `.csv` - Comma-delimited text
|
||||
- `.xml` - Prism XML format
|
||||
|
||||
**Behavior by Table Type:**
|
||||
- **Data/Results tables:** Exports entire table
|
||||
- **Info tables (`.txt`):** Exports notes only (not constants)
|
||||
- **Info tables (`.xml`):** Exports both constants and notes
|
||||
- **XML with ALL option:** Exports all data and info tables project-wide
|
||||
|
||||
**Note:** For info constants only, use WSheet command instead.
|
||||
|
||||
## Output to Tables and Files
|
||||
|
||||
### Writing to Prism Tables (Text/HTML/XML/SQL)
|
||||
Scripts can create and populate Prism tables in multiple formats for structured data output.
|
||||
|
||||
### Writing to Text Files
|
||||
Commands for writing data to external text files for export and integration.
|
||||
|
||||
### WBlock Command
|
||||
**Introduced:** Prism 6.04/6.0e
|
||||
**Purpose:** Write cell block (range) to text file opened via OpenOutput
|
||||
|
||||
**Syntax:** `WBlock [row(s)] [column(s)] <row label> <;>`
|
||||
|
||||
**Row Parameters:**
|
||||
| Parameter | Meaning |
|
||||
|-----------|---------|
|
||||
| Single number | One row |
|
||||
| `n-` | Row n through first blank row |
|
||||
| `n-m` | Rows n through m (inclusive) |
|
||||
| List | Multiple specific rows (any order) |
|
||||
|
||||
**Column Parameters:**
|
||||
| Parameter | Meaning |
|
||||
|-----------|---------|
|
||||
| Single letter | One column |
|
||||
| `A-` | Column A through first empty column |
|
||||
| `A-D` | Columns A through D (inclusive) |
|
||||
| List | Multiple specific columns (any order) |
|
||||
|
||||
**Row Label:** Optional label prepended to each row
|
||||
**Semicolon (`;`):** If present, label joins with first column (no delimiter)
|
||||
|
||||
**Examples:**
|
||||
```prism
|
||||
WBlock "7-", "6,4", "PSummary" // Rows 7-end, cols 6&4, labeled
|
||||
WBlock "7-", "6,3", "Significant?"; // Label joins column (no delimiter)
|
||||
WBlock "7-", "7,4", "PSummary" // Label in separate column
|
||||
```
|
||||
|
||||
**Output Format:** Tab-delimited by default (or comma if set in OpenOutput)
|
||||
|
||||
### WTBlock Command
|
||||
**Syntax:** `WTBlock [row(s)] [columns to include] <row label> <;>`
|
||||
|
||||
**Difference from WBlock:** Transposes output - each Prism column becomes a row in output, with label applied per output row
|
||||
|
||||
**Example:**
|
||||
```prism
|
||||
WTBlock "7-", "7,3,4" // Transpose specified rows/columns
|
||||
```
|
||||
|
||||
## Microsoft Office Integration
|
||||
|
||||
### SendToWord Command
|
||||
Sends current graph or layout to Microsoft Word document.
|
||||
|
||||
### SendToPP Command
|
||||
Sends current graph or layout to Microsoft PowerPoint presentation.
|
||||
|
||||
**Platform:** Windows only
|
||||
|
||||
## Special Purpose Commands
|
||||
|
||||
### SetProjectName
|
||||
**Syntax:** `SetProjectName ["new name"]`
|
||||
Changes project file name for next save operation.
|
||||
|
||||
### SetScriptDialogTitle
|
||||
**Syntax:** `SetScriptDialogTitle ["dialog title"]`
|
||||
Customizes script progress dialog title (useful for user-facing scripts).
|
||||
|
||||
### RecalcAll
|
||||
Recalculates all results in project. Required when opening files from prior Prism versions saved in large format.
|
||||
|
||||
### Beep
|
||||
Plays audible alert when script completes (useful for long-running scripts).
|
||||
|
||||
### CreateLog
|
||||
**Behavior:**
|
||||
- **Script dialog execution:** Ignored (log always created in dialog tab 2)
|
||||
- **File execution:** Creates `.log` file with same name as script file
|
||||
|
||||
Logs each script step for debugging and verification.
|
||||
|
||||
### SetSheetTitle
|
||||
**Syntax:** `SetSheetTitle [new_name] <K>`
|
||||
Renames current sheet.
|
||||
**K parameter:** Retains first K characters of existing name, replaces remainder.
|
||||
|
||||
### CloseScriptDialog
|
||||
Closes script progress dialog (useful for programmatic control).
|
||||
|
||||
### Print
|
||||
Prints current sheet only (not entire project).
|
||||
|
||||
### Exit
|
||||
**Syntax:** `Exit`
|
||||
**Platform:** Windows only
|
||||
Closes all open files without saving or prompting, then exits Prism.
|
||||
**Warning:** Data loss risk - use cautiously.
|
||||
|
||||
## Scripting Syntax Elements
|
||||
|
||||
### Comments
|
||||
```prism
|
||||
// Single line comment
|
||||
|
||||
/*
|
||||
Multi-line
|
||||
comment block
|
||||
*/
|
||||
```
|
||||
|
||||
### Punctuation Rules
|
||||
- **Command separation:** Space between command and arguments
|
||||
- **Argument separation:** Spaces or commas
|
||||
- **Case:** Insensitive (mix upper/lower freely)
|
||||
- **Whitespace:** Extra spaces allowed for readability
|
||||
|
||||
### Documentation Conventions
|
||||
- **Required arguments:** `[like this]` in square brackets
|
||||
- **Optional arguments:** `<like this>` in angle brackets
|
||||
- **Lowercase:** Placeholder for value you enter
|
||||
- **UPPERCASE:** Exact keyword to type
|
||||
|
||||
### Output Variables
|
||||
Available in commands that export text (especially useful in loops):
|
||||
|
||||
| Variable | Meaning |
|
||||
|----------|---------|
|
||||
| `%F` | Filename (before extension) |
|
||||
| `%X` | File extension (without period) |
|
||||
| `%S` | Current sheet name |
|
||||
| `%N` | Loop iteration number |
|
||||
| `%%` | Literal `%` symbol |
|
||||
|
||||
**Usage:** Can precede/follow with text
|
||||
**Context:** Must be inside script loop (except `%S`)
|
||||
**Additional:** More variables available for text writing commands
|
||||
|
||||
## Platform-Specific Features
|
||||
|
||||
### macOS Integration
|
||||
|
||||
#### Automator Support
|
||||
**Requirements:** macOS 10.4 (Tiger) or later
|
||||
**Input:** Script file path or script text
|
||||
**Output:** "Done" or error message
|
||||
Enables workflow automation with Prism scripts.
|
||||
|
||||
#### AppleScript/MacScript
|
||||
Launch Prism from Microsoft Office (Word/Excel) via VBA:
|
||||
|
||||
```vba
|
||||
MacScript "tell application ""HD:Prism4:Prism""" + Chr(13) + _
|
||||
"activate" + Chr(13) + _
|
||||
"open file ""Macintosh HD:Prism4:Scripts:dr2""" + Chr(13) + _
|
||||
"end tell"
|
||||
```
|
||||
|
||||
**Requirements:**
|
||||
- Full path to Prism application
|
||||
- Full path to script file
|
||||
|
||||
**Behavior:** VBA continues immediately (non-blocking)
|
||||
**Synchronization:** VBA program must manually wait for Prism completion (e.g., poll for output file creation)
|
||||
|
||||
## Key Limitations and Notes
|
||||
|
||||
1. **Exit command:** Windows only, no macOS support
|
||||
2. **SendToWord/SendToPP:** Windows-focused features
|
||||
3. **WBlock/WTBlock:** Requires prior OpenOutput command
|
||||
4. **Async execution:** AppleScript launches don't block - implement waiting logic
|
||||
5. **Info table exports:** Different behavior for TXT vs XML formats
|
||||
6. **File format dependencies:** Extension determines export format/behavior
|
||||
180
skills/graphpad-prism-skill/reference/data_operations.md
Normal file
180
skills/graphpad-prism-skill/reference/data_operations.md
Normal file
@@ -0,0 +1,180 @@
|
||||
# Data Operations - Summary
|
||||
|
||||
## Creating New Sheets
|
||||
|
||||
### Commands
|
||||
- `DuplicateDataTable <CLEAR>`
|
||||
- `DuplicateFamily [prepend_text] <CLEAR>`
|
||||
- `CreateLayout [#rows] [#columns] <orientation> <#StartingGraphIndex> <#Graphs>`
|
||||
|
||||
### Details
|
||||
**DuplicateDataTable**: Duplicates only a data table (no linked analyses/graphs). Can import data but cannot analyze or graph within script.
|
||||
|
||||
**DuplicateFamily**: Duplicates sheet plus all linked sheets. Import new data replaces existing, all analyses/graphs update automatically. Prepended text added to all new sheet names. Use `%F` as prepend text to use imported filename.
