Merge pull request #13 from giannisdoukas/visualise

add view magic command
giannisdoukas · Jul 10, 2020 · 2909ec0 · 2909ec0
2 parents cf0915e + 2109587
commit 2909ec0
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Showing 7 changed files with 291 additions and 24 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -6,8 +6,11 @@ python:
 os:
   - linux
 before_install:
+  - sudo apt-get update
+  - sudo apt-get install graphviz
   - python --version
 install:
+  - pip install -r requirements.txt
   - pip install -r test-requirements.txt
   - python setup.py install
 # command to run tests
@@ -23,6 +26,7 @@ matrix:
       osx_image: xcode9.4  # Python 3.7 running on macOS 10.13
       language: shell  # 'language: python' is an error on Travis CI macOS
       before_install:
+        - brew install graphviz
         - python3 --version
         - pip3 install virtualenv
         - virtualenv -p python3 venv

diff --git a/cwlkernel/kernel_magics.py b/cwlkernel/kernel_magics.py
@@ -6,6 +6,9 @@
 from pathlib import Path
 from typing import List
 
+import pydot
+from cwltool.cwlviewer import CWLViewer
+from cwltool.main import main as cwltool_main
 from ruamel.yaml import YAML
 
 from .CWLKernel import CONF as CWLKernel_CONF
@@ -342,6 +345,33 @@ def magics(kernel: CWLKernel, arg: str):
             )
 
 
+@CWLKernel.register_magic('view')
+def visualize_graph(kernel: CWLKernel, tool_id: str):
+    """Visualize a Workflow"""
+    tool_id = tool_id.strip()
+    path = kernel.workflow_repository.get_tools_path_by_id(tool_id)
+    rdf_stream = StringIO()
+    import logging
+    handler = logging.StreamHandler()
+    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')
+
+    kernel.send_response(
+        kernel.iopub_socket,
+        'display_data',
+        {
+            'data': {
+                "image/svg+xml": image.decode(),
+                "text/plain": image.decode()
+            },
+            'metadata': {},
+        },
+
+    )
+
+
 # import user's magic commands
 
 if CWLKernel_CONF.CWLKERNEL_MAGIC_COMMANDS_DIRECTORY is not None:

