287 clowder2 test extractor

.github/workflows/ci.yaml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.9, 3.11]
 
     steps:
     - uses: actions/checkout@v2

pyclowder/api/v1/files.py

@@ -348,7 +348,7 @@ def _upload_to_dataset_local(connector, client, datasetid, filepath):
     """
 
     logger = logging.getLogger(__name__)
-    url = '%s/api/uploadToDataset/%s?key=%s' % (client.host, datasetid, cliet.key)
+    url = '%s/api/uploadToDataset/%s?key=%s' % (client.host, datasetid, client.key)
 
     if os.path.exists(filepath):
         # Replace local path with remote path before uploading

pyclowder/api/v2/files.py

@@ -96,6 +96,22 @@ def download_info(connector, client, fileid):
 
     return result
 
+def download_summary(connector, client, fileid):
+    """Download file summary  from Clowder.
+
+    Keyword arguments:
+    connector -- connector information, used to get missing parameters and send status updates
+    client -- ClowderClient containing authentication credentials
+    fileid -- the file to fetch metadata of
+    """
+
+    url = '%s/api/v2/files/%s/summary' % (client.host, fileid)
+    headers = {"Authorization": "Bearer " + client.key}
+    # fetch data
+    result = connector.get(url, stream=True, verify=connector.ssl_verify if connector else True, headers=headers)
+
+    return result
+
 
 def download_metadata(connector,client, fileid, extractor=None):
     """Download file JSON-LD metadata from Clowder.
@@ -194,13 +210,13 @@ def upload_preview(connector, client, fileid, previewfile, previewmetadata=None,
 
     # associate uploaded preview with orginal file
     if fileid and not (previewmetadata and 'section_id' in previewmetadata and previewmetadata['section_id']):
-        url = '%s/api/files/%s/previews/%s?key=%s' % (host, fileid, previewid, key)
+        url = '%s/api/files/%s/previews/%s?key=%s' % (client.host, fileid, previewid, client.key)
         result = connector.post(url, headers=headers, data=json.dumps({}),
                                 verify=connector.ssl_verify if connector else True)
 
     # associate metadata with preview
     if previewmetadata is not None:
-        url = '%s/api/previews/%s/metadata?key=%s' % (host, previewid, key)
+        url = '%s/api/previews/%s/metadata?key=%s' % (client.host, previewid, client.key)
         result = connector.post(url, headers=headers, data=json.dumps(previewmetadata),
                                 verify=connector.ssl_verify if connector else True)
 

pyclowder/files.py

@@ -71,6 +71,21 @@ def download_info(connector, host, key, fileid):
         result = v1files.download_info(connector, client, fileid)
     return result.json()
 
+def download_summary(connector, host, key, fileid):
+    """Download file summary  from Clowder.
+
+    Keyword arguments:
+    connector -- connector information, used to get missing parameters and send status updates
+    host -- the clowder host, including http and port, should end with a /
+    key -- the secret key to login to clowder
+    fileid -- the file to fetch metadata of
+    """
+    client = ClowderClient(host=host, key=key)
+    if clowder_version == 2:
+        result = v2files.download_summary(connector, client, fileid)
+    else:
+        result = v1files.download_info(connector, client, fileid)
+    return result.json()
 
 def download_metadata(connector, host, key, fileid, extractor=None):
     """Download file JSON-LD metadata from Clowder.
@@ -287,7 +302,8 @@ def upload_to_dataset(connector, host, key, datasetid, filepath, check_duplicate
     """
     client = ClowderClient(host=host, key=key)
     if clowder_version == 2:
-        v2files.upload_to_dataset(connector, client, datasetid, filepath, check_duplicate)
+        uploadedfileid = v2files.upload_to_dataset(connector, client, datasetid, filepath, check_duplicate)
+        return uploadedfileid
     else:
         logger = logging.getLogger(__name__)
 

sample-extractors/test-dataset-extractor/Dockerfile

@@ -0,0 +1,8 @@
+FROM python:3.8
+
+WORKDIR /extractor
+COPY requirements.txt ./
+RUN pip install -r requirements.txt
+
+COPY test-dataset-extractor.py extractor_info.json ./
+CMD python test-dataset-extractor.py