|
||||
|
||||
**CreateLayout**: Creates new layout with array of placeholders.
|
||||
- Orientation: "portrait" or "landscape" (default: portrait)
|
||||
- Starting graph: rank order in navigator (1 = first graph)
|
||||
- GraphsCount: number of graphs to assign (optional; stops at last placeholder or last graph if omitted)
|
||||
|
||||
## Modifying Data Tables
|
||||
|
||||
### Commands
|
||||
- `SetYReplicates [#]`
|
||||
- `ClearTable <row>,<col>,<subcol>`
|
||||
- `DeleteAllDataSets <CLEAR>`
|
||||
|
||||
### Details
|
||||
Scripts have limited ability to modify data tables. Cannot change table structure or number format (only Y replicates).
|
||||
|
||||
**SetYReplicates**: Changes number of Y replicates (subcolumns).
|
||||
|
||||
**DeleteAllDataSets**: Deletes all data and all links to analyses/graphs.
|
||||
|
||||
**ClearTable**: Erases all data left and below designated cell (including cell itself). Maintains links to analyses/graphs.
|
||||
|
||||
## Info Constants
|
||||
|
||||
### Commands
|
||||
- `SetInfo ["value"] [rownumber] <position: 0 (name) or 1 (value) or 2 (notes)>`
|
||||
- `SetValueToInfo [infotable #] [inforow#] [datarow] [datacol] <datasubcol>`
|
||||
|
||||
### Details
|
||||
Both commands insert/change values in Info sheets.
|
||||
|
||||
**SetInfo**:
|
||||
- Position 0: change constant name
|
||||
- Position 1: change constant value (default)
|
||||
- Position 2: append to notes (row number ignored)
|
||||
|
||||
Examples:
|
||||
```
|
||||
SetInfo 5.3, 3 // Set 3rd constant = 5.3
|
||||
Setinfo "Notebook 25, page 34", 5 // Set 5th constant to text
|
||||
Setinfo "Experimenter", 3, 0 // Name 3rd constant
|
||||
Setinfo "Dennis", 3, 1 // Set value of 3rd constant
|
||||
Setinfo "Notebook 2007H, page 304", 1, 2 // Add to notes
|
||||
```
|
||||
|
||||
**SetValueToInfo**: Value comes from data/results/info table. Must first navigate using Goto command. Specify source cell (row, col, subcol) and destination (info table #, info row #).
|
||||
|
||||
Example:
|
||||
```
|
||||
SetValueToInfo 2, 4, 14, 0 // From row 14, col 0 (X value) → 4th row of 2nd info table
|
||||
```
|
||||
|
||||
## Importing Data
|
||||
|
||||
### From Text Files
|
||||
|
||||
#### Commands
|
||||
- `Import <"filename">, <row>, <col>, <subcol>`
|
||||
- `ImportLink <"filename">, <row>, <col>, <subcol>`
|
||||
|
||||
#### Details
|
||||
**Import**: Imports data from text file into data table.
|
||||
- If filename omitted in ForEach loop: uses current loop file
|
||||
- If filename without path: uses SetPath directory
|
||||
- Row 0 = title row, row 1 = first data row
|
||||
- Column 0 = X column, column 1 = first Y column
|
||||
- Column -1 = row titles
|
||||
- Cannot import subcolumn titles
|
||||
|
||||
**ImportLink**: Replaces data in data object using existing filter/rearrangement choices. Before scripting, manually import file and create link with Filter/Placement tab options (select rows/columns, transpose, etc.). Properties stored with data object. ImportLink then updates using same properties.
|
||||
- If single data object: omit row/col/subcol
|
||||
- If multiple data objects: specify upper-left corner
|
||||
- Only updates Prism→text file links (not Excel Paste Link)
|
||||
|
||||
### From Script File
|
||||
|
||||
#### Commands
|
||||
- `InsertData <row>, <col>, <subcol>`
|
||||
- `InsertDataLink <row>, <col>, <subcol>`
|
||||
|
||||
#### Details
|
||||
For scripts created within other programs, data can be included in same file as script commands.
|
||||
|
||||
**InsertData**: Imports data included within script file, starting at specified position. Data enclosed in `<Data>` and `</Data>` tags. Script continues after `</Data>` tag.
|
||||
|
||||
Example:
|
||||
```
|
||||
InsertData
|
||||
<Data>
|
||||
1, 2, 4
|
||||
5, 7, 9
|
||||
</Data>
|
||||
```
|
||||
|
||||
**InsertDataLink**: Imports data into data object at indicated position. Works similarly to ImportLink command.
|
||||
|
||||
Row/column indexing same as Import command (row 0 = title, col 0 = X, col -1 = row titles).
|
||||
|
||||
## Copy and Paste
|
||||
|
||||
### Commands
|
||||
- `Copy`
|
||||
- `Copy [#rows] [#columns] [first row] [first col] <first subcol>`
|
||||
- `Paste [first row] [first col] <first subcol>`
|
||||
- `Paste`
|
||||
|
||||
### Details
|
||||
From data/info/results table, copy selected values to clipboard.
|
||||
|
||||
**Copy**:
|
||||
- No arguments: copies entire sheet
|
||||
- With arguments: specify range to copy
|
||||
- #columns includes subcolumns (e.g., triplicate values in 2 columns = 6, or 7 with X)
|
||||
|
||||
**Paste**:
|
||||
- No arguments: pastes entire table at current insertion point
|
||||
- With arguments: specifies paste location
|
||||
|
||||
Copy/paste use system clipboard (overwrites other clipboard content).
|
||||
|
||||
Example:
|
||||
```
|
||||
Copy 1, 9, 5, 10 // Copies 1 row, 9 columns/subcolumns, starting row 5, col 10
|
||||
```
|
||||
|
||||
## Opening and Saving Files
|
||||
|
||||
### Commands
|
||||
- `Open ["filename"]`
|
||||
- `Close`
|
||||
- `Save <"filename">`
|
||||
|
||||
### Details
|
||||
Scripts can be saved in Prism file or separate .pzc file. When script runs from separate file, Open/Close switch between Prism files. Commands work on last opened file. Multiple files can be open; reissue Open to switch back.
|
||||
|
||||
**Open**:
|
||||
- Without disk/directory: uses SetPath directory (or temp folder if no SetPath)
|
||||
- Include extension: .PZF, .PZFX, .PZT, or .PZM
|
||||
- Unlike Import, doesn't auto-open next file in ForEach loop
|
||||
- For ForEach loop: use `Open %F.PZFX` (%F = next file)
|
||||
|
||||
**Close**: Does not save file.
|
||||
|
||||
**Save**:
|
||||
- Include filename: creates new file
|
||||
- Omit filename: saves changes to same name
|
||||
- Saves to .PZF or .PZFX based on extension
|
||||
|
||||
## Exporting Data
|
||||
|
||||
### Commands
|
||||
- `ExportTable [filename] <ALL>`
|
||||
|
||||
### Details
|
||||
Export format determined by file extension.
|
||||
|
||||
**From data/results table**: Exports entire table.
|
||||
- Formats: .txt (tab-delimited), .csv (comma-delimited), .xml (Prism XML)
|
||||
|
||||
**From info table**:
|
||||
- .txt file: exports only notes (not info constants)
|
||||
- .xml file: exports both info constants and notes
|
||||
- For info constants only: use WSheet command instead
|
||||
|
||||
**XML with ALL option**: Exports all data and info tables.
|
||||
|
||||
Can also export to script-created tables.
|
||||
249
skills/graphpad-prism-skill/reference/overview_and_running.md
Normal file
249
skills/graphpad-prism-skill/reference/overview_and_running.md
Normal file
@@ -0,0 +1,249 @@
|
||||
# GraphPad Prism Scripts - Overview & Running Scripts
|
||||
|
||||
## What are Prism Scripts?
|
||||
|
||||
**Purpose**: Automate analysis of multiple files or perform Monte Carlo simulations. Scripts (.pzc files) can open/close Prism files, import data, export/print results and graphs.
|
||||
|
||||
**Key Limitation**: Scripts do NOT control how Prism analyzes or graphs data - that's defined in the Prism project file. Scripts only import data, specify which results to export/print, and manage file operations.
|
||||
|
||||
**Automation Built-in**: Prism links data→graphs→analyses. Editing/replacing data or info constants auto-updates everything (analyses, graphs, paste-linked data). Scripts extend this for batch processing.
|
||||
|
||||
**Skill Level**: Creating scripts slightly harder than using Prism. Scripting/macro language experience helpful but not required.