diff --git a/examples/Compose.ipynb b/examples/Compose.ipynb
@@ -96,7 +96,13 @@
          "type": "File"
         }
        ],
-       "outputs": [],
+       "outputs": [
+        {
+         "id": "tailoutput",
+         "outputSource": "tailstepid/tailoutput",
+         "type": "File"
+        }
+       ],
        "requirements": {},
        "steps": {
         "headstepid": {
@@ -112,13 +118,15 @@
          "in": {
           "tailinput": "headstepid/headoutput"
          },
-         "out": [],
+         "out": [
+          "tailoutput"
+         ],
          "run": "tail.cwl"
         }
        }
       },
       "text/plain": [
-       "{\"cwlVersion\": \"v1.0\", \"class\": \"Workflow\", \"id\": \"main\", \"inputs\": [{\"id\": \"inputfile\", \"type\": \"File\"}], \"outputs\": [], \"steps\": {\"tailstepid\": {\"run\": \"tail.cwl\", \"in\": {\"tailinput\": \"headstepid/headoutput\"}, \"out\": []}, \"headstepid\": {\"run\": \"head.cwl\", \"in\": {\"headinput\": \"inputfile\"}, \"out\": [\"headoutput\"]}}, \"requirements\": {}}"
+       "{\"cwlVersion\": \"v1.0\", \"class\": \"Workflow\", \"id\": \"main\", \"inputs\": [{\"id\": \"inputfile\", \"type\": \"File\"}], \"outputs\": [{\"id\": \"tailoutput\", \"type\": \"File\", \"outputSource\": \"tailstepid/tailoutput\"}], \"steps\": {\"tailstepid\": {\"run\": \"tail.cwl\", \"in\": {\"tailinput\": \"headstepid/headoutput\"}, \"out\": [\"tailoutput\"]}, \"headstepid\": {\"run\": \"head.cwl\", \"in\": {\"headinput\": \"inputfile\"}, \"out\": [\"headoutput\"]}}, \"requirements\": {}}"
       ]
      },
      "metadata": {
@@ -139,6 +147,7 @@
     "type: File\n",
     "% newWorkflowAddStepIn tailstepid headstepid headoutput\n",
     "tailinput: headstepid/headoutput\n",
+    "% newWorkflowAddOutputSource tailstepid/tailoutput File\n",
     "% newWorkflowBuild"
    ]
   },
@@ -156,9 +165,22 @@
     },
     {
      "data": {
-      "application/json": {},
+      "application/json": {
+       "tailoutput": {
+        "basename": "tail.out",
+        "checksum": "sha1$e186f07099395040cf9d83ff1eb0a5dad4801937",
+        "class": "File",
+        "http://commonwl.org/cwltool#generation": 0,
+        "id": "tailoutput",
+        "location": "file:///private/tmp/CWLKERNEL_DATA/d8f78c63-0b6a-413b-b60e-03d8f96165c8/runtime_data/tail.out",
+        "nameext": ".out",
+        "nameroot": "tail",
+        "result_counter": 0,
+        "size": 688
+       }
+      },
       "text/plain": [
-       "{}"
+       "{\"tailoutput\": {\"location\": \"file:///private/tmp/CWLKERNEL_DATA/d8f78c63-0b6a-413b-b60e-03d8f96165c8/runtime_data/tail.out\", \"basename\": \"tail.out\", \"nameroot\": \"tail\", \"nameext\": \".out\", \"class\": \"File\", \"checksum\": \"sha1$e186f07099395040cf9d83ff1eb0a5dad4801937\", \"size\": 688, \"http://commonwl.org/cwltool#generation\": 0, \"id\": \"tailoutput\", \"result_counter\": 0}}"
       ]
      },
      "metadata": {
@@ -174,7 +196,157 @@
     "% execute main\n",
     "inputfile: \n",
     "    class: File\n",
-    "    location: /Users/dks/Desktop/data.csv"
+    "    location: /Users/dks/Workspaces/CWLKernel/tests/input_data/data.csv"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "image/svg+xml": [
+       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
+       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
+       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
+       "<!-- Generated by graphviz version 2.42.3 (20191010.1750)\n",
+       " -->\n",
+       "<!-- Title: G Pages: 1 -->\n",
+       "<svg width=\"143pt\" height=\"320pt\"\n",
+       " viewBox=\"0.00 0.00 143.00 320.00\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
+       "<g id=\"graph0\" class=\"graph\" transform=\"scale(1 1) rotate(0) translate(4 316)\">\n",
+       "<title>G</title>\n",
+       "<polygon fill=\"#eeeeee\" stroke=\"transparent\" points=\"-4,4 -4,-316 139,-316 139,4 -4,4\"/>\n",
+       "<g id=\"clust1\" class=\"cluster\">\n",
+       "<title>cluster_inputs</title>\n",
+       "<polygon fill=\"#eeeeee\" stroke=\"black\" stroke-dasharray=\"5,2\" points=\"12,-229 12,-304 122,-304 122,-229 12,-229\"/>\n",
+       "<text text-anchor=\"middle\" x=\"66.92\" y=\"-235.8\" font-family=\"Times,serif\" font-size=\"14.00\">Workflow Inputs</text>\n",
+       "</g>\n",
+       "<g id=\"clust2\" class=\"cluster\">\n",
+       "<title>cluster_outputs</title>\n",
+       "<polygon fill=\"#eeeeee\" stroke=\"black\" stroke-dasharray=\"5,2\" points=\"8,-8 8,-83 127,-83 127,-8 8,-8\"/>\n",
+       "<text text-anchor=\"middle\" x=\"67.25\" y=\"-14.8\" font-family=\"Times,serif\" font-size=\"14.00\">Workflow Outputs</text>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid -->\n",
+       "<g id=\"node1\" class=\"node\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid</title>\n",
+       "<polygon fill=\"lightgoldenrodyellow\" stroke=\"black\" points=\"40,-184.5 40,-220.5 94,-220.5 94,-184.5 40,-184.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"66.71\" y=\"-198.3\" font-family=\"Times,serif\" font-size=\"14.00\">head</text>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid -->\n",
+       "<g id=\"node2\" class=\"node\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid</title>\n",
+       "<polygon fill=\"lightgoldenrodyellow\" stroke=\"black\" points=\"40,-111.5 40,-147.5 94,-147.5 94,-111.5 40,-111.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"66.94\" y=\"-125.3\" font-family=\"Times,serif\" font-size=\"14.00\">tail</text>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid -->\n",
+       "<g id=\"edge1\" class=\"edge\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M67,-184.31C67,-176.29 67,-166.55 67,-157.57\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"70.5,-157.53 67,-147.53 63.5,-157.53 70.5,-157.53\"/>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailoutput -->\n",
+       "<g id=\"node4\" class=\"node\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailoutput</title>\n",