sample-extractors/test-dataset-extractor/README.md

@@ -0,0 +1,81 @@
+A simple test extractor that verifies the functions of file in pyclowder.
+
+# Docker
+
+This extractor is ready to be run as a docker container, the only dependency is a running Clowder instance. Simply build and run.
+
+1. Start Clowder V2. For help starting Clowder V2, see our [getting started guide](https://github.com/clowder-framework/clowder2/blob/main/README.md).
+
+2. First build the extractor Docker container:
+
+```
+# from this directory, run:
+
+docker build -t test-dataset-extractor .
+```
+
+3. Finally run the extractor:
+
+```
+docker run -t -i --rm --net clowder_clowder -e "RABBITMQ_URI=amqp://guest:guest@rabbitmq:5672/%2f" --name "test-dataset-extractor" test-dataset-extractor
+```
+
+Then open the Clowder web app and run the wordcount extractor on a .txt file (or similar)! Done.
+
+### Python and Docker details
+
+You may use any version of Python 3. Simply edit the first line of the `Dockerfile`, by default it uses `FROM python:3.8`.
+
+Docker flags:
+
+- `--net` links the extractor to the Clowder Docker network (run `docker network ls` to identify your own.)
+- `-e RABBITMQ_URI=` sets the environment variables can be used to control what RabbitMQ server and exchange it will bind itself to. Setting the `RABBITMQ_EXCHANGE` may also help.
+  - You can also use `--link` to link the extractor to a RabbitMQ container.
+- `--name` assigns the container a name visible in Docker Desktop.
+
+## Troubleshooting
+
+**If you run into _any_ trouble**, please reach out on our Clowder Slack in the [#pyclowder channel](https://clowder-software.slack.com/archives/CNC2UVBCP).
+
+Alternate methods of running extractors are below.
+
+# Commandline Execution
+
+To execute the extractor from the command line you will need to have the required packages installed. It is highly recommended to use python virtual environment for this. You will need to create a virtual environment first, then activate it and finally install all required packages.
+
+```
+  Step 1 - Start clowder docker-compose 
+  Step 2 - Starting heartbeat listener 
+          virtualenv clowder2-python (try pipenv)
+          source clowder2-python/bin/activate
+  Step 3 - Run heatbeat_listener_sync.py to register new extractor (This step will likely not be needed in future)
+            cd ~/Git/clowder2/backend
+	       pip install email_validator
+        copy heartbeat_listener_sync.py to /backend from /backend/app/rabbitmq
+	    python heartbeat_listener_sync.py
+
+  Step 4 - Installing pyclowder branch & running extractor
+	    source ~/clowder2-python/bin/activate
+	    pip uninstall pyclowder
+
+	    # the pyclowder Git repo should have Todd's branch activated (50-clowder20-submit-file-to-extractor)
+	    pip install -e ~/Git/pyclowder
+
+	    cd ~/Git/pyclowder/sample-extractors/test-dataset-extractor
+	    export CLOWDER_VERSION=2   
+	    export CLOWDER_URL=http://localhost:8000/
+
+	    python test-dataset-extractor.py
+
+
+  Step 5 = # post a particular File ID (text file) to the new extractor
+    POST http://localhost:3002/api/v2/files/639b31754241665a4fc3e513/extract?extractorName=ncsa.test-dataset-extractor
+
+    Or,
+    Go to Clowder UI and submit a file for extraction
+```
+
+# Run the extractor from Pycharm
+  You can run the heartbeat_listener_sync.py and test_file_extractor.py from pycharm. 
+  Create a pipenv (generally pycharm directs you to create one when you first open the file). To run test_file_extractor.py,
+  add 'CLOWDER_VERSION=2' to environment variable in run configuration.

