Initial commit

.github/workflows/docker.yml

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+name: Build Docker image
+
+on:
+  push:
+    branches:
+      - "main"
+    paths:
+      - "dockerfile"
+      - ".github/workflows/docker.yml"
+
+env:
+  REGISTRY: ghcr.io
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+
+    defaults:
+      run:
+        working-directory: "."
+
+    steps:
+      - name: Checkout GitHub Action
+        uses: actions/checkout@v3
+
+      - name: Login to GitHub Container Registry (GHCR)
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: metadata
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ github.repository }}
+          tags: |
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}} 
+            type=semver,pattern={{major}}
+            type=ref,event=branch
+            type=sha
+            latest
+
+      - name: Build and push to GHCR
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.metadata.outputs.tags }}
+          labels: ${{ steps.metadata.outputs.labels }}
+          provenance: false

.gitignore

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+makefile
+.secrets
+develop.ipynb

dockerfile

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+# Use an official Python runtime as a parent image
+FROM python:3.9-slim
+
+# Set the working directory in the container
+WORKDIR /usr/src/app
+
+# Install any needed packages specified in requirements.txt
+RUN pip install --no-cache-dir requests pandas synapseclient
+
+# Copy the current directory contents into the container at /usr/src/app
+COPY . .
+
+# Make the script run when the container launches
+CMD ["python", "./monitor.py"]

monitor.py

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+import json
+import requests
+import synapseclient
+from synapseclient import EntityViewSchema, EntityViewType, Synapse
+syn  = synapseclient.Synapse()
+
+import sys
+
+fileview = 'syn20446927'
+webhook_url = 'https://hooks.slack.com/services/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'
+fileview = sys.argv[1]
+webhook_url = sys.argv[2]
+
+syn.login()
+
+
+def find_modified_entities_fileview(
+    syn: Synapse, syn_id: str, value: int = 1, unit: str = "day"
+) -> list:
+    """Finds entities scoped in a fileview modified in the past {value} {unit}
+
+    Args:
+        syn: Synapse connection
+        syn_id: Synapse Fileview Id
+        value: number of time units
+        unit: time unit
+
+    Returns:
+        List of synapse ids
+    """
+    # Update the view
+    # _force_update_view(syn, view_id)
+
+    query = (
+        f"select id, projectId, parentId, createdBy, modifiedBy, Component from {syn_id} where "
+        f"modifiedOn > unix_timestamp(NOW() - INTERVAL {value} {unit})*1000"
+    )
+    results = syn.tableQuery(query)
+    resultsdf = results.asDataFrame()
+    return resultsdf
+
+
+def enrich_count(df, syn):
+    """
+    Enriches a DataFrame with user names, project names, and parent folder names from Synapse.
+
+    Args:
+    df (pd.DataFrame): DataFrame containing Synapse data with columns 'modifiedBy', 'projectId', and 'parentId'.
+    syn (synapseclient.Synapse): A logged-in Synapse client instance.
+
+    Returns:
+    pd.DataFrame: The enriched DataFrame.
+    """
+    # Add columns for user, project name, and parent folder name
+    df['userName'] = ''
+    df['projectName'] = ''
+    df['parentFolderName'] = ''
+
+    for index, row in df.iterrows():
+        # Get user info
+        user = syn.getUserProfile(row['modifiedBy'])
+        df.at[index, 'userName'] = user['userName']
+
+        # Get project info
+        project = syn.get(row['projectId'], downloadFile=False)
+        df.at[index, 'projectName'] = project.name
+
+        # Get parent folder info
+        parent_folder = syn.get(row['parentId'], downloadFile=False)
+        df.at[index, 'parentFolderName'] = parent_folder.name
+
+    return df
+
+
+def dataframe_to_slack_block_with_md_links(df):
+    base_synapse_url = "https://www.synapse.org/#!Synapse:"
+    blocks = [{"type": "section", "text": {"type": "mrkdwn", "text": "*Your daily update on HTAN activity on Synapse:*"}}]
+    for index, row in df.iterrows():
+        # Determine the correct pluralization
+        dataset_text = "dataset" if row['id'] == 1 else "datasets"
+
+        # Construct the Markdown URL for the parent folder
+        parent_folder_url = f"{base_synapse_url}{row['parentId']}"
+        parent_folder_link = f"<{parent_folder_url}|{row['parentFolderName']}>"
+
+        # Format the line with the Markdown link
+        line = f"{row['userName']} modified {row['id']} {dataset_text} in the {parent_folder_link} folder of the {row['projectName']} project."
+        block = {"type": "section", "text": {"type": "mrkdwn", "text": f"{line}"}}
+        blocks.append(block)
+    return {"blocks": blocks}
+
+
+def send_message_to_slack_blocks(webhook_url, blocks):
+    headers = {'Content-Type': 'application/json'}
+    data = json.dumps(blocks)
+    response = requests.post(webhook_url, headers=headers, data=data)
+    if response.status_code != 200:
+        raise ValueError(f"Request to slack returned an error {response.status_code}, the response is:\n{response.text}")
+
+
+
+count = find_modified_entities_fileview(syn, fileview).groupby(['modifiedBy','projectId','parentId']).count().reset_index()
+
+enriched_data = enrich_count(count, syn)
+
+slack_message_blocks = dataframe_to_slack_block_with_md_links(enriched_data)
+
+# Usage
+send_message_to_slack_blocks(webhook_url, slack_message_blocks)
+
+