+       "<polygon fill=\"#94ddf4\" stroke=\"black\" points=\"16.23,-38.5 16.23,-74.5 117.77,-74.5 117.77,-38.5 16.23,-38.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"67\" y=\"-52.3\" font-family=\"Times,serif\" font-size=\"14.00\">main/tailoutput</text>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailoutput -->\n",
+       "<g id=\"edge3\" class=\"edge\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailoutput</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M67,-111.31C67,-103.29 67,-93.55 67,-84.57\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"70.5,-84.53 67,-74.53 63.5,-84.53 70.5,-84.53\"/>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/inputfile -->\n",
+       "<g id=\"node3\" class=\"node\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/inputfile</title>\n",
+       "<polygon fill=\"#94ddf4\" stroke=\"black\" points=\"19.72,-259.5 19.72,-295.5 114.28,-295.5 114.28,-259.5 19.72,-259.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"67\" y=\"-273.3\" font-family=\"Times,serif\" font-size=\"14.00\">main/inputfile</text>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/inputfile&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid -->\n",
+       "<g id=\"edge2\" class=\"edge\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/inputfile&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M67,-259.2C67,-250.75 67,-240.37 67,-230.87\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"70.5,-230.68 67,-220.68 63.5,-230.68 70.5,-230.68\"/>\n",
+       "</g>\n",
+       "</g>\n",
+       "</svg>\n"
+      ],
+      "text/plain": [
+       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
+       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
+       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
+       "<!-- Generated by graphviz version 2.42.3 (20191010.1750)\n",
+       " -->\n",
+       "<!-- Title: G Pages: 1 -->\n",
+       "<svg width=\"143pt\" height=\"320pt\"\n",
+       " viewBox=\"0.00 0.00 143.00 320.00\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
+       "<g id=\"graph0\" class=\"graph\" transform=\"scale(1 1) rotate(0) translate(4 316)\">\n",
+       "<title>G</title>\n",
+       "<polygon fill=\"#eeeeee\" stroke=\"transparent\" points=\"-4,4 -4,-316 139,-316 139,4 -4,4\"/>\n",
+       "<g id=\"clust1\" class=\"cluster\">\n",
+       "<title>cluster_inputs</title>\n",
+       "<polygon fill=\"#eeeeee\" stroke=\"black\" stroke-dasharray=\"5,2\" points=\"12,-229 12,-304 122,-304 122,-229 12,-229\"/>\n",
+       "<text text-anchor=\"middle\" x=\"66.92\" y=\"-235.8\" font-family=\"Times,serif\" font-size=\"14.00\">Workflow Inputs</text>\n",
+       "</g>\n",
+       "<g id=\"clust2\" class=\"cluster\">\n",
+       "<title>cluster_outputs</title>\n",
+       "<polygon fill=\"#eeeeee\" stroke=\"black\" stroke-dasharray=\"5,2\" points=\"8,-8 8,-83 127,-83 127,-8 8,-8\"/>\n",
+       "<text text-anchor=\"middle\" x=\"67.25\" y=\"-14.8\" font-family=\"Times,serif\" font-size=\"14.00\">Workflow Outputs</text>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid -->\n",
+       "<g id=\"node1\" class=\"node\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid</title>\n",
+       "<polygon fill=\"lightgoldenrodyellow\" stroke=\"black\" points=\"40,-184.5 40,-220.5 94,-220.5 94,-184.5 40,-184.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"66.71\" y=\"-198.3\" font-family=\"Times,serif\" font-size=\"14.00\">head</text>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid -->\n",
+       "<g id=\"node2\" class=\"node\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid</title>\n",
+       "<polygon fill=\"lightgoldenrodyellow\" stroke=\"black\" points=\"40,-111.5 40,-147.5 94,-147.5 94,-111.5 40,-111.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"66.94\" y=\"-125.3\" font-family=\"Times,serif\" font-size=\"14.00\">tail</text>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid -->\n",
+       "<g id=\"edge1\" class=\"edge\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M67,-184.31C67,-176.29 67,-166.55 67,-157.57\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"70.5,-157.53 67,-147.53 63.5,-157.53 70.5,-157.53\"/>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailoutput -->\n",
+       "<g id=\"node4\" class=\"node\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailoutput</title>\n",
+       "<polygon fill=\"#94ddf4\" stroke=\"black\" points=\"16.23,-38.5 16.23,-74.5 117.77,-74.5 117.77,-38.5 16.23,-38.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"67\" y=\"-52.3\" font-family=\"Times,serif\" font-size=\"14.00\">main/tailoutput</text>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailoutput -->\n",
+       "<g id=\"edge3\" class=\"edge\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailstepid&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/tailoutput</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M67,-111.31C67,-103.29 67,-93.55 67,-84.57\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"70.5,-84.53 67,-74.53 63.5,-84.53 70.5,-84.53\"/>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/inputfile -->\n",
+       "<g id=\"node3\" class=\"node\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/inputfile</title>\n",
+       "<polygon fill=\"#94ddf4\" stroke=\"black\" points=\"19.72,-259.5 19.72,-295.5 114.28,-295.5 114.28,-259.5 19.72,-259.5\"/>\n",
+       "<text text-anchor=\"middle\" x=\"67\" y=\"-273.3\" font-family=\"Times,serif\" font-size=\"14.00\">main/inputfile</text>\n",
+       "</g>\n",
+       "<!-- file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/inputfile&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid -->\n",
+       "<g id=\"edge2\" class=\"edge\">\n",
+       "<title>file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/inputfile&#45;&gt;file:///private/tmp/CWLKERNEL_DATA/d8f78c63&#45;0b6a&#45;413b&#45;b60e&#45;03d8f96165c8/repo/main.cwl#main/headstepid</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M67,-259.2C67,-250.75 67,-240.37 67,-230.87\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"70.5,-230.68 67,-220.68 63.5,-230.68 70.5,-230.68\"/>\n",
+       "</g>\n",
+       "</g>\n",
+       "</svg>\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "% view main"
    ]
   }
  ],

