Allow artifact renaming

qiita_pet/handlers/api_proxy/__init__.py

@@ -30,7 +30,7 @@
                        artifact_post_req, artifact_get_req,
                        artifact_status_put_req, artifact_delete_req,
                        artifact_summary_get_request,
-                       artifact_summary_post_request)
+                       artifact_summary_post_request, artifact_patch_request)
 from .ontology import ontology_patch_handler
 from .processing import (
     list_commands_handler_get_req, process_artifact_handler_get_req,
@@ -61,4 +61,4 @@
            'list_commands_handler_get_req', 'process_artifact_handler_get_req',
            'list_options_handler_get_req', 'workflow_handler_post_req',
            'workflow_handler_patch_req', 'workflow_run_post_req',
-           'job_ajax_get_req']
+           'job_ajax_get_req', 'artifact_patch_request']

qiita_pet/handlers/api_proxy/artifact.py

@@ -308,6 +308,64 @@ def artifact_post_req(user_id, filepaths, artifact_type, name,
             'artifact': artifact.id}
 
 
+def artifact_patch_request(user_id, req_op, req_path, req_value=None,
+                           req_from=None):
+    """Modifies an attribute of the artifact
+
+    Parameters
+    ----------
+    user_id : str
+        The id of the user performing the patch operation
+    req_op : str
+        The operation to perform on the artifact
+    req_path : str
+        The prep information and attribute to patch
+    req_value : str, optional
+        The value that needs to be modified
+    req_from : str, optional
+        The original path of the element
+
+    Returns
+    -------
+    dict of {str, str}
+        A dictionary with the following keys:
+        - status: str, whether if the request is successful or not
+        - message: str, if the request is unsuccessful, a human readable error
+    """
+    if req_op == 'replace':
+        req_path = [v for v in req_path.split('/') if v]
+        if len(req_path) != 2:
+            return {'status': 'error',
+                    'message': 'Incorrect path parameter'}
+
+        artifact_id = req_path[0]
+        attribute = req_path[1]
+
+        # Check if the user actually has access to the artifact
+        artifact = Artifact(artifact_id)
+        access_error = check_access(artifact.study.id, user_id)
+        if access_error:
+            return access_error
+
+        if not req_value:
+            return {'status': 'error',
+                    'message': 'A value is required'}
+
+        if attribute == 'name':
+            artifact.name = req_value
+            return {'status': 'success',
+                    'message': ''}
+        else:
+            # We don't understand the attribute so return an error
+            return {'status': 'error',
+                    'message': 'Attribute "%s" not found. '
+                               'Please, check the path parameter' % attribute}
+    else:
+        return {'status': 'error',
+                'message': 'Operation "%s" not supported. '
+                           'Current supported operations: replace' % req_op}
+
+
 def artifact_types_get_req():
     """Gets artifact types and descriptions available
 

qiita_pet/handlers/api_proxy/tests/test_artifact.py

@@ -26,7 +26,8 @@
 from qiita_pet.handlers.api_proxy.artifact import (
     artifact_get_req, artifact_status_put_req, artifact_graph_get_req,
     artifact_delete_req, artifact_types_get_req, artifact_post_req,
-    artifact_summary_get_request, artifact_summary_post_request)
+    artifact_summary_get_request, artifact_summary_post_request,
+    artifact_patch_request)
 
 
 class TestArtifactAPIReadOnly(TestCase):
@@ -243,6 +244,47 @@ def test_artifact_summary_post_request(self):
                'job': [job.id, 'queued', None]}
         self.assertEqual(obs, exp)
 
