commit d4dea53771276adca2b6b86b7be8c8881faf8ebc Author: Zhongwei Li Date: Sun Nov 30 09:08:49 2025 +0800 Initial commit diff --git a/.claude-plugin/plugin.json b/.claude-plugin/plugin.json new file mode 100644 index 0000000..99f0414 --- /dev/null +++ b/.claude-plugin/plugin.json @@ -0,0 +1,11 @@ +{ + "name": "graphpad-prism", + "description": "Expert assistance with GraphPad Prism scientific graphing and statistics software, specializing in Prism scripting for automation, batch processing, and data analysis workflows.", + "version": "1.0.0", + "author": { + "name": "GraphPad Prism Tools" + }, + "skills": [ + "./skills" + ] +} \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..fae37b7 --- /dev/null +++ b/README.md @@ -0,0 +1,3 @@ +# graphpad-prism + +Expert assistance with GraphPad Prism scientific graphing and statistics software, specializing in Prism scripting for automation, batch processing, and data analysis workflows. diff --git 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When to Activate This Skill + +This skill should be used when users: +- Ask about GraphPad Prism scripting or automation +- Need help with Prism script syntax or commands +- Want to batch process multiple data files in Prism +- Need to integrate Prism with Excel, Python, or other tools +- Ask about Prism file formats (.pzfx, .pzc, .pzm) +- Want to export or import data programmatically +- Need guidance on automating graph generation or analysis + +## Core Capabilities + +### 1. Prism Script Commands +You have complete knowledge of all 71 Prism script commands including: +- **Navigation**: GoTo command for navigating sheets/sections +- **Loops**: ForEach, ForEachSheet for batch operations +- **File Operations**: Open, Close, Save, Import, Export +- **Data Operations**: Import, InsertData, Copy, Paste, SetInfo +- **Graph Export**: 10+ formats (PDF, SVG, PNG, JPG, EPS, etc.) +- **Text Output**: 14 W* commands for writing data to files +- **Special Commands**: AnalyzeData, Regenerate, Beep, etc. + +Reference the `command_reference.md` file for quick command lookup with syntax. + +### 2. Understanding Limitations + +**Critical**: Prism scripts have important limitations you must communicate: +- ❌ **No conditional logic** (no if/else statements) +- ❌ **No variables** (except %N, %F, %S for output) +- ❌ **Cannot read values** into variables for decisions +- ❌ **Cannot control analysis** (defined in project file, not script) +- ✅ Scripts are **purely procedural** - good for batch processing, not logic + +### 3. Workarounds for Reading Data + +When users need to read/query current Prism state, recommend the **PZFX XML approach**: + +**The PZFX Format**: +- Prism files saved as .pzfx are plain XML +- Data and info tables are readable/editable XML +- Analysis results are encrypted (readable but not editable) +- External programs (Python, R, etc.) can read/modify data +- Prism auto-updates when file is reopened + +**Workflow**: +1. Save Prism project as .pzfx +2. Use external tool (Python/R/etc.) to parse XML +3. Read data, make decisions, modify if needed +4. Reopen in Prism - everything updates automatically + +Reference `reference/xml_schemas.md` for XML structure details. + +### 4. Platform-Specific Integration + +**macOS**: +- AppleScript: Limited to launching scripts only (activate, open file, quit) +- Automator: Can run scripts via Automator Actions +- Recommendation: Use PZFX XML for data access, not AppleScript + +**Windows**: +- Shell command: Launch scripts from batch files +- OLE/ActiveX: More control, sequential execution +- Desktop shortcuts: User-friendly script launching +- Excel VBA integration: MacScript or OLE automation + +Reference the overview_and_running.md summary for detailed integration examples. + +## How to Help Users + +### For Script Writing Tasks: + +1. **Understand the goal**: What are they trying to automate? +2. **Check feasibility**: Is it possible with Prism's limitations? +3. **Suggest architecture**: + - Template-based (recommended): Create