Implemented upload_thumbnail to files and datasets

Author: ddey2

pyclowder/api/v1/datasets.py

@@ -260,6 +260,40 @@ def upload_metadata(connector, client, datasetid, metadata):
                            verify=connector.ssl_verify if connector else True)
     result.raise_for_status()
 
+def upload_thumbnail(connector, host, key, datasetid, thumbnailid):
+    """Upload thumbnail to 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
+        datasetid -- the dataset that the thumbnail should be associated with
+        thumbnailid -- the file containing the thumbnail
+        """
+    logger = logging.getLogger(__name__)
+    logger.info("Upload thumbnails to datasets is not available in V1")
+
+
+def upload_preview(connector, host, key, datasetid, previewfile, previewmetadata=None, preview_mimetype=None,
+                   visualization_name=None, visualization_description=None, visualization_config_data=None,
+                   visualization_component_id=None):
+    """Upload preview to 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
+    datasetid -- the dataset that is currently being processed
+    previewfile -- the file containing the preview
+    previewmetadata -- any metadata to be associated with preview, can contain a section_id
+                    to indicate the section this preview should be associated with.
+    preview_mimetype -- (optional) MIME type of the preview file. By default, this is obtained from the
+                    file itself and this parameter can be ignored. E.g. 'application/vnd.clowder+custom+xml'
+    """
+
+    logger = logging.getLogger(__name__)
+    logger.info("Upload preview to datasets is not available in V1")
+
 
 # TODO not done yet, need more testing
 class DatasetsApi(object):

pyclowder/api/v2/datasets.py

@@ -316,3 +316,22 @@ def upload_preview(connector, client, datasetid, previewfile, previewmetadata=No
 
     return preview_id
 
+def upload_thumbnail(connector, client, datasetid, thumbnailid):
+    """Upload thumbnail to 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
+            datasetid -- the dataset that the thumbnail should be associated with
+            thumbnailid -- the file containing the thumbnail
+            """
+
+    connector.message_process({"type": "dataset", "id": datasetid}, "Uploading thumbnail to dataset.")
+    headers = {'Content-Type': 'application/json',
+               'X-API-KEY': client.key}
+    url = '%s/api/v2/datasets/%s/thumbnail/%s' % (client.host, datasetid, thumbnailid)
+    result = connector.patch(url, headers=headers,
+                             verify=connector.ssl_verify if connector else True)
+    return result.json()["thumbnail_id"]
+

pyclowder/api/v2/files.py

@@ -94,6 +94,7 @@ def download_info(connector, client, fileid):
 
     return result
 
+
 def download_summary(connector, client, fileid):
     """Download file summary  from Clowder.
 
@@ -272,22 +273,24 @@ def upload_tags(connector, client, fileid, tags):
                             verify=connector.ssl_verify if connector else True)
 
 
-# TODO not implemented in v2
-def upload_thumbnail(connector, client, fileid, thumbnail):
+def upload_thumbnail(connector, client, fileid, thumbnailid):
     """Upload thumbnail to 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 that the thumbnail should be associated with
-    thumbnail -- the file containing the thumbnail
+    thumbnailid -- the file containing the thumbnail
     """
 
-    # TODO: Update the code below after V2 endpoint for uploading a thumbnail is ready.
-    logger = logging.getLogger(__name__)
-    logger.info("Thumbnail upload is under construction and currently skipped in Clowder V2 extractors!")
-    pass
+    connector.message_process({"type": "file", "id": fileid}, "Uploading thumbnail to file.")
+    headers = {'Content-Type': 'application/json',
+               'X-API-KEY': client.key}
+    url = '%s/api/v2/files/%s/thumbnail/%s' % (client.host, fileid, thumbnailid)
+    result = connector.patch(url, headers=headers,
+                             verify=connector.ssl_verify if connector else True)
+    return result.json()["thumbnail_id"]
 
 
 def upload_to_dataset(connector, client, datasetid, filepath, check_duplicate=False):

pyclowder/connectors.py

@@ -565,6 +565,23 @@ def post(self, url, data=None, json_data=None, raise_status=True, **kwargs):
 
         return response
 
+    def patch(self, url, data=None, json_data=None, raise_status=True, **kwargs):
+        """
+        This methods wraps the Python requests PATCH method
+        :param url: URl to use in PATCH request
+        :param data: (optional) data (Dictionary, bytes, or file-like object) to send in the body of PATCH request
+        :param json_data: (optional) json data to send with PATCH request
+        :param raise_status: (optional) If set to True, call raise_for_status. Default is True.
+        :param kwargs: List of other optional arguments to pass to PATCH call
+        :return: Response of the PATCH request
+        """
+
+        response = requests.patch(url, data=data, json=json_data, **kwargs)
+        if raise_status:
+            response.raise_for_status()
+
+        return response
+
     def put(self, url, data=None, raise_status=True, **kwargs):
         """
         This methods wraps the Python requests PUT method

pyclowder/datasets.py

@@ -250,3 +250,19 @@ def upload_preview(connector, host, key, datasetid, previewfile, previewmetadata
                                          visualization_config_data=visualization_config_data,
                                          visualization_component_id=visualization_component_id)
     return preview_id
+
+
+def upload_thumbnail(connector, host, key, datasetid, thumbnailid):
+    """Upload thumbnail to 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
+            datasetid -- the dataset that the thumbnail should be associated with
+            thumbnailid -- the file containing the thumbnail
+            """
+    logger = logging.getLogger(__name__)
+
+    client = ClowderClient(host=host, key=key)
+    return datasets.upload_thumbnail(connector, client, datasetid, thumbnailid)

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

@@ -76,6 +76,14 @@ def process_message(self, connector, host, secret_key, resource, parameters):
         else:
             logger.info("Preview %s uploaded to dataset successfully ", preview_id)
 
+        # Uploaing thumbnail
+        thumbnailid = "64e4bed765b3b301d4965820"
+        thumbnail_id = pyclowder.datasets.upload_thumbnail(connector, host, secret_key, dataset_id, thumbnailid)
+        if thumbnail_id == thumbnailid:
+            logger.info("Success in uploading thumbnail to file")
+        else:
+            logger.error("Error in uploading thumbnail to file")
+
 
 
 

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

@@ -62,6 +62,14 @@ def process_message(self, connector, host, secret_key, resource, parameters):
         else:
             logger.error("Error in downloading file summary")
 
+        # Uploaing thumbnail
+        thumbnailid = "64ac275727c83a6786dd9fd4"
+        thumbnail_id = pyclowder.files.upload_thumbnail(connector, host, secret_key, file_id, thumbnailid)
+        if thumbnail_id == thumbnailid:
+            logger.info("Success in uploading thumbnail to file")
+        else:
+            logger.error("Error in uploading thumbnail to file")
+
 
 
 if __name__ == "__main__":