|
||||
|
||||
## Alternatives to Scripting
|
||||
|
||||
**PZFX File Format**: Other programs can manipulate Prism files without scripts:
|
||||
1. Prism saves project files in PZFX format (plain text XML)
|
||||
2. Analysis/graphing sections encrypted, but data/info tables are plain XML
|
||||
3. External programs can:
|
||||
- Open PZFX file with text editor
|
||||
- Edit/replace data and info constants in XML
|
||||
- Resave file
|
||||
- When user opens in Prism, graphs/analyses auto-update
|
||||
|
||||
**Workflow**:
|
||||
1. Create Prism file with desired analysis/graphs
|
||||
2. Save as PZFX
|
||||
3. Open in text editor - see encrypted analysis + plain XML data
|
||||
4. Edit XML data
|
||||
5. Resave
|
||||
6. Open in Prism - updates automatically
|
||||
|
||||
**Advantages**: Cross-platform, no need for simultaneous execution, simpler for some use cases.
|
||||
|
||||
## Running Scripts from Prism (Development/Testing)
|
||||
|
||||
**Access**: Prism button → File menu → Run Script
|
||||
|
||||
### Creating New Script:
|
||||
1. Choose "Run Script"
|
||||
2. Select "New Script"
|
||||
3. Choose blank screen or copy existing script
|
||||
4. Edit script in left pane, view syntax reference in right pane
|
||||
5. Test with "1 step" button (step through line-by-line)
|
||||
6. Use "12 steps" for batch testing
|
||||
7. Click "Run" when ready - Prism and dialog minimize during execution
|
||||
|
||||
### Editing Existing Script:
|
||||
1. Choose "Run Script"
|
||||
2. Select from script list OR "Open Script file" for external file
|
||||
3. Follow steps 4-7 above
|
||||
|
||||
## Running Scripts on Mac (Automator, MacScript, AppleScript)
|
||||
|
||||
### Automator (OSX 10.4+)
|
||||
- Prism installs Automator Action for script launching
|
||||
- **Input**: File containing script OR script text
|
||||
- **Output**: "Done" or error message
|
||||
|
||||
### MacScript (from Microsoft Office VBA)
|
||||
**Launch syntax**:
|
||||
```vb
|
||||
MacScript "tell application ""HD:Prism4:Prism""" + Chr(13) + _
|
||||
"activate" + Chr(13) + _
|
||||
"open file ""Macintosh HD:Prism4:Scripts:dr2""" + Chr(13) + _
|
||||
"end tell"
|
||||
```
|
||||
|
||||
**Synchronization Pattern** (VBA doesn't wait for Prism):
|
||||
1. Prism script creates completion file:
|
||||
```
|
||||
OpenOutput "done.txt"
|
||||
WText "done"
|
||||
CloseOutput
|
||||
```
|
||||
2. VBA deletes done.txt before launching Prism
|
||||
3. VBA loops until done.txt exists:
|
||||
```vb
|
||||
Do Until Dir$("HD:prism 5:done.txt") > ""
|
||||
Application.Wait Now + TimeValue("00:00:1")
|
||||
Loop
|
||||
```
|
||||
4. VBA quits Prism:
|
||||
```vb
|
||||
MacScript "tell application ""HD:Prism4:Prism""" + Chr(13) + _
|
||||
"quit" + Chr(13) + _
|
||||
"end tell"
|
||||
```
|
||||
|
||||
### AppleScript
|
||||
|
||||
**HFS Path Example**:
|
||||
```applescript
|
||||
tell application "HD:Applications:Prism4 Folder:Prism"
|
||||
activate
|
||||
open file "HD:P4scripts:DR2.pzc"
|
||||
end tell
|
||||
```
|
||||
|
||||
**POSIX Path Example**:
|
||||
```applescript
|
||||
tell application "HD:Applications:Prism4 Folder:Prism"
|
||||
activate
|
||||
open POSIX file "/P4scripts/DR2.pzc"
|
||||
end tell
|
||||
```
|
||||
|
||||
**Note**: POSIX paths use slashes (not colons), must start with `/`.
|
||||
|
||||
## Running Scripts on Windows
|
||||
|
||||
### Desktop Shortcut
|
||||
**Syntax**:
|
||||
```
|
||||
"C:\PRISM5\PRISM.EXE" @"C:\PROGRAM FILES\PRISM 6\SCRIPTS\DOIT.PZC"
|
||||
```
|
||||
- Use `@` symbol before script path
|
||||
- Quote paths containing spaces
|
||||
|
||||
### Shell Command (from VBA/other programs)
|
||||
**Basic syntax**:
|
||||
```vb
|
||||
Shell ("C:\prism 5\prism.exe @C:\prism 6\dr2.pzc")
|
||||
```
|
||||
|
||||
**Behavior**:
|
||||
- Prism runs invisibly
|
||||
- Shell returns immediately (doesn't wait for completion)
|
||||
|
||||
**Synchronization Pattern** (same as Mac):
|
||||
1. Prism script creates done.txt:
|
||||
```
|
||||
OpenOutput "done.txt"
|
||||
WText "done"
|
||||
CloseOutput
|
||||
```
|
||||
2. VBA deletes done.txt, launches Prism, then loops:
|
||||
```vb
|
||||
Do Until Dir$("C:\prism 6\done.txt") > ""
|
||||
Application.Wait Now + TimeValue("00:00:1")
|
||||
Loop
|
||||
```
|
||||
|
||||
### OLE/ActiveX Automation
|
||||
**Full example**:
|
||||
```vb
|
||||
Set Prism = CreateObject("Prism.command")
|
||||
Prism.SetPath ("C:\data\july99")
|
||||
Prism.visible
|
||||
Prism.runcommand ("c:\prism5\doseresp.pzc")
|
||||
Prism.quit
|
||||
Set Prism = Nothing
|
||||
```
|
||||
|
||||
**Commands**:
|
||||
- `CreateObject("Prism.command")` - Creates Prism object (Windows finds prism.exe via registry)
|
||||
- `SetPath (path)` - Optional, sets working directory for data files/templates
|
||||
- `visible` - Shows progress dialog (remove for invisible operation)
|
||||
- `runcommand (scriptpath)` - Launches script (requires full path)
|
||||
- `quit` - Exits Prism
|
||||
|
||||
**Advantages over Shell**:
|
||||
1. Sequential execution - VBA waits for Prism completion (no synchronization file needed)
|
||||
2. Can set working directory without modifying script
|
||||
|
||||
### Intranet Launch (Batch File)
|
||||
**Create StartPrism.bat**:
|
||||
```batch
|
||||
Call "N:\Program Files\PRISM5\PRISM.EXE" -OC:\WINDOWS\prism5.cnf
|
||||
```
|
||||
OR:
|
||||
```batch
|
||||
Call F:\Prism\Prism.exe @"F:\PRISM\PRISMSCRIPTS\DOIT.PZC"
|
||||
```
|
||||
|
||||
**HTML link**: Link text to StartPrism.bat file.
|
||||
|
||||
## Excel Integration
|
||||
|
||||
### Export Excel Data to CSV (VBA)
|
||||
```vb
|
||||
Open "C:\data\july97\dr2.csv" For Output As #1
|
||||
For I = 1 To 12
|
||||
For J = 1 to 6
|
||||
Print #1, Worksheets(1).Cells(I,J).Value; ",";
|
||||
Next
|
||||
Write #1,
|
||||
Next
|
||||
Close #1
|
||||
```
|
||||
**Note**: Exporting to CSV faster than opening Excel files directly from Prism.
|
||||
|
||||
### Generate PZC File from Excel (VBA)
|
||||
```vb
|
||||
Open "C:\Prism4\auto.pzc" For Output As #1
|
||||
Print #1, "Shortlog"
|
||||
Print #1, "SetPath C:\gp\prism25\"
|
||||
Print #1, "Open generate.pzm"
|
||||
Print #1, "openOutput fit.txt"
|
||||
Print #1, " ForEach 500"
|
||||
Print #1, " GoTo R 1"
|
||||
Print #1, " Regenerate"
|
||||
Print #1, " GoTo R 2"
|
||||
Print #1, " WCell 5,1"
|
||||
Print #1, " Next"
|
||||
Close #1
|
||||
Shell ("C:\program files\prism5\prism.exe @C:\prism5\auto.pzc")
|
||||
```
|
||||
|
||||
**Workflow**:
|
||||
- All script commands in one Excel VBA file
|
||||
- Each line prefaced with `Print #1,` and in quotes
|
||||
- Simplifies editing (one file vs two)
|
||||
- Trade-off: More complex syntax
|
||||
|
||||
### Import Prism Graph to Excel (VBA)
|
||||
**Prerequisites**:
|
||||
1. Manually create picture object in Excel (Control toolbar → Image button → drag)
|
||||
2. Name the object (e.g., "DRGraph")
|
||||
|
||||
**VBA code**:
|
||||
```vb
|
||||
Sheet2.DRGraph.Picture = LoadPicture(Path$ + "dr2.wmf")
|
||||
```
|
||||
|
||||
**Note**: Prism script must export graph as WMF first. No VBA command to directly import pictures, so must change existing picture object's contents.
