[RAW] functional pipeline graph editor, added docs update

README.md

@@ -1,5 +1,5 @@
 <div align="center">
-  <img src=".github/logo.png" width="512">
+  <img src=".github/logo-title.png" width="512">
 </div>
 
 ---

candis/__init__.py

@@ -1,7 +1,7 @@
 # module - candis
 from candis.config  import Config, get_config, CONFIG
 from candis.manager import Cache
-from candis.data    import entrez
+# from candis.data    import entrez
 from candis.ios     import cdata, pipeline
 from candis.cli     import main
 

candis/app/client/app/action/AsynchronousAction.jsx

@@ -30,7 +30,7 @@ const getResource     = (dispatch) => {
        })
 }
 
-const write            = (output, format, buffer = { }) => {
+const write            = (output, format, buffer = null) => {
   const dispatch       = (dispatch) => {
     const action       = requestWrite(output, format, buffer)
     const parameters   = { output: output, format: format, buffer: buffer }

candis/app/client/app/action/DocumentProcessorAction.jsx

@@ -18,13 +18,13 @@ const removeDocument    = (dokument) => {
   return action
 }
 
-const pushStage         = (stage) => {
+const setStage          = (stage) => {
   const action          = {
-       type: ActionType.DocumentProcessor.PUSH_STAGE,
+       type: ActionType.DocumentProcessor.SET_STAGE,
     payload: stage
   }
 
   return action
 }
 
-export { setActiveDocument, removeDocument, pushStage }
+export { setActiveDocument, removeDocument, setStage }

candis/app/client/app/component/widget/GraphEditor.jsx

@@ -14,7 +14,7 @@ class GraphEditor extends React.Component {
 
     return (
       <div className={classNames("panel panel-default no-border no-shadow no-background")}>
-        <div className="panel-body" style={{ height: "100vh" }}>
+        <div className="panel-body" style={{ height: "100%" }}>
           {
             graph.nodes().map((ID, index) => {
               let meta = graph.node(ID)
@@ -26,7 +26,7 @@ class GraphEditor extends React.Component {
                   <span>
                     <h2 className="no-margin">
                       <span className="label label-default">
-                        {meta.label}
+                        {meta.name}
                       </span>
                     </h2>
                   </span>
@@ -48,4 +48,4 @@ const mapStateToProps   = (state) => {
   }
 }
 
-export default connect(mapStateToProps)(GraphEditor)
+export default connect()(GraphEditor)

candis/app/client/app/component/widget/document/DocumentPanel.jsx

@@ -40,7 +40,9 @@ class DocumentPanel extends React.Component {
           </div>
           <div className="panel-body">
             {
-
+              active ?
+                <GraphEditor
+                  graph={active.data}/> : null
             }
           </div>
         </div>

candis/app/client/app/constant/ActionType.jsx

@@ -22,7 +22,7 @@ const ActionType =
   {
     SET_ACTIVE_DOCUMENT: 'ACTION_TYPE_SET_ACTIVE_DOCUMENT',
         REMOVE_DOCUMENT: 'ACTION_TYPE_DOCUMENT_PROCESSOR_REMOVE_DOCUMENT',
-             PUSH_STAGE: 'ACTION_TYPE_DOCUMENT_PUSH_STAGE'
+              SET_STAGE: 'ACTION_TYPE_DOCUMENT_SET_STAGE'
   },
 
                INSERT_TOOL: 'ACTION_TYPE_INSERT_TOOL',

candis/app/client/app/meta/Compartments.jsx

@@ -1,7 +1,7 @@
-import axios         from 'axios'
+import axios        from 'axios'
 
-import config        from '../config'
-import { pushStage } from '../action/DocumentProcessorAction'
+import config       from '../config'
+import { setStage } from '../action/DocumentProcessorAction'
 
 import { showDialog, hideDialog } from '../action/DialogAction'
 import Dialog     from '../component/widget/Dialog'
@@ -18,7 +18,7 @@ const Compartments = [
              icon: `${config.routes.icons}/edit.png`,
           tooltip: 'Create a new DataSet',
           onClick: (dispatch) => {
-            const action = pushStage({
+            const action = setStage({
                    name: 'Create',
                 onClick: (dispatch) => {
                   // dialog action

candis/app/client/app/reducer/DocumentProcessorReducer.jsx

@@ -1,4 +1,6 @@
 import shortid    from 'shortid'
+import graphlib   from 'graphlib'
+import cloneDeep  from 'lodash.clonedeep'
 
 import ActionType from '../constant/ActionType'
 import FileFormat from '../constant/FileFormat'
@@ -16,11 +18,13 @@ const documentProcessor = (state = initialState, action) => {
 
       if ( file.format == FileFormat.PIPELINE ) {
         const data      = action.payload.data
+        const graph     = new graphlib.Graph()
 
         const dokument  =
         {
               ID: shortid.generate(),
-          output: data.output
+          output: data.output,
+            data: graph
         }
 
         const documents = state.documents.slice()
@@ -46,11 +50,16 @@ const documentProcessor = (state = initialState, action) => {
       return {...state, documents: documents }
     }
 
