set max-width on visualizing images

set max-width on visualising images
giannisdoukas · Jul 21, 2020 · 4c4a18f · 4c4a18f
2 parents 592981f + 4f22d58
commit 4c4a18f
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Showing 3 changed files with 30 additions and 16 deletions.
diff --git a/cwlkernel/cwlrepository/CWLComponent.py b/cwlkernel/cwlrepository/CWLComponent.py
@@ -4,7 +4,7 @@
 from io import StringIO
 from typing import Dict, List, Union, Optional
 
-import yaml
+from ruamel import yaml
 
 
 class WorkflowComponent(ABC):

diff --git a/cwlkernel/kernel_magics.py b/cwlkernel/kernel_magics.py
@@ -3,6 +3,8 @@
 import os
 import random
 import subprocess
+import traceback
+import xml.etree.ElementTree as ET
 from collections import OrderedDict
 from copy import deepcopy
 from io import StringIO
@@ -254,7 +256,7 @@ def display_data_image(kernel: CWLKernel, data_name: str):
         mime = 'image/svg+xml'
     else:
         raise ValueError(f'unsupported type {result}')
-    image = f"""<image src="data:{mime}; base64, {image}" alt="{result}">"""
+    image = f"""<image src="data:{mime}; base64, {image}" alt="{result}" style="max-width: 100%">"""
     kernel.send_response(
         kernel.iopub_socket,
         'display_data',
@@ -324,14 +326,20 @@ def data(kernel: CWLKernel, *args):
 def github_import(kernel: CWLKernel, url: str):
     cwl_factory = WorkflowComponentFactory()
     for cwl_file in kernel._github_resolver.resolve(url):
-        with open(cwl_file) as f:
-            file_data = f.read()
-        cwl_component = cwl_factory.get_workflow_component(file_data)
-        cwl_component._id = os.path.splitext(os.path.basename(cwl_file))[0]
-        relative_dir = Path(os.path.relpath(cwl_file, kernel._github_resolver._local_root_directory.as_posix()))
-        kernel.workflow_repository.register_tool(cwl_component, relative_dir)
-        kernel.send_response(kernel.iopub_socket, 'stream',
-                             {'name': 'stdout', 'text': f"tool '{cwl_component.id}' registered\n"})
+        try:
+            with open(cwl_file) as f:
+                file_data = f.read()
+            cwl_component = cwl_factory.get_workflow_component(file_data)
+            cwl_component._id = os.path.splitext(os.path.basename(cwl_file))[0]
+            relative_dir = Path(os.path.relpath(cwl_file, kernel._github_resolver._local_root_directory.as_posix()))
+            kernel.workflow_repository.register_tool(cwl_component, relative_dir)
+            kernel.send_response(kernel.iopub_socket, 'stream',
+                                 {'name': 'stdout', 'text': f"tool '{cwl_component.id}' registered\n"})
+        except Exception as e:
+            kernel.send_error_response(f'Error on loading tool "{cwl_file}"\n')
+            stacktrace_error = StringIO()
+            traceback.print_exc(file=stacktrace_error)
+            kernel.send_error_response(f'Error: {e}\n{stacktrace_error.getvalue()}')
 
 
 @CWLKernel.register_magic('viewTool')
@@ -386,15 +394,16 @@ def visualize_graph(kernel: CWLKernel, tool_id: str):
     cwltool_main(['--print-rdf', os.path.abspath(path)], stdout=rdf_stream, logger_handler=handler)
     cwl_viewer = CWLViewer(rdf_stream.getvalue())
     (dot_object,) = pydot.graph_from_dot_data(cwl_viewer.dot())
-    image = dot_object.create('dot', 'svg')
-
+    ET.register_namespace('', 'http://www.w3.org/2000/svg')
+    image_xml = ET.fromstring(dot_object.create('dot', 'svg').decode())
+    image_container = f'<div style="max-width: 100%;">{ET.tostring(image_xml, method="html").decode()}</div>'
     kernel.send_response(
         kernel.iopub_socket,
         'display_data',
         {
             'data': {
-                "image/svg+xml": image.decode(),
-                "text/plain": image.decode()
+                "text/html": image_container,
+                "text/plain": image_container
             },
             'metadata': {},
         },

diff --git a/tests/test_CWLKernel_magics.py b/tests/test_CWLKernel_magics.py
@@ -4,6 +4,7 @@
 import tarfile
 import tempfile
 import unittest
+import xml.etree.ElementTree as ET
 from io import StringIO
 from pathlib import Path
 
@@ -448,7 +449,7 @@ def test_githubImport_without_id(self):
         )
 
     @unittest.skipIf("TRAVIS_IGNORE_DOCKER" in os.environ and os.environ["TRAVIS_IGNORE_DOCKER"] == "true",
-            "Skipping this test on Travis CI.")
+                     "Skipping this test on Travis CI.")
     def test_githubImport_walk_paths(self):
         when(requests) \
             .get(
@@ -720,9 +721,13 @@ def test_view_magic_command(self):
         )
 
         self.assertIn(
-            'image/svg+xml',
+            'text/html',
             responses[-1][0][2]['data'])
 
+        # should not raise an exception
+        tree = ET.fromstring(responses[-1][0][2]['data']['text/html'])
+        self.assertEqual(len(tree.findall("./{http://www.w3.org/2000/svg}svg")), 1)
+
     def test_scatter_tool(self):
         kernel = CWLKernel()
         # cancel send_response