|
||||
|
||||
## Key Concepts Summary
|
||||
|
||||
**File Extensions**:
|
||||
- `.pzc` - Prism script file
|
||||
- `.pzfx` - Prism XML format file (editable data)
|
||||
- `.pzm` - Prism template/master file
|
||||
|
||||
**Script Execution Modes**:
|
||||
1. **From Prism**: Interactive testing/development
|
||||
2. **Desktop/Shortcuts**: User-initiated batch processing
|
||||
3. **Shell/Automation**: Programmatic integration
|
||||
4. **Intranet**: Web-based launching
|
||||
|
||||
**Cross-Platform Differences**:
|
||||
- **Windows**: Shell, OLE/ActiveX, batch files
|
||||
- **Mac**: Automator, MacScript, AppleScript (HFS/POSIX paths)
|
||||
|
||||
**Synchronization**:
|
||||
- Shell/MacScript return immediately
|
||||
- Use completion file pattern (done.txt) with polling loop
|
||||
- OLE automation waits automatically
|
||||
|
||||
**No API**: Prism has no direct API - use scripts or PZFX file manipulation instead.
|
||||
304
skills/graphpad-prism-skill/reference/reading_current_data.md
Normal file
304
skills/graphpad-prism-skill/reference/reading_current_data.md
Normal file
@@ -0,0 +1,304 @@
|
||||
# Reading Current Prism Data State
|
||||
|
||||
## The Problem
|
||||
|
||||
Prism scripts **cannot read data values** into variables or use them for conditional logic. This is a fundamental limitation of the scripting language.
|
||||
|
||||
**What you CANNOT do:**
|
||||
- Read a cell value into a variable
|
||||
- Use if/else conditionals based on data
|
||||
- Make script decisions based on analysis results
|
||||
- Loop until a condition is met
|
||||
- Compare values or perform calculations in the script
|
||||
|
||||
**The only "read" command** is `SetValueToInfo`, which copies a value from one location to another but doesn't let you use it in logic.
|
||||
|
||||
## The Solution: PZFX XML Files
|
||||
|
||||
Since Prism's scripting language can't read data, use the **PZFX file format** instead.
|
||||
|
||||
### What is PZFX?
|
||||
|
||||
- **PZFX** = Prism's XML file format
|
||||
- Plain text XML structure (human and machine readable)
|
||||
- **Data tables**: Fully readable and editable in XML
|
||||
- **Info tables**: Fully readable and editable in XML
|
||||
- **Analysis results**: Encrypted but readable as XML
|
||||
- **Graph/analysis settings**: Encrypted (not editable externally)
|
||||
|
||||
### How Prism Automation Works
|
||||
|
||||
```
|
||||
Prism's Built-in Automation:
|
||||
Data → Auto-updates → Graphs
|
||||
Data → Auto-updates → Analyses
|
||||
Data → Auto-updates → Paste-linked tables
|
||||
```
|
||||
|
||||
When you edit data in a PZFX file externally, Prism sees it as a data change and **auto-updates everything**.
|
||||
|
||||
## Workflow Patterns
|
||||
|
||||
### Pattern 1: Read-Only Analysis (Python/R)
|
||||
|
||||
**Use case**: Extract data/results for external analysis
|
||||
|
||||
```python
|
||||
# Python example
|
||||
import xml.etree.ElementTree as ET
|
||||
|
||||
# Read PZFX file
|
||||
tree = ET.parse('experiment.pzfx')
|
||||
root = tree.getroot()
|
||||
|
||||
# Extract data from table
|
||||
for table in root.findall('.//Table'):
|
||||
table_name = table.get('ID')
|
||||
# Parse data cells
|
||||
for cell in table.findall('.//d'):
|
||||
value = cell.text
|
||||
# Analyze, plot, whatever you need
|
||||
```
|
||||
|
||||
### Pattern 2: Modify Data, Let Prism Analyze
|
||||
|
||||
**Use case**: Pre-process data externally, let Prism do analysis/graphing
|
||||
|
||||
```python
|
||||
# Python example
|
||||
import xml.etree.ElementTree as ET
|
||||
|
||||
# 1. Read PZFX template
|
||||
tree = ET.parse('template.pzfx')
|
||||
|
||||
# 2. Modify data in XML
|
||||
for table in tree.findall('.//Table[@ID="Data 1"]'):
|
||||
# Update cell values
|
||||
cells = table.findall('.//d')
|
||||
cells[0].text = str(new_value)
|
||||
|
||||
# 3. Save modified file
|
||||
tree.write('processed.pzfx')
|
||||
|
||||
# 4. Open in Prism - graphs/analyses auto-update!
|
||||
```
|
||||
|
||||
### Pattern 3: Conditional Logic + Prism Script
|
||||
|
||||
**Use case**: Make decisions based on data, then run appropriate Prism script
|
||||
|
||||
```python
|
||||
# Python: Read data and decide what to do
|
||||
tree = ET.parse('results.pzfx')
|
||||
p_value = float(tree.find('.//Cell[@Row="5"][@Col="3"]').text)
|
||||
|
||||
if p_value < 0.05:
|
||||
script_to_run = "significant.pzc"
|
||||
else:
|
||||
script_to_run = "not_significant.pzc"
|
||||
|
||||
# Launch appropriate Prism script
|
||||
import subprocess
|
||||
subprocess.run(['prism', script_to_run])
|
||||
```
|
||||
|
||||
### Pattern 4: Full Integration (Python + Prism)
|
||||
|
||||
**Complete workflow**:
|
||||
|
||||
```python
|
||||
#!/usr/bin/env python3
|
||||
import xml.etree.ElementTree as ET
|
||||
import subprocess
|
||||
import os
|
||||
|
||||
# 1. Prepare data externally
|
||||
data = process_experimental_data()
|
||||
|
||||
# 2. Create/modify PZFX file
|
||||
tree = ET.parse('template.pzfx')
|
||||
# ... populate data in XML ...
|
||||
tree.write('experiment.pzfx')
|
||||
|
||||
# 3. Run Prism script to generate graphs
|
||||
subprocess.run(['prism', '@export_graphs.pzc'])
|
||||
|
||||
# 4. Read results back from PZFX
|
||||
tree = ET.parse('experiment.pzfx')
|
||||
results = extract_results(tree)
|
||||
|
||||
# 5. Make decisions, generate reports
|
||||
if results['significant']:
|
||||
generate_report(results)
|
||||
```
|
||||
|
||||
## Platform-Specific Integration
|
||||
|
||||
### macOS Approach
|
||||
|
||||
**Problem**: AppleScript can only launch Prism scripts, not read data.
|
||||
|
||||
**Solution**: Use PZFX + external tool
|
||||
|
||||
```applescript
|
||||
-- Save current work (user does this manually or via script)
|
||||
tell application "Prism"
|
||||
-- Prism must already have file open, saved as PZFX
|
||||
end tell
|
||||
|
||||
-- Process with Python/R/etc
|
||||
do shell script "python3 ~/scripts/analyze_prism.py"
|
||||
|
||||
-- Reopen in Prism (optional - user can do manually)
|
||||
tell application "Prism"
|
||||
activate
|
||||
open POSIX file "/path/to/processed.pzfx"
|
||||
end tell
|
||||
```
|
||||
|
||||
### Windows Approach
|
||||
|
||||
**Same principle**, but can use VBA, PowerShell, or Python:
|
||||
|
||||
```vbnet
|
||||
' Excel VBA example
|
||||
Sub ProcessPrismData()
|
||||
' 1. Tell Prism to save as PZFX
|
||||
' (user must do manually or via Save command in script)
|
||||
|
||||
' 2. Parse XML (using MSXML2.DOMDocument)
|
||||
Dim xmlDoc As Object
|
||||
Set xmlDoc = CreateObject("MSXML2.DOMDocument")
|
||||
xmlDoc.Load "C:\Data\experiment.pzfx"
|
||||
|
||||
' 3. Read values
|
||||
Dim pValue As Double
|
||||
pValue = CDbl(xmlDoc.SelectSingleNode("//Cell[@Row='5']").Text)
|
||||
|
||||
' 4. Make decision
|
||||
If pValue < 0.05 Then
|
||||
Shell "C:\Prism\prism.exe @C:\Scripts\significant.pzc"
|
||||
End If
|
||||
End Sub
|
||||
```
|
||||
|
||||
## XML Structure Reference
|
||||
|
||||
### Data Table Structure
|
||||
```xml
|
||||
<Table ID="Data 1" XFormat="none" YFormat="replicates">
|
||||
<Title>Dose Response</Title>
|
||||
<ColumnTitlesRow>
|
||||
<d>Dose</d>
|
||||
<d>Response</d>
|
||||
</ColumnTitlesRow>
|
||||
<YColumn>
|
||||
<Title>Control</Title>
|
||||
<Subcolumn>
|
||||
<d>10.5</d>
|
||||
<d>12.3</d>
|
||||
<d>11.8</d>
|
||||
</Subcolumn>
|
||||
</YColumn>
|
||||
</Table>
|
||||
```
|
||||
|
||||
### Info Constants Structure
|
||||
```xml
|
||||
<InfoSequence>
|
||||
<Ref ID="Info0" />
|
||||
</InfoSequence>
|
||||
|
||||
<Info ID="Info0">
|
||||
<Title>Experiment Details</Title>
|
||||
<Constant>
|
||||
<Name>Date</Name>
|
||||
<Value>2024-01-15</Value>
|
||||
</Constant>
|
||||
<Constant>
|
||||
<Name>Experimenter</Name>
|
||||
<Value>Jane Smith</Value>
|
||||
</Constant>
|
||||
</Info>
|
||||
```
|
||||
|
||||
## Complete Example: Batch Processing with Conditionals
|
||||
|
||||
```python
|
||||
#!/usr/bin/env python3
|
||||
"""
|
||||
Process multiple data files through Prism with conditional logic.
