Remove PUT Model Table. Closes #414.

docs/POST-Model-Files.rst

@@ -0,0 +1,31 @@
+POST Model Files
+================
+
+.. http:post /models/(mid)/files
+
+  Upload files for addition to a model, either from the client to the server or
+  a remote host to the server using a remote session. To upload files from the
+  client, specify the "files" parameter with one or more files. To upload
+  remote files, specify the "sids" and "paths" parameters with a session id and
+  remote filepath for each file to upload. In either case specify the
+  boolean "input" parameter, the name of a parsing plugin in "parser", and one
+  or more artifact names using "names".
+
+  :param mid: Unique model identifier.
+  :type mid: string
+
+  :requestheader Content-Type: form/multipart
+
+  :form files: Local files for upload.
+  :form input: Set to "true" to store results as input artifacts.
+  :form names: Artifact names for storage.
+  :form parser: Parsing plugin name.
+  :form paths: Remote host absolute filesystem paths.
+  :form sids: Remote session ids.
+
+
+See Also
+--------
+
+-  :http:post:`/remotes/(sid)/browse(path)`
+

docs/rest-api.rst

@@ -39,6 +39,7 @@ any programming language or library that supports HTTP requests.
   GET-User.rst
   POST-Events.rst
   POST-Model-Command.rst
+  POST-Model-Files.rst
   POST-Model-Finish.rst
   POST-Project-Bookmark.rst
   POST-Project-Models.rst
@@ -53,7 +54,6 @@ any programming language or library that supports HTTP requests.
   PUT-Model-File.rst
   PUT-Model-Inputs.rst
   PUT-Model-Parameter.rst
-  PUT-Model-Table.rst
   PUT-Model.rst
   PUT-Project.rst
 

packages/slycat/web/server/engine.py

@@ -161,7 +161,6 @@ def abspath(path):
   dispatcher.connect("put-model-inputs", "/models/:mid/inputs", slycat.web.server.handlers.put_model_inputs, conditions={"method" : ["PUT"]})
   dispatcher.connect("put-model", "/models/:mid", slycat.web.server.handlers.put_model, conditions={"method" : ["PUT"]})
   dispatcher.connect("put-model-parameter", "/models/:mid/parameters/:name", slycat.web.server.handlers.put_model_parameter, conditions={"method" : ["PUT"]})
-  dispatcher.connect("put-model-table", "/models/:mid/tables/:name", slycat.web.server.handlers.put_model_table, conditions={"method" : ["PUT"]})
   dispatcher.connect("put-project", "/projects/:pid", slycat.web.server.handlers.put_project, conditions={"method" : ["PUT"]})
 
   def log_configuration(tree, indent=""):

packages/slycat/web/server/handlers.py

@@ -456,14 +456,6 @@ def post_model_finish(mid):
   cherrypy.response.status = "202 Finishing model."
 
 def post_model_files(mid, input=None, files=None, sids=None, paths=None, names=None, parser=None, **kwargs):
-  cherrypy.log.error("input %s" % input)
-  cherrypy.log.error("files %s" % files)
-  cherrypy.log.error("sids %s" % sids)
-  cherrypy.log.error("paths %s" % paths)
-  cherrypy.log.error("names %s" % names)
-  cherrypy.log.error("parser %s" % parser)
-  cherrypy.log.error("kwargs %s" % kwargs)
-
   if input is None:
     raise cherrypy.HTTPError("400 Required input parameter is missing.")
   input = True if input == "true" else False
@@ -473,6 +465,10 @@ def post_model_files(mid, input=None, files=None, sids=None, paths=None, names=N
       files = [files]
     files = [file.file.read() for file in files]
   elif files is None and sids is not None and paths is not None:
+    if not isinstance(sids, list):
+      sids = [sids]
+    if not isinstance(paths, list):
+      paths = [paths]
     if len(sids) != len(paths):
       raise cherrypy.HTTPError("400 sids and paths parameters must have the same length.")
     files = []
@@ -537,47 +533,6 @@ def put_model_inputs(mid):
 
   slycat.web.server.put_model_inputs(database, model, source, deep_copy)
 