Prism file with analysis, script just imports data + - Script-driven: Script handles file operations, Prism handles analysis +4. **Provide syntax**: Use exact command syntax from reference files +5. **Include examples**: Adapt from script_examples.md +6. **Warn about limitations**: No conditionals, no reading values, etc. + +### For Integration Tasks: + +1. **Identify platform**: macOS or Windows? +2. **Choose method**: + - Simple batch: Direct script execution + - Excel integration: VBA examples in summaries + - Complex logic: Recommend PZFX + external tool +3. **Provide complete workflow**: Include synchronization patterns (done.txt polling) + +### For Troubleshooting: + +1. **Check syntax**: Commands are case-insensitive, but syntax matters +2. **Verify navigation**: Always GoTo before operating on a sheet +3. **Check file paths**: SetPath or full paths required +4. **Review limitations**: Often users expect features that don't exist + +## Reference Files + +Access these files for detailed information: + +- `command_reference.md` - Quick command syntax reference (all 71 commands) +- `reference/overview_and_running.md` - Overview & running scripts +- `reference/script_examples.md` - 7 script examples +- `reference/syntax_and_basics.md` - Syntax & basics +- `reference/data_operations.md` - Data operations +- `reference/advanced_features.md` - Advanced features +- `reference/xml_schemas.md` - PZFX file format & XML schemas +- `reference/reading_current_data.md` - How to query Prism state + +## Common Use Cases + +### Batch Import Multiple Files +```prism +SetPath "C:\Data\Experiment1" +GoTo D +ForEach *.csv + GoTo %N + Import + Next +``` + +### Monte Carlo Simulation +```prism +ForEach 1000 + GoTo R, 1 + Regenerate + AnalyzeData + GoTo R, 2 + WCell 5, 3 + Next +``` + +### Export All Graphs +```prism +GoTo G +ForEachSheet + ExportPDF "%S.pdf" + Next +``` + +### Template-Based Workflow +```prism +Open "template.pzfx" +GoTo D, 1 +Import "newdata.csv" +SaveAs "results_%F.pzfx" +GoTo L, 1 +Print +``` + +## Key Syntax Reminders + +- **Numbering**: Sheets start at 1 (not 0), first data row is 1, X column is 0 +- **Sections**: D (data), I (info), R (results), G (graphs), L (layouts) +- **Variables**: %N (loop number), %F (filename), %S (sheet name) +- **Comments**: `//` single line or `/* */` multi-line +- **Data blocks**: `...` for embedded data +- **Arguments**: `[required]` `` + +## Important Notes + +1. **No nested loops**: Only one loop level allowed +2. **No API**: Must use scripts or PZFX manipulation +3. **Sequential only**: No parallel processing +4. **Template recommended**: Store analysis in .pzm template, script imports data +5. **Cross-platform**: Scripts work on both Mac/Windows but integration differs + +## Response Style + +- Be concise but complete +- Always show actual syntax, not pseudocode +- Warn about limitations upfront +- Suggest workarounds when features don't exist +- Provide complete, runnable examples +- Reference partition summaries for complex scenarios diff --git a/skills/graphpad-prism-skill/command_reference.md b/skills/graphpad-prism-skill/command_reference.md new file mode 100644 index 0000000..eea2eed --- /dev/null +++ b/skills/graphpad-prism-skill/command_reference.md @@ -0,0 +1,192 @@ +# GraphPad Prism Script Commands - Quick Reference + +## All Commands + +**AnalyzeData** - Execute analysis + +**ApplyColorScheme** ["scheme name"] + +**Beep** - Play alert sound + +**ClearTable** ,, + +**Close** - Close current file + +**CloseOutput** - Close output file + +**CloseScriptDialog** - Close script dialog + +**Copy** - Copy entire sheet to clipboard +**Copy** [#rows] [#columns] [first row] [first col] + +**CreateLayout** [#rows] [#columns] <#StartingGraphIndex> <#Graphs> + +**CreateLog** - Create log file + +**DeleteAllDataSets** + +**DuplicateDataTable** + +**DuplicateFamily** [prepend_text] + +**EndTable** - End table definition + +**Exit** - Exit Prism (Windows