|
||||
Prism scripts can't do conditionals, so we use Python + PZFX.
|
||||
"""
|
||||
|
||||
import xml.etree.ElementTree as ET
|
||||
import subprocess
|
||||
import glob
|
||||
|
||||
# 1. Process each data file
|
||||
for data_file in glob.glob('data/*.csv'):
|
||||
# 2. Read data to make decision
|
||||
data = read_csv(data_file)
|
||||
|
||||
# 3. Choose appropriate Prism template based on data
|
||||
if len(data) > 100:
|
||||
template = 'large_dataset_template.pzfx'
|
||||
else:
|
||||
template = 'small_dataset_template.pzfx'
|
||||
|
||||
# 4. Load template and populate data
|
||||
tree = ET.parse(template)
|
||||
populate_prism_data(tree, data)
|
||||
|
||||
# 5. Save as new PZFX file
|
||||
output_file = f'processed/{data_file}.pzfx'
|
||||
tree.write(output_file)
|
||||
|
||||
# 6. Run Prism script to export graphs
|
||||
# Script is simple: just exports graphs, no logic needed
|
||||
subprocess.run(['prism', '@export_graphs.pzc', output_file])
|
||||
|
||||
# 7. Read results back if needed
|
||||
tree = ET.parse(output_file)
|
||||
results = extract_results(tree)
|
||||
|
||||
# 8. Store in database, generate report, etc.
|
||||
save_to_database(results)
|
||||
```
|
||||
|
||||
## Key Takeaways
|
||||
|
||||
1. **Prism scripts are write-only**: They can import/export but not read for logic
|
||||
2. **PZFX is the read interface**: Use external tools to parse XML
|
||||
3. **Prism auto-updates**: Changing data in PZFX updates graphs/analyses
|
||||
4. **Hybrid approach**: External tool for logic, Prism script for automation
|
||||
5. **XML is documented**: Use the schema files in `prism-xml-schema/` directory
|
||||
|
||||
## Tools for PZFX Processing
|
||||
|
||||
### Python
|
||||
- `xml.etree.ElementTree` - Built-in XML parser
|
||||
- `lxml` - More powerful XML processing
|
||||
- `pandas` - Can read XML tables
|
||||
|
||||
### R
|
||||
- `xml2` package - XML parsing
|
||||
- `XML` package - Alternative parser
|
||||
|
||||
### Excel VBA
|
||||
- `MSXML2.DOMDocument` - Microsoft's XML parser
|
||||
|
||||
### Command Line
|
||||
- `xmllint` - Validate and query XML
|
||||
- `xq` - jq for XML (requires installation)
|
||||
|
||||
## When to Use Each Approach
|
||||
|
||||
| Scenario | Best Approach |
|
||||
|----------|---------------|
|
||||
| Simple batch import | Prism script alone |
|
||||
| Conditional processing | Python/R + PZFX |
|
||||
| Read analysis results | Python/R + PZFX |
|
||||
| Complex data prep | External tool → PZFX → Prism |
|
||||
| Integration with LIMS | Python/R reads/writes PZFX |
|
||||
| Decision trees | External tool, not Prism script |
|
||||
245
skills/graphpad-prism-skill/reference/script_examples.md
Normal file
245
skills/graphpad-prism-skill/reference/script_examples.md
Normal file
@@ -0,0 +1,245 @@
|
||||
# GraphPad Prism Script Examples
|
||||
|
||||
## Overview
|
||||
|
||||
Seven examples demonstrating scripting use cases: repeated imports, Monte Carlo analysis, multi-file consolidation, template workflows, embedded data, multi-table operations, and batch graph formatting.
|
||||
|
||||
## Example 1: Repeatedly Import Data
|
||||
|
||||
**Use case**: Import multiple data files sequentially into separate tables.
|
||||
|
||||
**Key commands**:
|
||||
- `GoTo D, N` - Navigate to data table N
|
||||
- `Import filename.txt` - Import external file
|
||||
- Manual repetition of commands for each file/table
|
||||
|
||||
**Workflow**:
|
||||
1. Navigate to target table
|
||||
2. Import file
|
||||
3. Repeat for each additional file
|
||||
|
||||
**Limitation**: No loop construct in this basic example; requires explicit command repetition.
|
||||
|
||||
## Example 2: Monte Carlo Analysis
|
||||
|
||||
**Use case**: Perform iterative simulations with randomization.
|
||||
|
||||
**Key commands**:
|
||||
- `ForEach N` - Loop N times
|
||||
- `GoTo R, N` - Navigate to results table N
|
||||
- `AnalyzeData` - Execute analysis
|
||||
- `Next` - End loop iteration
|
||||
|
||||
**Workflow**:
|
||||
1. Set up analysis on initial data
|
||||
2. Loop through iterations:
|
||||
- Generate random data variation
|
||||
- Execute analysis
|
||||
- Store results in indexed table
|
||||
3. Aggregate results across iterations
|
||||
|
||||
**Pattern**:
|
||||
```
|
||||
ForEach 100
|
||||
GoTo R, %N
|
||||
AnalyzeData
|
||||
Next
|
||||
```
|
||||
|
||||
**Variable**: `%N` holds current iteration number (1-based).
|
||||
|
||||
## Example 3: Import Several Files onto One Table
|
||||
|
||||
**Use case**: Consolidate multiple data files into columns of single table.
|
||||
|
||||
**Key commands**:
|
||||
- `GoTo D, 1` - Navigate to data table 1
|
||||
- `Import filename.txt, column=N` - Import into specific column N
|
||||
- Column parameter specifies destination
|
||||
|
||||
**Workflow**:
|
||||
1. Navigate to target table
|
||||
2. Import first file to column 1
|
||||
3. Import subsequent files to columns 2, 3, etc.
|
||||
|
||||
**Syntax**: `Import Data1.txt, column=1`
|
||||
|
||||
**Note**: Files must have compatible row structure.
|
||||
|
||||
## Example 4: Open Template and Import Data
|
||||
|
||||
**Use case**: Automate data import into pre-configured analysis template.
|
||||
|
||||
**Key commands**:
|
||||
- `Open template.pzfx` - Load template file
|
||||
- `GoTo D, 1` - Navigate to data table
|
||||
- `Import datafile.txt` - Import data
|
||||
- `SaveAs output.pzfx` - Save populated file
|
||||
|
||||
**Workflow**:
|
||||
1. Open template with pre-configured graphs/analyses
|
||||
2. Navigate to data table
|
||||
3. Import new data
|
||||
4. Save as new file (preserves template)
|
||||
|
||||
**Advantage**: Template contains all formatting, analysis settings, and graph configurations.
|
||||
|
||||
## Example 5: Import Data and Info Constants from Script File
|
||||
|
||||
**Use case**: Embed data and metadata directly in script (no external files).
|
||||
|
||||
**Key commands**:
|
||||
- `<DATA>...</DATA>` - Data block delimiter
|
||||
- `InsertData N, M` - Insert data block N starting at column M
|
||||
- `SetInfo constant_name, value` - Set info constant
|
||||
|
||||
**Data block syntax**:
|
||||
```
|
||||
<DATA>
|
||||
value1\tvalue2\tvalue3
|
||||
value4\tvalue5\tvalue6
|
||||
</DATA>
|
||||
```
|
||||
|
||||
**Info constant syntax**:
|
||||
```
|
||||
SetInfo Experiment, "Drug Study A"
|
||||
SetInfo Date, "2024-01-15"