sample-extractors/test-dataset-extractor/extractor_info.json

@@ -0,0 +1,29 @@
+{
+  "@context": "http://clowder.ncsa.illinois.edu/contexts/extractors.jsonld",
+  "name": "ncsa.test-dataset-extractor",
+  "version": "2.0",
+  "description": "Test Dataset extractor. Test to verify all functionalities of dataset in pyclowder.",
+  "author": "Dipannita Dey <[email protected]>",
+  "contributors": [],
+  "contexts": [
+    {
+      "lines": "http://clowder.ncsa.illinois.edu/metadata/sample_metadata#lines",
+      "words": "http://clowder.ncsa.illinois.edu/metadata/sample_metadata#words",
+      "characters": "http://clowder.ncsa.illinois.edu/metadata/sample_metadata#characters"
+    }
+  ],
+  "repository": [
+    {
+      "repType": "git",
+      "repUrl": "https://opensource.ncsa.illinois.edu/stash/scm/cats/pyclowder.git"
+    }
+  ],
+  "process": {
+    "dataset": [
+    "*"
+  ]
+  },
+  "external_services": [],
+  "dependencies": [],
+  "bibtex": []
+}

sample-extractors/test-dataset-extractor/requirements.txt

@@ -0,0 +1 @@
+pyclowder==2.6.0

sample-extractors/test-dataset-extractor/test-dataset-extractor.py

@@ -0,0 +1,72 @@
+#!/usr/bin/env python
+
+"""Example extractor based on the clowder code."""
+
+import logging
+import subprocess
+import os
+
+from pyclowder.extractors import Extractor
+import pyclowder.files
+
+
+class TestDatasetExtractor(Extractor):
+    """Test the functionalities of an extractor."""
+    def __init__(self):
+        Extractor.__init__(self)
+
+        # add any additional arguments to parser
+        # self.parser.add_argument('--max', '-m', type=int, nargs='?', default=-1,
+        #                          help='maximum number (default=-1)')
+
+        # parse command line and load default logging configuration
+        self.setup()
+
+        # setup logging for the exctractor
+        logging.getLogger('pyclowder').setLevel(logging.DEBUG)
+        logging.getLogger('__main__').setLevel(logging.DEBUG)
+
+    def process_message(self, connector, host, secret_key, resource, parameters):
+        # Process the file and upload the results
+
+        logger = logging.getLogger(__name__)
+        dataset_id = resource['id']
+
+        # Local file path to file which you want to upload to dataset
+        file_path = os.path.join(os.getcwd(), 'test_dataset_extractor_file.txt')
+
+        # Upload a new file to dataset
+        file_id = pyclowder.files.upload_to_dataset(connector, host, secret_key, dataset_id, file_path, True)
+        if file_id is None:
+            logger.error("Error uploading file")
+        else:
+            logger.info("File uploaded successfully")
+
+        # Get file list under dataset
+        file_list = pyclowder.datasets.get_file_list(connector, host, secret_key, dataset_id)
+        logger.info("File list : %s", file_list)
+        is_in = file_id in [file['id'] for file in file_list]
+        if file_id in [file['id'] for file in file_list]:
+            logger.info("File uploading and retrieving file list succeeded")
+        else:
+            logger.error("File uploading/retrieving file list didn't succeed")
+
+        # Download info of dataset
+        dataset_info = pyclowder.datasets.get_info(connector, host, secret_key, dataset_id)
+        logger.info("Dataset info: %s", dataset_info)
+        if dataset_id == dataset_info['id']:
+            logger.info("Success in downloading dataset info")
+        else:
+            logger.error("Error in downloading dataset info")
+
+        # Downloading metadata of dataset
+        dataset_metadata = pyclowder.datasets.download_metadata(connector, host, secret_key, dataset_id)
+        if dataset_metadata is None:
+            logger.info("No metadata found for dataset %s", dataset_id)
+        else:
+            logger.info("Metadata: %s", dataset_metadata)
+
+
+if __name__ == "__main__":
+    extractor = TestDatasetExtractor()
+    extractor.start()

sample-extractors/test-dataset-extractor/test_dataset_extractor_file.txt

@@ -0,0 +1 @@
+This is a test file for the test dataset extractor.

