@galaxyproject/orbit 0.0.0 → 0.9.0

package/extensions/orbit/vendor/skills/skills/galaxy-integration/jupyterlite/SKILL.md

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+---
+name: jupyterlite-galaxy
+description: Write JupyterLite notebooks that read and write Galaxy datasets in the browser with the gxy package. Use when the analysis needs custom Python over data already in a history -- plotting, reshaping, ad-hoc inspection -- rather than a Galaxy tool run, or when the user asks for a notebook inside Galaxy.
+user_invocable: true
+---
+
+# JupyterLite Galaxy Notebook Skill
+
+When helping users write JupyterLite notebooks for Galaxy:
+
+## Quick Reference
+
+### Import
+```python
+import gxy
+```
+
+### Download Datasets
+```python
+# By HID (history item number)
+path = await gxy.get(1)           # single dataset
+paths = await gxy.get([1, 2, 3])  # multiple
+
+# By name (partial match)
+path = await gxy.get("sample", identifier_type="name")
+
+# By tag
+path = await gxy.get("input_data", identifier_type="tag")
+
+# By regex
+paths = await gxy.get(r".*\.fastq$", identifier_type="regex")
+
+# By dataset ID
+path = await gxy.get("f9cad7b01a472135", identifier_type="id")
+
+# Get datatype too
+path, dtype = await gxy.get(1, retrieve_datatype=True)
+```
+
+### Upload Results
+```python
+# Upload file to history
+await gxy.put("output.csv")
+
+# Custom name and extension
+await gxy.put("results.txt", output="My Analysis Results", ext="tabular")
+
+# With genome build
+await gxy.put("variants.vcf", ext="vcf", dbkey="hg38")
+```
+
+### API Calls (GET and POST only)
+```python
+# GET request (default)
+user = await gxy.api("/api/users/current")
+
+# POST request
+result = await gxy.api("/api/histories", method="POST", data={"name": "New History"})
+
+# NOTE: Only GET and POST supported. No PUT, DELETE, PATCH.
+```
+
+### History Info
+```python
+# Get current history ID
+history_id = await gxy.get_history_id()
+
+# Get visible datasets in history (not deleted/hidden)
+datasets = await gxy.get_history()
+for ds in datasets:
+    print(f"{ds['hid']}: {ds['name']} ({ds['extension']})")
+```
+
+## Common Patterns
+
+### Read tabular data with pandas
+```python
+import gxy
+import pandas as pd
+
+path = await gxy.get(1)
+df = pd.read_csv(path, sep="\t")
+```
+
+### Process FASTA
+```python
+import gxy
+
+path = await gxy.get("sequences", identifier_type="name")
+with open(path) as f:
+    for line in f:
+        if line.startswith(">"):
+            print(line.strip())
+```
+
+### Save plot to Galaxy
+```python
+import gxy
+import matplotlib.pyplot as plt
+
+plt.plot([1, 2, 3], [1, 4, 9])
+plt.savefig("plot.png")
+await gxy.put("plot.png", output="My Plot", ext="png")
+```
+
+### Batch processing
+```python
+import gxy
+
+paths = await gxy.get(r".*\.fastq$", identifier_type="regex")
+for path in paths:
+    # process each file
+    result = process(path)
+    await gxy.put(result)
+```
+
+## Important Notes
+
+1. All gxy functions are **async** - use `await`
+2. Downloaded files go to Pyodide virtual filesystem
+3. File naming: `{hid}.{ext}.{id}.{txt|dat}`
+4. Collections (`hdca`) not yet supported
+5. Pre-installed packages: pandas, numpy, matplotlib, seaborn, plotly
+6. Source: [galaxy-visualizations/jupyterlite/gxy](https://github.com/galaxyproject/galaxy-visualizations/blob/main/packages/jupyterlite/gxy/gxy/__init__.py)
+
+## Workflow with MCP
+
+Before writing notebook code, use Galaxy MCP tools to discover datasets:
+
+```
+# In Claude Code, use MCP to find dataset IDs:
+get_history_contents(history_id="...")
+
+# Then reference those IDs in notebook code:
+path = await gxy.get("dataset_id_here", identifier_type="id")
+```
+
+## Examples
+
+See `examples/` for complete notebooks:
+- `average_col3.ipynb` - Simple tabular data processing
+- `extract_sample_metadata.ipynb` - Metadata extraction with regex
+- `variant_annotation.ipynb` - Complex analysis with Biopython + visualization
+- `vcp_variant_map.ipynb` - Geographic visualization with Altair