only) + +**ExportAllPDF** [filename] + +**ExportBMP** [filename] + +**ExportEMF** [filename] (Windows only) + +**ExportEPS** [filename] + +**ExportJPG** [filename] + +**ExportPDF** [filename] + +**ExportPNG** [filename] + +**ExportSVG** [filename] + +**ExportTable** [filename] + +**ExportTIF** [filename] + +**ExportWMF** [filename] (Windows only) + +**ForEach** [# of loops] +**ForEach** [filespec, i.e. "C:\data\DR*.txt"] + +**ForEachSheet** - Loop over all sheets in current section + +**GoTo** , , V +**GoTo** + (next sheet) +**GoTo** - (previous sheet) + +**Import** <"filename">, , , + +**ImportLink** <"filename">, , , + +**InsertData** , , + +**InsertDataLink** , , + +**Next** - End loop iteration + +**NextRow** - Move to next table row + +**Open** ["filename"] + +**OpenOutput** ["filename"] ,, <"delimiter"> + +**Paste** - Paste from clipboard at current position +**Paste** [first row] [first col] + +**Print** - Print current sheet + +**RecalcAll** - Recalculate all results + +**Regenerate** - Regenerate random numbers (Monte Carlo) + +**Save** <"filename"> + +**SendToPP** - Send to PowerPoint (Windows only) + +**SendToWord** - Send to Word (Windows only) + +**SetAxisLimits** [which axis: X, Y, or Y2] [Top/Bottom/Interval] [value] + +**SetAxisTitle** [which axis: X, Y, or Y2] ["new title"] + +**SetGraphTitle** ["new title"] + +**SetInfo** ["value"] [rownumber] + +**SetPath** ["drive and folder path"] + +**SetProjectName** ["new name"] + +**SetScriptDialogTitle** ["dialog title"] + +**SetSheetTitle** [new_name] + +**SetValueToInfo** [infotable #] [inforow#] [datarow] [datacol] + +**SetYReplicates** [#] + +**Table** Prism [datatable number] +**Table** SQL [datasource] +**Table** XML [filename] + +**WBlock** [row(s)] [column(s)] <;> + +**WCell** [row], [col], <;&> + +**WCol** [row], , <;&> + +**WDate** <;&> + +**WRow** [row], , <;&> + +**WSheet** <;&> + +**WTable** [column title] [row] [col] +**WTable** [column title] [text or %F or %N] + +**WText** <"text"> <;&> + +**WTBlock** [row(s)] [columns to include] <;> + +**WTCol** [row, col] <, subcolumn><;&> + +**WTitle** - Write sheet title + +**WTRow** [row] <,col, subcol> <;&> + +**WTSheet** <;&> + +**WVersion** - Write Prism version + +## Variables + +%N - Loop iteration number +%F - Filename (without extension) +%X - File extension +%S - Sheet name +%D - Date and time file was last saved +%P - Prism project filename +%% - Literal percent sign + +## Syntax Notation + +[required] - Required parameter + - Optional parameter +<;&> - Optional semicolon (continue on same line with tab) or ampersand (continue without tab) +<;> - Optional semicolon (joins text without delimiter) +CLEAR - Keyword to clear existing content + +## Section Codes + +D - Data tables +I - Info tables +R - Results tables +G - Graphs +L - Layouts + +## Column/Row Numbering + +Columns: -1 (Row titles), 0 (X column), 1 (Column A), 2 (Column B)... +Rows: 0 or -1 (Column titles), 1 (First data row), 2 (Second data row)... + +## Data Block Syntax + + +value1 value2 value3 +value4 value5 value6 + + +## Comments + +// Single line comment +/* Multi-line comment */ diff --git a/skills/graphpad-prism-skill/reference/Prism7XMLSchema.xml b/skills/graphpad-prism-skill/reference/Prism7XMLSchema.xml new file mode 100644 index 0000000..a653ca2 --- /dev/null +++ b/skills/graphpad-prism-skill/reference/Prism7XMLSchema.xml @@ -0,0 +1,299 @@ + + + + XML Schema for storing data and info tables from GraphPad Prism 7.0. + Copyright 1992-2016 GraphPad Software, Inc. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/skills/graphpad-prism-skill/reference/Prism7XMLStyleSheet.xml b/skills/graphpad-prism-skill/reference/Prism7XMLStyleSheet.xml new file mode 100644 index 0000000..e5916e5 --- /dev/null +++ b/skills/graphpad-prism-skill/reference/Prism7XMLStyleSheet.xml @@ -0,0 +1,419 @@ + + + + + + + + + + + + + + + +
+ + + + +
 Notes
+ + + + + + + + +
ConstantName
  
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+ + + + + + + + + + +

This file can be opened by GraphPad Prism (version + or later).