sample-extractors/test-file-extractor/Dockerfile

@@ -0,0 +1,8 @@
+FROM python:3.8
+
+WORKDIR /extractor
+COPY requirements.txt ./
+RUN pip install -r requirements.txt
+
+COPY test-file-extractor.py extractor_info.json ./
+CMD python test-file-extractor.py

sample-extractors/test-file-extractor/README.md

@@ -0,0 +1,81 @@
+A simple test extractor that verifies the functions of file in pyclowder.
+
+# Docker
+
+This extractor is ready to be run as a docker container, the only dependency is a running Clowder instance. Simply build and run.
+
+1. Start Clowder V2. For help starting Clowder V2, see our [getting started guide](https://github.com/clowder-framework/clowder2/blob/main/README.md).
+
+2. First build the extractor Docker container:
+
+```
+# from this directory, run:
+
+docker build -t test-file-extractor .
+```
+
+3. Finally run the extractor:
+
+```
+docker run -t -i --rm --net clowder_clowder -e "RABBITMQ_URI=amqp://guest:guest@rabbitmq:5672/%2f" --name "test-file-extractor" test-file-extractor
+```
+
+Then open the Clowder web app and run the wordcount extractor on a .txt file (or similar)! Done.
+
+### Python and Docker details
+
+You may use any version of Python 3. Simply edit the first line of the `Dockerfile`, by default it uses `FROM python:3.8`.
+
+Docker flags:
+
+- `--net` links the extractor to the Clowder Docker network (run `docker network ls` to identify your own.)
+- `-e RABBITMQ_URI=` sets the environment variables can be used to control what RabbitMQ server and exchange it will bind itself to. Setting the `RABBITMQ_EXCHANGE` may also help.
+  - You can also use `--link` to link the extractor to a RabbitMQ container.
+- `--name` assigns the container a name visible in Docker Desktop.
+
+## Troubleshooting
+
+**If you run into _any_ trouble**, please reach out on our Clowder Slack in the [#pyclowder channel](https://clowder-software.slack.com/archives/CNC2UVBCP).
+
+Alternate methods of running extractors are below.
+
+# Commandline Execution
+
+To execute the extractor from the command line you will need to have the required packages installed. It is highly recommended to use python virtual environment for this. You will need to create a virtual environment first, then activate it and finally install all required packages.
+
+```
+  Step 1 - Start clowder docker-compose 
+  Step 2 - Starting heartbeat listener 
+          virtualenv clowder2-python (try pipenv)
+          source clowder2-python/bin/activate
+  Step 3 - Run heatbeat_listener_sync.py to register new extractor (This step will likely not be needed in future)
+            cd ~/Git/clowder2/backend
+	       pip install email_validator
+        copy heartbeat_listener_sync.py to /backend from /backend/app/rabbitmq
+	    python heartbeat_listener_sync.py
+
+  Step 4 - Installing pyclowder branch & running extractor
+	    source ~/clowder2-python/bin/activate
+	    pip uninstall pyclowder
+
+	    # the pyclowder Git repo should have Todd's branch activated (50-clowder20-submit-file-to-extractor)
+	    pip install -e ~/Git/pyclowder
+
+	    cd ~/Git/pyclowder/sample-extractors/test-file-extractor
+	    export CLOWDER_VERSION=2   
+	    export CLOWDER_URL=http://localhost:8000/
+
+	    python test-file-extractor.py
+
+
+  Step 5 = # post a particular File ID (text file) to the new extractor
+    POST http://localhost:3002/api/v2/files/639b31754241665a4fc3e513/extract?extractorName=ncsa.test-file-extractor
+
+    Or,
+    Go to Clowder UI and submit a file for extraction
+```
+
+# Run the extractor from Pycharm
+  You can run the heartbeat_listener_sync.py and test_file_extractor.py from pycharm. 
+  Create a pipenv (generally pycharm directs you to create one when you first open the file). To run test_file_extractor.py,
+  add 'CLOWDER_VERSION=2' to environment variable in run configuration.