package/extensions/orbit/vendor/skills/skills/galaxy-integration/jupyterlite/examples/average_col3.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Average of Column 3 from Dataset #13437\n",
+    "\n",
+    "This notebook reads dataset #13437 from Galaxy history and computes the average of column 3."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import gxy\n",
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Download dataset #13437 from Galaxy history\n",
+    "path = await gxy.get(13437)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Read into pandas dataframe\n",
+    "df = pd.read_csv(path, sep=\"\\t\", header=None)\n",
+    "df.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Compute average of column 3 (0-indexed as column 2)\n",
+    "avg_col3 = df[2].mean()\n",
+    "print(f\"Average of column 3: {avg_col3}\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.10.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

package/extensions/orbit/vendor/skills/skills/galaxy-integration/jupyterlite/examples/extract_sample_metadata.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Extract Sample Metadata\n",
+    "\n",
+    "This notebook extracts key metadata columns (Sample ID, Location, Collection Date) from the full sample metadata table.\n",
+    "\n",
+    "- For US samples: parses state from strain name (e.g., `MVs/Virginia.USA/...`)\n",
+    "- For Canadian samples: parses province from strain name (e.g., `MVs/Ontario.CAN/...`)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import gxy\n",
+    "import pandas as pd\n",
+    "import re\n",
+    "\n",
+    "# Suppress warnings\n",
+    "import warnings\n",
+    "warnings.filterwarnings('ignore')\n",
+    "\n",
+    "print(\"Libraries loaded\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Dataset ID - change this to match your metadata file\n",
+    "METADATA_DATASET = 13674"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Download the metadata file\n",
+    "path = await gxy.get(METADATA_DATASET)\n",
+    "print(f\"Downloaded: {path}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load the full metadata\n",
+    "df = pd.read_csv(path, sep='\\t')\n",
+    "print(f\"Loaded {len(df)} samples with {len(df.columns)} columns\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def extract_location(row):\n",
+    "    \"\"\"\n",
+    "    Extract location from sample metadata.\n",
+    "    \n",
+    "    - USA samples: parse state from strain (MVs/Virginia.USA/... -> USA:Virginia)\n",
+    "    - Canada samples: parse province from strain (MVs/Ontario.CAN/... -> Canada:Ontario)\n",
+    "    - Other countries: use country field as-is\n",
+    "    \"\"\"\n",
+    "    country = str(row.get('country', '')).strip()\n",
+    "    strain = str(row.get('strain', ''))\n",
+    "    \n",
+    "    # USA: parse state\n",
+    "    if country == 'USA' and strain:\n",
+    "        match = re.search(r'MVs/([A-Za-z ]+)\\.USA/', strain)\n",
+    "        if match:\n",
+    "            state = match.group(1).strip()\n",
+    "            return f\"USA:{state}\"\n",
+    "    \n",
+    "    # Canada: parse province\n",
+    "    if country == 'Canada' and strain:\n",
+    "        match = re.search(r'MVs/([A-Za-z ]+)\\.CAN/', strain)\n",
+    "        if match:\n",
+    "            province = match.group(1).strip()\n",
+    "            return f\"Canada:{province}\"\n",
+    "    \n",
+    "    return country\n",
+    "\n",
+    "# Test on a few rows\n",
+    "print(\"Testing location extraction:\")\n",
+    "test_indices = [0, 5, 45, 55, 103]  # USA, USA, Canada Alberta, Canada BC, Romania\n",
+    "for idx in test_indices:\n",
+    "    if idx < len(df):\n",
+    "        loc = extract_location(df.iloc[idx])\n",
+    "        print(f\"  {df.iloc[idx]['Sample']}: {loc}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Extract the 3 columns we need, with enhanced location\n",
+    "result = pd.DataFrame({\n",
+    "    'sample_id': df['Sample'],\n",
+    "    'location': df.apply(extract_location, axis=1),\n",
+    "    'collection_date': df['collection_date']\n",
+    "})\n",
+    "\n",
+    "print(f\"Extracted {len(result)} rows\")\n",
+    "result.head(10)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Filter out samples missing location or date\n",
+    "before = len(result)\n",
+    "result = result.dropna(subset=['location', 'collection_date'])\n",
+    "result = result[result['location'].str.strip() != '']\n",
+    "result = result[result['collection_date'].str.strip() != '']\n",
+    "after = len(result)\n",
+    "\n",
+    "print(f\"Filtered: {before} -> {after} samples\")\n",
+    "print(f\"Removed {before - after} samples with missing data\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Summary\n",
+    "print(\"=== SUMMARY ===\")\n",
+    "print(f\"Total samples: {len(result)}\")\n",
+    "print(f\"\\nLocations:\")\n",
+    "print(result['location'].value_counts().to_string())\n",
+    "print(f\"\\nDate range: {result['collection_date'].min()} to {result['collection_date'].max()}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# View final table\n",
+    "result"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Save to Galaxy\n",
+    "result.to_csv('sample_metadata_clean.tsv', sep='\\t', index=False)\n",
+    "await gxy.put('sample_metadata_clean.tsv', output='Sample Metadata (Clean)', ext='tabular')\n",
+    "print(\"Saved to Galaxy history!\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.10.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}