+ This file contains data tables and + info tables: + + + +
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    + + 2 +
    +     		+ + 2 + + +   + + X-Title +   + + + 2 + + +   + + X-Title +   + + + + 2 + +   + + + + + + + + +   +
    +   + + + + X + Err.Bar + + +   + +   + + + + Starting Date + Ending Date + + +   + +   + + + + + + + + + + + + + + + + + + :Y + + + + + + + + + + + :Y + + + + + + + + + + :Y + + + + + + + + :Y + + + + + + + Mean + + + SD + + + SEM + + + %CV + + + SD + N + + + SEM + N + + + %CV + N + + + +Error + -Error + + + UpperLimit + LowerLimit + + + + + + +   +
    + % + +
    +     		+ % + +
    +     		+ % + +
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    +     + + + +     + + + + + + + + + + + * + + + + + + + + + + + + + +
    +     + + + + + + + + + + + + + + + + + + font-size:pt + + + + + + + + + + + + + + + + diff --git a/skills/graphpad-prism-skill/reference/advanced_features.md b/skills/graphpad-prism-skill/reference/advanced_features.md new file mode 100644 index 0000000..d89c14d --- /dev/null +++ b/skills/graphpad-prism-skill/reference/advanced_features.md @@ -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] ` + +**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 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] <;>` + +**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] ` +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:** `` 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 diff --git a/skills/graphpad-prism-skill/reference/data_operations.md b/skills/graphpad-prism-skill/reference/data_operations.md new file mode 100644 index 0000000..5085cb4 --- /dev/null +++ b/skills/graphpad-prism-skill/reference/data_operations.md @@ -0,0 +1,180 @@ +# Data Operations - Summary + +## Creating New Sheets + +### Commands +- `DuplicateDataTable ` +- `DuplicateFamily [prepend_text] ` +- `CreateLayout [#rows] [#columns] <#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 ,,` +- `DeleteAllDataSets ` + +### 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] ` +- `SetValueToInfo [infotable #] [inforow#] [datarow] [datacol] ` + +### 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">, , , ` +- `ImportLink <"filename">, , , ` + +#### 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 , , ` +- `InsertDataLink , , ` + +#### 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 `` and `` tags. Script continues after `` tag. + +Example: +``` +InsertData + +1, 2, 4 +5, 7, 9 + +``` + +**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] ` +- `Paste [first row] [first col] ` +- `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] ` + +### 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. diff --git a/skills/graphpad-prism-skill/reference/overview_and_running.md b/skills/graphpad-prism-skill/reference/overview_and_running.md new file mode 100644 index 0000000..f95ad7b --- /dev/null +++ b/skills/graphpad-prism-skill/reference/overview_and_running.md @@ -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. diff --git a/skills/graphpad-prism-skill/reference/reading_current_data.md b/skills/graphpad-prism-skill/reference/reading_current_data.md new file mode 100644 index 0000000..7b1daa2 --- /dev/null +++ b/skills/graphpad-prism-skill/reference/reading_current_data.md @@ -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 + + Dose Response + + Dose + Response + + + Control + + 10.5 + 12.3 + 11.8 + + +
    +``` + +### Info Constants Structure +```xml + + + + + + Experiment Details + + Date + 2024-01-15 + + + Experimenter + Jane Smith + + +``` + +## 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 | diff --git a/skills/graphpad-prism-skill/reference/script_examples.md b/skills/graphpad-prism-skill/reference/script_examples.md new file mode 100644 index 0000000..f4f30ee --- /dev/null +++ b/skills/graphpad-prism-skill/reference/script_examples.md @@ -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 block delimiter +- `InsertData N, M` - Insert data block N starting at column M +- `SetInfo constant_name, value` - Set info constant + +**Data block syntax**: +``` + +value1\tvalue2\tvalue3 +value4\tvalue5\tvalue6 + +``` + +**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 `` 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 +- `...` - 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 `` 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 `` 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 diff --git a/skills/graphpad-prism-skill/reference/syntax_and_basics.md b/skills/graphpad-prism-skill/reference/syntax_and_basics.md new file mode 100644 index 0000000..7a14851 --- /dev/null +++ b/skills/graphpad-prism-skill/reference/syntax_and_basics.md @@ -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: `` +- 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 , , V` +- `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. diff --git a/skills/graphpad-prism-skill/reference/xml_schemas.md b/skills/graphpad-prism-skill/reference/xml_schemas.md new file mode 100644 index 0000000..05c7e0c --- /dev/null +++ b/skills/graphpad-prism-skill/reference/xml_schemas.md @@ -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 + + + + + + + + + +
    + + + + + + +     +``` + +### Data Table Elements + +#### Basic Data Table +```xml + + Dose Response Data + + + + X + Y + + + + + 0.1 + 1.0 + 10.0 + + + + + Control + + 10.5 + 12.3 + 11.8 + + + + + Treatment + + 8.2 + 9.1 + 8.7 + + +
    +``` + +#### 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 + + Experiment Information + + + + Date + 2024-01-15 + + + + Experimenter + Jane Smith + + + + Concentration + 10.5 + + + + + Experiment notes go here. + Multiple lines allowed. + + +``` + +### Results Tables (Encrypted) + +```xml + + + + + + + + +``` + +**Note**: Results are readable as XML but values are encrypted. You can see structure but not values without Prism. + +### Data Types + +#### Numeric Values +```xml +10.5 +1.23e-4 + +``` + +#### Text Values +```xml +Sample A +Control +``` + +#### Formatted Text +```xml + + Bold text + Italic text + Underlined + Superscript + Subscript + +``` + +#### Dates +```xml + + ExperimentDate + 2024-01-15 + +``` + +## 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 `` 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 `` 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