-    case ActionType.DocumentProcessor.PUSH_STAGE: {
-      const dokument   = state.active
+    case ActionType.DocumentProcessor.SET_STAGE: {
+      const dokument   = cloneDeep(state.active)
 
       if ( dokument !== null ) {
+        const ID       = shortid.generate()
         const stage    = action.payload
+
+        dokument.data.setNode(ID, stage)
+
+        return {...state, active: dokument }
       }
     }
   }

candis/app/server/api/data.py

@@ -111,12 +111,12 @@ def resource(filter_ = ['cdata', 'csv', 'cel', 'pipeline'], level = None):
 def read():
     response    = Response()
 
-    parameters  = request.get_json()
+    parameters  = addict.Dict(request.get_json())
 
     if 'path' in parameters:
         if 'name' in parameters:
-            path    = parameters['path']
-            name    = parameters['name']
+            path    = parameters.path
+            name    = parameters.name
 
             relpath = os.path.join(path, name)
 
@@ -141,49 +141,50 @@ def read():
 
 @app.route(CONFIG.App.Routes.Api.Data.WRITE, methods = ['POST'])
 def write():
-    response   = Response()
+    response    = Response()
 
-    parameters = addict.Dict(request.get_json())
+    parameters  = addict.Dict(request.get_json())
 
     if 'format' in parameters:
-        if 'buffer' in parameters:
-            format_ = parameters['format']
-            buffer_ = parameters['buffer']
-
-            if format_   == 'cdata':
-                extension = 'cdata'
-                prefix    = 'CDAT'
-                writer    = cdata
-            elif format_ == 'pipeline':
-                extension = 'cpipe'
-                prefix    = 'PIPE'
-                writer    = pipeline
-
-            if 'output' in parameters and 'name' in parameters.output:
-                if parameters.output.name:
-                    name = parameters.output.name
-                else:
-                    name = prefix + get_timestamp_str('%Y%m%d%H%M%S')
-            else:
-                name = prefix + get_timestamp_str('%Y%m%d%H%M%S')
-
-            fname  = '{name}.{ext}'.format(name = name, ext = extension)
-            path   = os.path.join(ABSPATH_STARTDIR, fname)
-            path   = get_filename_if_exists(path)
-
-            try:
-                writer.write(path, buffer_)
-
-                path, fname = os.path.split(path)
-
-                data        = addict.Dict()
-                data.output.path = path
-                data.output.name   = fname
-
-                response.set_data(data)
-            except TypeError as e:
-                response.set_error(Response.Error.UNPROCESSABLE_ENTITY)
+        format_ = parameters.format
+
+        if 'buffer' in parameters and parameters.buffer:
+            buffer_ = parameters.buffer
+        else:
+            buffer_ = None
+
+        if format_   == 'cdata':
+            extension = 'cdata'
+            prefix    = 'CDAT'
+            handler   = cdata
+        elif format_ == 'pipeline':
+            extension = 'cpipe'
+            prefix    = 'PIPE'
+            handler   = pipeline
+
+        if 'output' in parameters and 'name' in parameters.output and parameters.output.name:
+            name = parameters.output.name
         else:
+            name = prefix + get_timestamp_str('%Y%m%d%H%M%S')
+
+        fname  = '{name}.{ext}'.format(name = name, ext = extension)
+        path   = os.path.join(ABSPATH_STARTDIR, fname)
+        path   = get_filename_if_exists(path)
+
+        try:
+            handler.write(path, buffer_)
+
+            data             = addict.Dict()
+
+            data.data        = handler.read(path)
+
+            path, fname      = os.path.split(path)
+
+            data.output.path = path
+            data.output.name = fname
+
+            response.set_data(data)
+        except TypeError as e:
             response.set_error(Response.Error.UNPROCESSABLE_ENTITY)
     else:
         response.set_error(Response.Error.UNPROCESSABLE_ENTITY)

candis/ios/cdata/writer.py

@@ -18,7 +18,7 @@ def get_attribute_tag(attr):
     return tag
 
 def write(path, dataset, delimiter = ','):
-    with open(path, 'w') as f:
+    with open(path, mode = 'w') as f:
         writer  = csv.writer(f, delimiter = delimiter)
         cnames  = [ ]
 

candis/ios/pipeline/reader.py

@@ -1,2 +1,7 @@
+# imports - module imports
+from candis.util import json_load
+
 def read(path):
-    pass
+    pipeline = json_load(path)
+
+    return pipeline

candis/ios/pipeline/writer.py

@@ -1,3 +1,17 @@
-def write(path, pipeline):
-    with open(path, "w") as f:
-        pass
+# imports - standard imports
+import json
+
+# imports - third-party imports
+import addict
+
+# imports - module imports
+from candis.util import assign_if_none
+
+def write(path, pipeline = None):
+    pipeline = assign_if_none(pipeline, addict.Dict({
+        'stages': [ ],
+         'links': [ ]
+    }))
+
+    with open(path, mode = 'w') as f:
+        json.dump(pipeline, f, indent = 4)

docs/source/_templates/sidebar.html

@@ -1,5 +1,9 @@
-<div class="wrapper">
-  <a href="#">
-    <img src="" alt="candis-logo">
+<p class="logo">
+  <a href="{{ pathto(master_doc) }}">
+    <img class="logo" src="{{ pathto('_static/img/logo-title.png', 1) }}"/>
   </a>
-</div>
+</p>
+
+<p>
+  <iframe src="https://ghbtns.com/github-btn.html?user=achillesrasquinha&repo=candis&type=star&count=true&size=large" frameborder="0" scrolling="0" width="160px" height="30px"></iframe>
+</p>