diff --git a/examples/multipleSteps.ipynb b/examples/multipleSteps.ipynb
@@ -276,6 +276,15 @@
    "source": [
     "% displayData tailoutput"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "% view main"
+   ]
   }
  ],
  "metadata": {

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-cwltool>=3.0.20200706173533
+git+https://github.com/giannisdoukas/cwltool.git@cwl-view#egg=cwltool
 jsonschema>=3.2.0
 jupyter-client>=5.3.4
 jupyter-core>=4.6.3
@@ -8,4 +8,5 @@ PyYAML>=5.3.1
 pandas>=1.0.4
 notebook>=6.0.3
 requests>=2.23.0
-pygtrie>=2.3.3
+pygtrie>=2.3.3
+pydot>=1.4.1
diff --git a/setup.py b/setup.py
@@ -59,16 +59,6 @@ def get_version(rel_path):
 with open(os.sep.join([os.path.abspath(os.path.dirname(__file__)), "README.md"]), "r") as fh:
     long_description = fh.read()
 
-with open('requirements.txt') as f:
-    req = f.readlines()
-
-for i, r in enumerate(req):
-    r = r.rstrip()
-    if r.startswith('git+https://'):
-        egg_position = r.rfind("#egg=")
-        dependency_name = r[egg_position + 5:]
-        req[i] = f"{dependency_name} @ {r[:egg_position]}"
-
 setup(
     name=name,
     version=get_version(f"{name}/CWLKernel.py"),
@@ -91,9 +81,4 @@ def get_version(rel_path):
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
     ],
-    # cmdclass={
-    #     'develop': PostDevelopCommand,
-    #     'install': PostInstallCommand,
-    # },
-    install_requires=req
 )