-def put_model_table(mid, name, input=None, file=None, sid=None, path=None):
-  """Deprecated."""
-  database = slycat.web.server.database.couchdb.connect()
-  model = database.get("model", mid)
-  project = database.get("project", model["project"])
-  slycat.web.server.authentication.require_project_writer(project)
-
-  if input is None:
-    raise cherrypy.HTTPError("400 Required input parameter is missing.")
-  input = True if input == "true" else False
-
-  if file is not None and sid is None and path is None:
-    data = file.file.read()
-    filename = file.filename
-  elif file is None and sid is not None and path is not None:
-    with slycat.web.server.remote.get_session(sid) as session:
-      filename = "%s@%s:%s" % (session.username, session.hostname, path)
-      if stat.S_ISDIR(session.sftp.stat(path).st_mode):
-        raise cherrypy.HTTPError("400 Cannot load directory %s." % filename)
-      data = session.sftp.file(path).read()
-  else:
-    raise cherrypy.HTTPError("400 Must supply a file parameter, or sid and path parameters.")
-
-  slycat.web.server.update_model(database, model, message="Loading table %s from %s." % (name, filename))
-  try:
-    array = slycat.table.parse(data)
-  except:
-    raise cherrypy.HTTPError("400 Could not parse file %s" % filename)
-
-  storage = uuid.uuid4().hex
-  with slycat.web.server.hdf5.lock:
-    with slycat.web.server.hdf5.create(storage) as file:
-      database.save({"_id" : storage, "type" : "hdf5"})
-      model["artifact:%s" % name] = storage
-      model["artifact-types"][name] = "hdf5"
-      if input:
-        model["input-artifacts"] = list(set(model["input-artifacts"] + [name]))
-      database.save(model)
-      arrayset = slycat.hdf5.ArraySet(file)
-      arrayset.store_array(0, array)
-
 @cherrypy.tools.json_in(on = True)
 def put_model_parameter(mid, name):
   database = slycat.web.server.database.couchdb.connect()

web-server/js/slycat-web-client.js

@@ -717,40 +717,6 @@ define("slycat-web-client", ["slycat-server-root", "jquery", "URI"], function(se
     });
   }
 
-  module.put_model_table = function(params)
-  {
-    var data = new FormData();
-    data.append("input", params.input === undefined ? true: params.input ? true: false);
-    if(params.sid && params.path)
-    {
-      data.append("sid", params.sid);
-      data.append("path", params.path);
-    }
-    else if(params.file)
-    {
-      data.append("file", params.file);
-    }
-
-    $.ajax(
-    {
-      contentType: false,
-      processData: false,
-      data: data,
-      type: "PUT",
-      url: server_root + "models/" + params.mid + "/tables/" + params.name,
-      success: function()
-      {
-        if(params.success)
-          params.success();
-      },
-      error: function(request, status, reason_phrase)
-      {
-        if(params.error)
-          params.error(request, status, reason_phrase);
-      },
-    });
-  }
-
   module.put_project = function(params)
   {
     var project = {};

web-server/plugins/slycat-cca/js/local-ui.js

@@ -55,7 +55,7 @@ define(["slycat-server-root", "slycat-web-client", "slycat-dialog", "knockout",
         files: component.browser.selection(),
         input: true,
         names: ["data-table"],
-        parser: "slycat-csv-parser",
+        parser: component.parser(),
         success: function()
         {
           client.get_model_table_metadata(

web-server/plugins/slycat-cca/js/remote-ui.js

@@ -9,6 +9,7 @@ define(["slycat-server-root", "slycat-web-client", "slycat-dialog", "knockout",
     component.remote = mapping.fromJS({hostname: null, username: null, password: null, status: null, status_type: null, enable: true, focus: false, sid: null});
     component.remote.focus.extend({notify: "always"});
     component.browser = mapping.fromJS({path:null, selection: []});
+    component.parser = ko.observable(null);
     component.attributes = mapping.fromJS([]);
     component.scale_inputs = ko.observable(true);
 
@@ -76,13 +77,14 @@ define(["slycat-server-root", "slycat-web-client", "slycat-dialog", "knockout",
     }
     component.load_table = function()
     {
-      client.put_model_table(
+      client.post_model_files(
       {
         mid: component.model._id(),
-        sid: component.remote.sid(),
-        path: component.browser.selection()[0],
+        sids: [component.remote.sid()],
+        paths: [component.browser.selection()],
         input: true,
-        name: "data-table",
+        names: ["data-table"],
+        parser: component.parser(),
         success: function()
         {
           client.get_model_table_metadata(

web-server/plugins/slycat-cca/remote-ui.html

@@ -23,6 +23,7 @@ <h3 class="modal-title">New Remote CCA Model</h3>
     </div>
     <div data-bind="visible:tab() == 2" style="height: 400px">
       <slycat-remote-browser params="type:'remote',sid:remote.sid,hostname:remote.hostname,selection:browser.selection,path:browser.path,open_file_callback:load_table"></slycat-remote-browser>
+      <slycat-parser-controls params="parser:parser"></slycat-parser-controls>
     </div>
     <div data-bind="visible:tab() == 3">
       <table style="width:100%">

web-server/plugins/slycat-csv-parser.py

@@ -25,8 +25,7 @@ def parse(database, model, input, files, names, **kwargs):
 
     slycat.web.server.put_model_arrayset(database, model, name, input)
     slycat.web.server.put_model_array(database, model, name, 0, attributes, dimensions)
-    for attribute_index, column in enumerate(data):
-      slycat.web.server.put_model_arrayset_data(database, model, name, "%s/%s/..." % (array_index, attribute_index), [column])
+    slycat.web.server.put_model_arrayset_data(database, model, name, "%s/.../..." % array_index, data)
 
 def register_slycat_plugin(context):
   context.register_parser("slycat-csv-parser", "Comma separated values (CSV)", ["table"], parse)