|
||||
SetInfo Concentration, 10.5
|
||||
```
|
||||
|
||||
**Workflow**:
|
||||
1. Define data blocks in script using `<DATA>` tags
|
||||
2. Navigate to target table: `GoTo D, 1`
|
||||
3. Insert data: `InsertData 1, 0` (block 1, starting column 0)
|
||||
4. Navigate to info table: `GoTo I, 2`
|
||||
5. Set info constants with name/value pairs
|
||||
|
||||
**Data format**: Tab-delimited values within DATA tags, numbered sequentially (1-based).
|
||||
|
||||
**Info types**: String (quoted), numeric (unquoted), date (quoted).
|
||||
|
||||
## Example 6: Import Data into Several Tables
|
||||
|
||||
**Use case**: Batch import multiple files into multiple tables using loop.
|
||||
|
||||
**Prerequisites**: Prism file with N data tables, each linked to graph, all graphs on one layout.
|
||||
|
||||
**Key commands**:
|
||||
- `ForEach N` - Loop N times
|
||||
- `GoTo %N` - Navigate to table using iteration variable
|
||||
- `Import Data%N.txt` - Dynamic filename with variable substitution
|
||||
- `Next` - End loop
|
||||
- `GoTo L, 1` - Navigate to layout
|
||||
- `Print` - Print layout
|
||||
|
||||
**Script pattern**:
|
||||
```
|
||||
GoTo D
|
||||
ForEach 9
|
||||
GoTo %N
|
||||
Import Data%N.txt
|
||||
Next
|
||||
GoTo L, 1
|
||||
Print
|
||||
```
|
||||
|
||||
**Variable substitution**: `%N` replaced with current iteration number (1, 2, 3, ..., 9).
|
||||
|
||||
**Dynamic filenames**: `Data1.txt`, `Data2.txt`, ..., `Data9.txt` matched to tables 1-9.
|
||||
|
||||
**Result**: All tables populated, layout printed with all graphs updated.
|
||||
|
||||
## Example 7: Changing X-Axis Title of All Graphs
|
||||
|
||||
**Use case**: Apply uniform formatting change across all graphs in file.
|
||||
|
||||
**Key commands**:
|
||||
- `GoTo G` - Navigate to graphs family
|
||||
- `ForEachSheet` - Iterate over all sheets in current family
|
||||
- `SetAxisTitle axis, "title"` - Set axis title
|
||||
- `Next` - End loop
|
||||
|
||||
**Script pattern**:
|
||||
```
|
||||
GoTo G
|
||||
ForEachSheet
|
||||
SetAxisTitle X, "Time (minutes)"
|
||||
Next
|
||||
```
|
||||
|
||||
**Axis parameter**: `X` (X-axis), `Y` (Y-axis), `Y2` (secondary Y-axis).
|
||||
|
||||
**Scope**: Operates on all graph sheets in current family.
|
||||
|
||||
**Alternative axes**: `SetAxisTitle Y, "Response (units)"` for Y-axis.
|
||||
|
||||
## Common Scripting Patterns
|
||||
|
||||
### Loop Constructs
|
||||
- `ForEach N` / `Next` - Fixed iteration count
|
||||
- `ForEachSheet` / `Next` - Iterate over sheets in family
|
||||
- `%N` variable - Current iteration number (1-based)
|
||||
|
||||
### Navigation
|
||||
- `GoTo family, N` - Navigate to specific sheet
|
||||
- `D, N` - Data table N
|
||||
- `R, N` - Results table N
|
||||
- `G, N` - Graph N
|
||||
- `I, N` - Info table N
|
||||
- `L, N` - Layout N
|
||||
- `GoTo family` - Navigate to family without specific sheet
|
||||
- `GoTo %N` - Navigate using iteration variable
|
||||
|
||||
### Data Operations
|
||||
- `Import filename.txt` - Import external file
|
||||
- `Import filename.txt, column=N` - Import to specific column
|
||||
- `InsertData N, M` - Insert embedded data block N at column M
|
||||
- `<DATA>...</DATA>` - Embed data in script (tab-delimited)
|
||||
|
||||
### Info Constants
|
||||
- `SetInfo name, value` - Set named constant
|
||||
- String values: quoted
|
||||
- Numeric values: unquoted
|
||||
|
||||
### File Operations
|
||||
- `Open filename.pzfx` - Load Prism file
|
||||
- `SaveAs filename.pzfx` - Save with new name
|
||||
|
||||
### Analysis and Output
|
||||
- `AnalyzeData` - Execute analysis
|
||||
- `Print` - Print current sheet/layout
|
||||
|
||||
## Variable Substitution
|
||||
|
||||
`%N` - Current iteration number in loops
|
||||
- Use in navigation: `GoTo %N`
|
||||
- Use in filenames: `Import Data%N.txt`
|
||||
- Use in any string context requiring iteration number
|
||||
- 1-based indexing (first iteration = 1)
|
||||
|
||||
## Data Formats
|
||||
|
||||
**External files**: Tab-delimited or comma-delimited text files.
|
||||
|
||||
**Embedded data**: Tab-delimited within `<DATA>` tags, multiple blocks numbered sequentially.
|
||||
|
||||
**Info constants**: Name/value pairs, supports strings (quoted), numbers (unquoted), dates (quoted).
|
||||
|
||||
## Script Structure Best Practices
|
||||
|
||||
1. Navigate before operating: Always `GoTo` target before import/analysis
|
||||
2. Use loops for repetitive operations: `ForEach` with `%N` variable
|
||||
3. Embed small datasets: Use `<DATA>` blocks for portability
|
||||
4. Template workflows: Separate data from analysis configuration
|
||||
5. Batch operations: Combine loops with variable substitution for file series
|
||||
6. Layout printing: Navigate to layout after updating all graphs
|
||||
|
||||
## Limitations and Notes
|
||||
|
||||
- No automatic file discovery: Must specify exact filenames or use predictable naming pattern
|
||||
- Fixed iteration counts: `ForEach N` requires known count, no dynamic termination
|
||||
- Sequential execution: No parallel processing
|
||||
- Column compatibility: Multi-file imports require matching row structures
|
||||
- Variable scope: `%N` only valid within loop construct
|
||||
- 1-based indexing: All sheet numbers, iteration counts, and data blocks start at 1
|
||||
114
skills/graphpad-prism-skill/reference/syntax_and_basics.md
Normal file
114
skills/graphpad-prism-skill/reference/syntax_and_basics.md
Normal file
@@ -0,0 +1,114 @@
|
||||
# GraphPad Prism Scripting - Syntax & Basics Summary
|
||||
|
||||
## Script Syntax
|
||||
|
||||
### Punctuation Rules
|
||||
- Command name followed by space, then arguments
|
||||
- Separate arguments with spaces or commas
|
||||
- Case-insensitive
|
||||
- Extra spaces allowed for readability
|
||||
|
||||
### Documentation Notation
|
||||
- Required arguments: `[like this]`
|
||||
- Optional arguments: `<like this>`
|
||||
- Lowercase: value to enter
|
||||
- UPPERCASE: exact word to type
|
||||
|
||||
## Comments
|
||||
|
||||
### Syntax
|
||||
```
|
||||
// single line comment
|
||||
|
||||
/*
|
||||
multiple lines
|
||||
of comments
|
||||
*/
|
||||
```
|
||||
|
||||
## Row and Column Numbering
|
||||
|
||||
### Columns
|
||||
- Row Title column: -1
|
||||
- X Column: 0
|
||||
- Column A: 1
|
||||
- Column B: 2, etc.
|
||||
|
||||
### Rows
|
||||
- Column Title row: 0 or -1
|
||||
- First data row: 1 (not 0)
|
||||
- Subcolumn titles: not accessible via script
|
||||
|
||||
## General Commands
|
||||
|
||||
### GoTo Command
|
||||
Navigate between sheets and sections.
|
||||
|
||||
**Syntax:**
|
||||
- `GoTo <section: D, I, R, G, or L>, <sheet#>, V<tab#>`
|
||||
- `GoTo +` (next sheet)
|
||||
- `GoTo -` (previous sheet)
|
||||
|
||||
**Examples:**
|
||||
- `GoTo G` - go to graphs section, most recent graph
|
||||
- `GoTo 3` - third sheet of current section
|
||||
- `GoTo G, 3` - third graph
|
||||
- `GoTo V2` - second analysis tab of current results
|
||||
- `GoTo R, 3, V2` - second tab of third results sheet
|
||||
|
||||
**Notes:**
|
||||
- Sheet numbering starts at 1 (not 0)
|
||||
- Space required between results and view: `R4V2` fails, use `R, 4, V2`
|
||||
|
||||
## Loops and Simulations
|
||||
|
||||
### Loop Commands
|
||||
- `ForEach [# of loops]` - loop specified number of times
|
||||
- `ForEach [filespec]` - loop over files (e.g., `ForEach *.CSV` or `ForEach "C:\data\DR*.txt"`)
|
||||
- `ForEachSheet` - loop over all sheets in current section
|
||||
- `Next` - end loop statement
|
||||
- `Regenerate` - regenerate random numbers (for Monte Carlo simulations)
|
||||
|
||||
**Notes:**
|
||||
- Cannot nest loops
|
||||
- Used for simulations and repeated file imports
|
||||
|
||||
### Monte Carlo Pattern
|
||||
1. Create Prism file with "Simulate data with random scatter" analysis
|
||||
2. Link simulated data to another analysis (e.g., nonlinear regression)
|
||||
3. In loop: GoTo simulation analysis → Regenerate → GoTo results → write output → Next
|
||||
|
||||
## Variables for Text Output
|
||||
|
||||
Available in any command that exports text, primarily useful in loops:
|
||||
|
||||
- `%F` - file name (before period)
|
||||
- `%X` - file extension (without period)
|
||||
- `%S` - current sheet name (works inside or outside loops)
|
||||
- `%N` - loop number
|
||||
- `%%` - literal percent symbol (%)
|
||||
|
||||
Variables can be preceded/followed by other text. Additional variables available when writing text files.
