Expose cert and ca_bundle in CLI

Allow users to specify the path to a CA bundle and client certificate file via the command line interface to facilitate working with SSL secured archives.
ImagingDataCommons · Nov 1, 2018 · 204b810 · 204b810
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diff --git a/docs/usage.rst b/docs/usage.rst
@@ -321,28 +321,51 @@ Retrieve bulk data given a URL:
 Command Line Interface (CLI)
 ----------------------------
 
-Search for instances:
+Search for studies:
 
 .. code-block:: none
 
-    dicomweb_client --url https://dicomcloud.azurewebsites.net/qidors search instances
+    dicomweb_client --url https://dicomcloud.azurewebsites.net/qidors search studies
 
 Retrieve metadata for all instances of a given study:
 
 .. code-block:: none
 
-    dicomweb_client --url https://dicomcloud.azurewebsites.net/wadors retrieve studies --study 1.2.826.0.1.3680043.8.1055.1.20111103111148288.98361414.79379639 metadata
-
+    dicomweb_client --url https://dicomcloud.azurewebsites.net/wadors \
+        retrieve studies \
+        --study 1.2.826.0.1.3680043.8.1055.1.20111103111148288.98361414.79379639 \
+        metadata
 
 The output can be *dicomized* for human interpretation:
 
 .. code-block:: none
 
-    dicomweb_client --url https://dicomcloud.azurewebsites.net/wadors retrieve studies --study 1.2.826.0.1.3680043.8.1055.1.20111103111148288.98361414.79379639 metadata --dicomize
+    dicomweb_client --url https://dicomcloud.azurewebsites.net/wadors \
+        retrieve studies \
+        --study 1.2.826.0.1.3680043.8.1055.1.20111103111148288.98361414.79379639 \
+        metadata \
+        --dicomize
+
+Retrieve the full Part 3.10 files for all instances of a given study:
+
+.. code-block:: none
+
+    dicomweb_client --url https://dicomcloud.azurewebsites.net/wadors \
+        retrieve studies \
+        --study 1.2.826.0.1.3680043.8.1055.1.20111103111148288.98361414.79379639 \
+        full
+
 
-Retrieve a single frame of a given instances as JPEG compressed image and show it:
+Retrieve a single frame of a given instances as JPEG compressed image:
 
 .. code-block:: none
 
-    dicomweb_client --url https://dicomcloud.azurewebsites.net/wadors retrieve instances --study 1.2.826.0.1.3680043.8.1055.1.20111103111148288.98361414.79379639 --series 1.2.826.0.1.3680043.8.1055.1.20111103111208937.49685336.24517034 --instance 1.2.826.0.1.3680043.8.1055.1.20111103111208937.40440871.13152534 frames --numbers 1 --image-format jpeg --show
+    dicomweb_client --url https://dicomcloud.azurewebsites.net/wadors \
+        retrieve instances \
+        --study 1.2.826.0.1.3680043.8.1055.1.20111103111148288.98361414.79379639 \
+        --series 1.2.826.0.1.3680043.8.1055.1.20111103111208937.49685336.24517034 \
+        --instance 1.2.826.0.1.3680043.8.1055.1.20111103111208937.40440871.13152534 \
+        frames \
+        --numbers 1 \
+        --image-format jpeg
 
diff --git a/src/dicomweb_client/cli.py b/src/dicomweb_client/cli.py
@@ -50,6 +50,14 @@ def _get_parser():
         '-p', '--password', dest='password', metavar='PASSWORD',
         help='password for authentication with the DICOMweb service'
     )
+    parser.add_argument(
+        '--ca', dest='ca_bundle', metavar='CERT-FILE',
+        help='path to a CA bundle file'
+    )
+    parser.add_argument(
+        '--cert', dest='cert', metavar='CERT-FILE',
+        help='path to a client certificate file in PEM format'
+    )
     parser.add_argument(
         '--url', dest='url', metavar='URL',
         help='uniform resource locator of the DICOMweb service'
@@ -459,23 +467,41 @@ def _print_pixeldata(pixels):
 def _search_for_studies(args):
     '''Searches for *Studies* and writes metadata to standard output.'''
     params = _parse_search_parameters(args)
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     studies = client.search_for_studies(**params)
     _print_metadata(studies, args.prettify, args.dicomize)
 
 
 def _search_for_series(args):
     '''Searches for Series and writes metadata to standard output.'''
     params = _parse_search_parameters(args)
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     series = client.search_for_series(args.study_instance_uid, **params)
     _print_metadata(series, args.prettify, args.dicomize)
 
 
 def _search_for_instances(args):
     '''Searches for Instances and writes metadata to standard output.'''
     params = _parse_search_parameters(args)
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     instances = client.search_for_instances(
         args.study_instance_uid, args.series_instance_uid, **params
     )
@@ -486,7 +512,13 @@ def _retrieve_study(args):
     '''Retrieves all Instances of a given Study and either writes them to
     standard output or to files on disk.
     '''
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     instances = client.retrieve_study(args.study_instance_uid)
     for inst in instances:
         sop_instance_uid = inst.SOPInstanceUID
@@ -500,7 +532,13 @@ def _retrieve_series(args):
     '''Retrieves all Instances of a given Series and either writes them to
     standard output or to files on disk.
     '''
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     instances = client.retrieve_series(
         args.study_instance_uid, args.series_instance_uid
     )
@@ -516,7 +554,13 @@ def _retrieve_instance(args):
     '''Retrieves an Instances and either writes it to standard output or to a
     file on disk.
     '''
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     instance = client.retrieve_instance(
         args.study_instance_uid, args.series_instance_uid,
         args.sop_instance_uid
@@ -531,7 +575,13 @@ def _retrieve_study_metadata(args):
     '''Retrieves metadata for all Instances of a given Study and either
     writes it to standard output or to files on disk.
     '''
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     metadata = client.retrieve_study_metadata(args.study_instance_uid)
     if args.save:
         for md in metadata:
@@ -549,7 +599,13 @@ def _retrieve_series_metadata(args):
     '''Retrieves metadata for all Instances of a given Series and either
     writes it to standard output or to files on disk.
     '''
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     metadata = client.retrieve_series_metadata(
         args.study_instance_uid, args.series_instance_uid
     )
@@ -569,7 +625,13 @@ def _retrieve_instance_metadata(args):
     '''Retrieves metadata for an individual Instances and either
     writes it to standard output or to a file on disk.
     '''
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     metadata = client.retrieve_instance_metadata(
         args.study_instance_uid, args.series_instance_uid,
         args.sop_instance_uid
@@ -588,7 +650,13 @@ def _retrieve_instance_frames(args):
     writes it to standard output or to a file on disk or displays it
     (depending on the requested content type).
     '''
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     pixeldata = client.retrieve_instance_frames(
         args.study_instance_uid, args.series_instance_uid,
         args.sop_instance_uid, args.frame_numbers,
@@ -640,15 +708,27 @@ def _retrieve_bulkdata(args):
     '''Retrieves bulk data and either writes them to standard output or to a
     file on disk.
     '''
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     data = client.retrieve_bulkdata(args.bulkdata_uri, args.image_format)
     print(data)
     print('\n')
 
 
 def _store_instances(args):
     '''Loads Instances from files on disk and stores them.'''
-    client = DICOMwebClient(args.url, args.username, args.password)
+    client = DICOMwebClient(
+        args.url,
+        username=args.username,
+        password=args.password,
+        ca_bundle=args.ca_bundle,
+        cert=args.cert
+    )
     datasets = list()
     for f in args.files:
         ds = pydicom.dcmread(f)