web-server/plugins/slycat-linear-regression-demo/wizard-ui.html

@@ -17,6 +17,7 @@ <h3 class="modal-title">New Linear Regression Model</h3>
     </div>
     <div data-bind="visible:tab() == 1">
       <slycat-local-browser params="selection:browser.selection"></slycat-local-browser>
+      <slycat-parser-controls params="parser:parser"></slycat-parser-controls>
     </div>
     <div data-bind="visible:tab() == 2">
       <table style="width:100%">

web-server/plugins/slycat-linear-regression-demo/wizard-ui.js

@@ -7,6 +7,7 @@ define(["slycat-server-root", "slycat-web-client", "slycat-dialog", "knockout",
     component.project = params.projects()[0];
     component.model = mapping.fromJS({_id: null, name: "New Linear Regression Demo Model", description: "This model demonstrates plotting with d3.js", marking: null});
     component.browser = mapping.fromJS({selection: []});
+    component.parser = ko.observable(null);
     component.attributes = mapping.fromJS([]);
     component.x_column = ko.observable(null);
     component.y_column = ko.observable(null);
@@ -37,12 +38,13 @@ define(["slycat-server-root", "slycat-web-client", "slycat-dialog", "knockout",
     {
       console.log("upload_table", component.browser.selection());
 
-      client.put_model_table(
+      client.post_model_files(
       {
         mid: component.model._id(),
-        file: component.browser.selection()[0],
+        files: component.browser.selection(),
         input: true,
-        name: "data-table",
+        names: ["data-table"],
+        parser: component.parser(),
         success: function()
         {
           client.get_model_table_metadata(

web-server/plugins/slycat-parameter-image/js/wizard-ui.js

@@ -9,6 +9,7 @@ define(["slycat-server-root", "slycat-web-client", "slycat-dialog", "knockout",
     component.remote = mapping.fromJS({hostname: null, username: null, password: null, status: null, status_type: null, enable: true, focus: false, sid: null});
     component.remote.focus.extend({notify: "always"});
     component.browser = mapping.fromJS({path:null, selection: []});
+    component.parser = ko.observable(null);
     component.attributes = mapping.fromJS([]);
 
     component.cancel = function()
@@ -63,13 +64,14 @@ define(["slycat-server-root", "slycat-web-client", "slycat-dialog", "knockout",
     }
     component.load_table = function()
     {
-      client.put_model_table(
+      client.post_model_files(
       {
         mid: component.model._id(),
-        sid: component.remote.sid(),
-        path: component.browser.selection()[0],
+        sids: [component.remote.sid()],
+        paths: component.browser.selection(),
         input: true,
-        name: "data-table",
+        names: ["data-table"],
+        parser: component.parser(),
         success: function()
         {
           client.get_model_command(

web-server/plugins/slycat-parameter-image/wizard-ui.html

@@ -23,6 +23,7 @@ <h3 class="modal-title">Remote Parameter Image Model</h3>
     </div>
     <div data-bind="visible:tab() == 2" style="height: 400px">
       <slycat-remote-browser params="type:'remote',sid:remote.sid,hostname:remote.hostname,selection:browser.selection,path:browser.path,open_file_callback:load_table"></slycat-remote-browser>
+      <slycat-parser-controls params="parser:parser"></slycat-parser-controls>
     </div>
     <div data-bind="visible:tab() == 3">
       <table style="width:100%">

web-server/plugins/slycat-tracer-image/js/wizard-ui.js

@@ -9,6 +9,7 @@ define(["slycat-server-root", "slycat-web-client", "slycat-dialog", "knockout",
     component.remote = mapping.fromJS({hostname: null, username: null, password: null, status: null, status_type: null, enable: true, focus: false, sid: null});
     component.remote.focus.extend({notify: "always"});
     component.browser = mapping.fromJS({path:null, selection: []});
+    component.parser = ko.observable(null);
     component.attributes = mapping.fromJS([]);
 
     component.cancel = function()
@@ -63,13 +64,14 @@ define(["slycat-server-root", "slycat-web-client", "slycat-dialog", "knockout",
     }
     component.load_table = function()
     {
-      client.put_model_table(
+      client.post_model_files(
       {
         mid: component.model._id(),
-        sid: component.remote.sid(),
-        path: component.browser.selection()[0],
+        sids: [component.remote.sid()],
+        paths: component.browser.selection(),
         input: true,
-        name: "data-table",
+        names: ["data-table"],
+        parser: component.parser(),
         success: function()
         {
           client.get_model_command(

web-server/plugins/slycat-tracer-image/wizard-ui.html

@@ -23,6 +23,7 @@ <h3 class="modal-title">New Remote Tracer Image Model</h3>
     </div>
     <div data-bind="visible:tab() == 2" style="height: 400px">
       <slycat-remote-browser params="type:'remote',sid:remote.sid,hostname:remote.hostname,selection:browser.selection,path:browser.path,open_file_callback:load_table"></slycat-remote-browser>
+      <slycat-parser-controls params="parser:parser"></slycat-parser-controls>
     </div>
     <div data-bind="visible:tab() == 3">
       <table style="width:100%">