|
||||
|
||||
## File Path Management
|
||||
|
||||
### SetPath Command
|
||||
**Syntax:** `SetPath ["drive and folder path"]`
|
||||
|
||||
Sets default path for file read/write commands unless overridden in individual commands.
|
||||
|
||||
**Windows Examples:**
|
||||
```
|
||||
SetPath "C:\Users\(current user)\Documents\007\goldfinger\oddjob"
|
||||
SetPath "(local drive):\DataFiles\August2005\"
|
||||
SetPath "\\LabServer\DDrive\PrismFiles"
|
||||
```
|
||||
|
||||
**Mac Example:**
|
||||
```
|
||||
SetPath "Hard Drive:Prism 4:Data:June21"
|
||||
```
|
||||
|
||||
**Network drives:** Use `\\ServerName\DriveName\path` format without "C:" notation.
|
||||
|
||||
Individual commands can specify full paths to override SetPath.
|
||||
418
skills/graphpad-prism-skill/reference/xml_schemas.md
Normal file
418
skills/graphpad-prism-skill/reference/xml_schemas.md
Normal file
@@ -0,0 +1,418 @@
|
||||
# Prism XML File Format & Schemas
|
||||
|
||||
## Overview
|
||||
|
||||
GraphPad Prism uses XML-based file formats that allow external programs to read and modify data without using Prism's limited scripting language.
|
||||
|
||||
## File Formats
|
||||
|
||||
### PZFX - Prism XML Format
|
||||
- **Extension**: `.pzfx`
|
||||
- **Format**: Plain text XML
|
||||
- **Readable**: Yes - open in any text editor
|
||||
- **Data tables**: Fully accessible as XML
|
||||
- **Info tables**: Fully accessible as XML
|
||||
- **Analysis results**: Encrypted but readable as XML
|
||||
- **Graphs/settings**: Encrypted (not editable externally)
|
||||
- **Use case**: Primary format for external data access
|
||||
|
||||
### PZF - Prism Binary Format
|
||||
- **Extension**: `.pzf`
|
||||
- **Format**: Binary (not human-readable)
|
||||
- **Use case**: Smaller file size, faster loading
|
||||
- **External access**: None - must convert to PZFX first
|
||||
|
||||
### PZM - Prism Template/Master
|
||||
- **Extension**: `.pzm`
|
||||
- **Format**: Can be PZFX or PZF
|
||||
- **Use case**: Templates for repeated analysis
|
||||
- **Scripting**: Open with `Open "template.pzm"`
|
||||
|
||||
### PZC - Prism Script
|
||||
- **Extension**: `.pzc`
|
||||
- **Format**: Plain text script commands
|
||||
- **Use case**: Automation scripts
|
||||
|
||||
## Official XML Schemas
|
||||
|
||||
GraphPad provides official XML schemas for Prism 7.0+ format.
|
||||
|
||||
**Schema files included in this skill:**
|
||||
- `Prism7XMLSchema.xml` - Complete schema definition
|
||||
- `Prism7XMLStyleSheet.xml` - XSLT for transforming Prism XML
|
||||
|
||||
**Schema location**: `../../prism-xml-schema/`
|
||||
|
||||
**Schema covers**:
|
||||
- Data table structure
|
||||
- Info table structure
|
||||
- Formatting elements (fonts, colors, alignment)
|
||||
- Metadata (version, creation date, user info)
|
||||
- Text formatting (bold, italic, underline, super/subscript)
|
||||
|
||||
## PZFX File Structure
|
||||
|
||||
### Root Structure
|
||||
```xml
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<GraphPadPrismFile>
|
||||
<OriginalVersion CreatedByProgram="Prism" CreatedByVersion="10.0.0" />
|
||||
<TableSequence>
|
||||
<Ref ID="Table0" />
|
||||
<Ref ID="Table1" />
|
||||
</TableSequence>
|
||||
<Table ID="Table0" ...>
|
||||
<!-- Data table content -->
|
||||
</Table>
|
||||
<InfoSequence>
|
||||
<Ref ID="Info0" />
|
||||
</InfoSequence>
|
||||
<Info ID="Info0" ...>
|
||||
<!-- Info constants -->
|
||||
</Info>
|
||||
</GraphPadPrismFile>
|
||||
```
|
||||
|
||||
### Data Table Elements
|
||||
|
||||
#### Basic Data Table
|
||||
```xml
|
||||
<Table ID="Data 1" XFormat="none" YFormat="replicates" Replicates="3">
|
||||
<Title>Dose Response Data</Title>
|
||||
|
||||
<!-- Column titles -->
|
||||
<ColumnTitlesRow>
|
||||
<d>X</d>
|
||||
<d>Y</d>
|
||||
</ColumnTitlesRow>
|
||||
|
||||
<!-- X Column -->
|
||||
<XColumn Width="81">
|
||||
<d>0.1</d>
|
||||
<d>1.0</d>
|
||||
<d>10.0</d>
|
||||
</XColumn>
|
||||
|
||||
<!-- Y Column with replicates -->
|
||||
<YColumn Width="81">
|
||||
<Title>Control</Title>
|
||||
<Subcolumn>
|
||||
<d>10.5</d>
|
||||
<d>12.3</d>
|
||||
<d>11.8</d>
|
||||
</Subcolumn>
|
||||
</YColumn>
|
||||
|
||||
<YColumn Width="81">
|
||||
<Title>Treatment</Title>
|
||||
<Subcolumn>
|
||||
<d>8.2</d>
|
||||
<d>9.1</d>
|
||||
<d>8.7</d>
|
||||
</Subcolumn>
|
||||
</YColumn>
|
||||
</Table>
|
||||
```
|
||||
|
||||
#### Table Attributes
|
||||
- `ID` - Unique identifier (e.g., "Data 1", "Table0")
|
||||
- `XFormat` - X column format: "none", "numbers", "text", "date"
|
||||
- `YFormat` - Y format: "replicates", "SD", "SEM", "mean"
|
||||
- `Replicates` - Number of subcolumns per Y column
|
||||
- `RowTitlesWidth` - Width of row titles column
|
||||
|
||||
### Info Table Elements
|
||||
|
||||
```xml
|
||||
<Info ID="Info0">
|
||||
<Title>Experiment Information</Title>
|
||||
|
||||
<!-- Individual constants -->
|
||||
<Constant>
|
||||
<Name>Date</Name>
|
||||
<Value>2024-01-15</Value>
|
||||
</Constant>
|
||||
|
||||
<Constant>
|
||||
<Name>Experimenter</Name>
|
||||
<Value>Jane Smith</Value>
|
||||
</Constant>
|
||||
|
||||
<Constant>
|
||||
<Name>Concentration</Name>
|
||||
<Value>10.5</Value>
|
||||
</Constant>
|
||||
|
||||
<!-- Notes section -->
|
||||
<Notes>
|
||||
Experiment notes go here.
|
||||
Multiple lines allowed.
|
||||
</Notes>
|
||||
</Info>
|
||||
```
|
||||
|
||||
### Results Tables (Encrypted)
|
||||
|
||||
```xml
|
||||
<HugeResults ID="HugeResults0">
|
||||
<!-- Results are encrypted but structure is visible -->
|
||||
<OriginalVersion ... />
|
||||
<AnalysisParams ...>
|
||||
<!-- Some parameters visible -->
|
||||
</AnalysisParams>
|
||||
<!-- Actual results encrypted -->
|
||||
</HugeResults>
|
||||
```
|
||||
|
||||
**Note**: Results are readable as XML but values are encrypted. You can see structure but not values without Prism.
|
||||
|
||||
### Data Types
|
||||
|
||||
#### Numeric Values
|
||||
```xml
|
||||
<d>10.5</d> <!-- Regular number -->
|
||||
<d>1.23e-4</d> <!-- Scientific notation -->
|
||||
<d></d> <!-- Missing/empty value -->
|
||||
```
|
||||
|
||||
#### Text Values
|
||||
```xml
|
||||
<d>Sample A</d> <!-- Plain text -->
|
||||
<d>Control</d> <!-- Text in row/column titles -->
|
||||
```
|
||||
|
||||
#### Formatted Text
|
||||
```xml
|
||||
<d>
|
||||
<b>Bold text</b>
|
||||
<i>Italic text</i>
|
||||
<u>Underlined</u>
|
||||
<sup>Superscript</sup>
|
||||
<sub>Subscript</sub>
|
||||
</d>
|
||||
```
|
||||
|
||||
#### Dates
|
||||
```xml
|
||||
<Constant>
|
||||
<Name>ExperimentDate</Name>
|
||||
<Value>2024-01-15</Value>
|
||||
</Constant>
|
||||
```
|
||||
|
||||
## Parsing PZFX Files
|
||||
|
||||
### Python Example
|
||||
|
||||
```python
|
||||
import xml.etree.ElementTree as ET
|
||||
|
||||
# Parse file
|
||||
tree = ET.parse('experiment.pzfx')
|
||||
root = tree.getroot()
|
||||
|
||||
# Find all data tables
|
||||
for table in root.findall('.//Table'):
|
||||
table_id = table.get('ID')
|
||||
title = table.find('Title').text
|
||||
|
||||
print(f"Table: {table_id} - {title}")
|
||||
|
||||
# Get X values
|
||||
x_column = table.find('XColumn')
|
||||
if x_column is not None:
|
||||
x_values = [d.text for d in x_column.findall('d')]
|
||||
print(f" X values: {x_values}")
|
||||
|
||||
# Get Y values
|
||||
for y_column in table.findall('YColumn'):
|
||||
y_title = y_column.find('Title').text
|
||||
subcolumn = y_column.find('Subcolumn')
|
||||
y_values = [d.text for d in subcolumn.findall('d')]
|
||||
print(f" {y_title}: {y_values}")
|
||||
```
|
||||
|
||||
### Reading Info Constants
|
||||
|
||||
```python
|
||||
# Find info tables
|
||||
for info in root.findall('.//Info'):
|
||||
info_id = info.get('ID')
|
||||
print(f"Info table: {info_id}")
|
||||
|
||||
# Get all constants
|
||||
for constant in info.findall('Constant'):
|
||||
name = constant.find('Name').text
|
||||
value = constant.find('Value').text
|
||||
print(f" {name}: {value}")
|
||||
|
||||
# Get notes
|
||||
notes = info.find('Notes')
|
||||
if notes is not None:
|
||||
print(f" Notes: {notes.text}")
|
||||
```
|
||||
|
||||
### Modifying Data
|
||||
|
||||
```python
|
||||
# Load template
|
||||
tree = ET.parse('template.pzfx')
|
||||
|
||||
# Find first data table
|
||||
table = tree.find('.//Table[@ID="Data 1"]')
|
||||
|
||||
# Modify X values
|
||||
x_column = table.find('XColumn')
|
||||
x_cells = x_column.findall('d')
|
||||
x_cells[0].text = "0.5"
|
||||
x_cells[1].text = "5.0"
|
||||
|
||||
# Modify Y values
|
||||
y_column = table.find('YColumn')
|
||||
subcolumn = y_column.find('Subcolumn')
|
||||
y_cells = subcolumn.findall('d')
|
||||
y_cells[0].text = "15.2"
|
||||
|
||||
# Save modified file
|
||||
tree.write('modified.pzfx', encoding='UTF-8', xml_declaration=True)
|
||||
```
|
||||
|
||||
## XPath Query Examples
|
||||
|
||||
### Find specific table
|
||||
```python
|
||||
table = root.find(".//Table[@ID='Data 1']")
|
||||
```
|
||||
|
||||
### Find all Y columns
|
||||
```python
|
||||
y_columns = root.findall(".//Table[@ID='Data 1']/YColumn")
|
||||
```
|
||||
|
||||
### Find specific info constant
|
||||
```python
|
||||
date = root.find(".//Info/Constant[Name='Date']/Value").text
|
||||
```
|
||||
|
||||
### Count data points
|
||||
```python
|
||||
num_points = len(root.findall(".//Table[@ID='Data 1']/XColumn/d"))
|
||||
```
|
||||
|
||||
## Validation
|
||||
|
||||
### Using xmllint (command line)
|
||||
```bash
|
||||
# Validate against schema
|
||||
xmllint --schema Prism7XMLSchema.xml experiment.pzfx
|
||||
|
||||
# Pretty print
|
||||
xmllint --format experiment.pzfx
|
||||
|
||||
# Extract specific elements
|
||||
xmllint --xpath "//Table/@ID" experiment.pzfx
|
||||
```
|
||||
|
||||
### Python Validation
|
||||
```python
|
||||
from lxml import etree
|
||||
|
||||
# Load schema
|
||||
schema_doc = etree.parse('Prism7XMLSchema.xml')
|
||||
schema = etree.XMLSchema(schema_doc)
|
||||
|
||||
# Validate file
|
||||
doc = etree.parse('experiment.pzfx')
|
||||
is_valid = schema.validate(doc)
|
||||
|
||||
if not is_valid:
|
||||
print(schema.error_log)
|
||||
```
|
||||
|
||||
## Common Patterns
|
||||
|
||||
### Extract all data to CSV
|
||||
```python
|
||||
import csv
|
||||
|
||||
tree = ET.parse('experiment.pzfx')
|
||||
|
||||
for table in tree.findall('.//Table'):
|
||||
table_id = table.get('ID')
|
||||
|
||||
with open(f'{table_id}.csv', 'w', newline='') as csvfile:
|
||||
writer = csv.writer(csvfile)
|
||||
|
||||
# Write column titles
|
||||
titles = [d.text for d in table.find('ColumnTitlesRow').findall('d')]
|
||||
writer.writerow(titles)
|
||||
|
||||
# Write data rows
|
||||
x_column = table.find('XColumn')
|
||||
x_values = [d.text for d in x_column.findall('d')]
|
||||
|
||||
for i, x_val in enumerate(x_values):
|
||||
row = [x_val]
|
||||
for y_column in table.findall('YColumn'):
|
||||
subcolumn = y_column.find('Subcolumn')
|
||||
y_values = [d.text for d in subcolumn.findall('d')]
|
||||
row.append(y_values[i] if i < len(y_values) else '')
|
||||
writer.writerow(row)
|
||||
```
|
||||
|
||||
### Batch update info constants
|
||||
```python
|
||||
import glob
|
||||
|
||||
for pzfx_file in glob.glob('*.pzfx'):
|
||||
tree = ET.parse(pzfx_file)
|
||||
|
||||
# Find or create date constant
|
||||
info = tree.find('.//Info')
|
||||
date_constant = info.find("./Constant[Name='Date']")
|
||||
|
||||
if date_constant is None:
|
||||
# Create new constant
|
||||
constant = ET.SubElement(info, 'Constant')
|
||||
ET.SubElement(constant, 'Name').text = 'Date'
|
||||
ET.SubElement(constant, 'Value').text = '2024-01-15'
|
||||
else:
|
||||
# Update existing
|
||||
date_constant.find('Value').text = '2024-01-15'
|
||||
|
||||
tree.write(pzfx_file, encoding='UTF-8', xml_declaration=True)
|
||||
```
|
||||
|
||||
## Limitations
|
||||
|
||||
**What you CAN access**:
|
||||
- ✅ All data values in tables
|
||||
- ✅ All info constants
|
||||
- ✅ Table structure and format
|
||||
- ✅ Column/row titles
|
||||
- ✅ File metadata
|
||||
|
||||
**What you CANNOT access**:
|
||||
- ❌ Analysis parameter details (encrypted)
|
||||
- ❌ Calculated results values (encrypted)
|
||||
- ❌ Graph appearance settings (encrypted)
|
||||
- ❌ Analysis method details (encrypted)
|
||||
|
||||
**Workaround**: Let Prism do the analysis. You modify data, Prism recalculates everything when opened.
|
||||
|
||||
## Best Practices
|
||||
|
||||
1. **Always preserve XML declaration**: Keep `<?xml version="1.0"?>` header
|
||||
2. **Maintain structure**: Don't remove or reorder major elements
|
||||
3. **Validate after modification**: Use xmllint or schema validation
|
||||
4. **Backup originals**: Keep copy before programmatic modification
|
||||
5. **Use proper encoding**: Save as UTF-8 with XML declaration
|
||||
6. **Handle missing values**: Empty `<d></d>` tags for missing data
|
||||
7. **Test with Prism**: Open modified files in Prism to verify
|
||||
|
||||
## Resources
|
||||
|
||||
- **Schema files**: `../../prism-xml-schema/Prism7XMLSchema.xml`
|
||||
- **Stylesheet**: `../../prism-xml-schema/Prism7XMLStyleSheet.xml`
|
||||
- **GraphPad documentation**: https://www.graphpad.com/
|
||||
- **XML tools**: xmllint, Python lxml, R xml2 package
|
||||
Reference in New Issue
Block a user