+    def test_artifact_patch_request(self):
+        obs = artifact_patch_request('test@foo.bar', 'replace', '/1/name/',
+                                     req_value='NEW_NAME')
+        exp = {'status': 'success', 'message': ''}
+        self.assertEqual(obs, exp)
+
+        self.assertEqual(Artifact(1).name, 'NEW_NAME')
+
+    def test_artifact_patch_request_errors(self):
+        # No access to the study
+        obs = artifact_patch_request('demo@microbio.me', 'replace',
+                                     '/1/name/', req_value='NEW_NAME')
+        exp = {'status': 'error',
+               'message': 'User does not have access to study'}
+        self.assertEqual(obs, exp)
+        # Incorrect path parameter
+        obs = artifact_patch_request('test@foo.bar', 'replace',
+                                     '/1/name/oops/', req_value='NEW_NAME')
+        exp = {'status': 'error',
+               'message': 'Incorrect path parameter'}
+        self.assertEqual(obs, exp)
+        # Missing value
+        obs = artifact_patch_request('test@foo.bar', 'replace', '/1/name/')
+        exp = {'status': 'error',
+               'message': 'A value is required'}
+        self.assertEqual(obs, exp)
+        # Wrong attribute
+        obs = artifact_patch_request('test@foo.bar', 'replace', '/1/oops/',
+                                     req_value='NEW_NAME')
+        exp = {'status': 'error',
+               'message': 'Attribute "oops" not found. Please, check the '
+                          'path parameter'}
+        self.assertEqual(obs, exp)
+        # Wrong operation
+        obs = artifact_patch_request('test@foo.bar', 'add', '/1/name/',
+                                     req_value='NEW_NAME')
+        exp = {'status': 'error',
+               'message': 'Operation "add" not supported. Current supported '
+                          'operations: replace'}
+        self.assertEqual(obs, exp)
+
     def test_artifact_delete_req(self):
         obs = artifact_delete_req(3, 'test@foo.bar')
         exp = {'status': 'success', 'message': ''}

qiita_pet/handlers/study_handlers/artifact.py

@@ -15,7 +15,8 @@
 from qiita_pet.handlers.api_proxy import (
     artifact_graph_get_req, artifact_types_get_req, artifact_post_req,
     artifact_status_put_req, artifact_get_req, artifact_delete_req,
-    artifact_summary_get_request, artifact_summary_post_request)
+    artifact_summary_get_request, artifact_summary_post_request,
+    artifact_patch_request)
 from qiita_core.util import execute_as_transaction
 from qiita_core.qiita_settings import qiita_config
 
@@ -57,30 +58,52 @@ def post(self):
 
 
 class ArtifactSummaryAJAX(BaseHandler):
+    @authenticated
     def get(self):
         artifact_id = self.get_argument('artifact_id')
         res = artifact_summary_get_request(self.current_user.id, artifact_id)
         res['artifact_id'] = artifact_id
         self.render("study_ajax/artifact_summary.html", **res)
 
+    @authenticated
     def post(self):
         artifact_id = self.get_argument('artifact_id')
         res = artifact_summary_post_request(self.current_user.id, artifact_id)
         self.write(res)
 
 
 class ArtifactAJAX(BaseHandler):
+    @authenticated
     def get(self):
         artifact_id = to_int(self.get_argument('artifact_id'))
         name = artifact_get_req(self.current_user.id, artifact_id)['name']
         self.write(name)
 
+    @authenticated
     def post(self):
         artifact_id = to_int(self.get_argument('artifact_id'))
         self.write(artifact_delete_req(artifact_id, self.current_user.id))
 
+    @authenticated
+    def patch(self):
+        """Patches a prep template in the system
+
+        Follows the JSON PATCH specification:
+        https://tools.ietf.org/html/rfc6902
+        """
+        req_op = self.get_argument('op')
+        req_path = self.get_argument('path')
+        req_value = self.get_argument('value', None)
+        req_from = self.get_argument('from', None)
+
+        response = artifact_patch_request(
+            self.current_user.id, req_op, req_path, req_value, req_from)
+
+        self.write(response)
+
 
 class ArtifactAdminAJAX(BaseHandler):
+    @authenticated
     def get(self):
         artifact_id = to_int(self.get_argument('artifact_id'))
         info = artifact_get_req(self.current_user.id, artifact_id)
@@ -130,6 +153,7 @@ def get(self):
 
         self.write(' '.join(buttons))
 
+    @authenticated
     def post(self):
         visibility = self.get_argument('visibility')
         artifact_id = int(self.get_argument('artifact_id'))

qiita_pet/templates/study_ajax/artifact_summary.html

@@ -45,12 +45,52 @@
         load_artifact_summary(aid);
       });
   }
+
+  /*
+   *
+   * Function to update the artifact name
+   *
+   * @param artifact_id int the artifact to be changed
+   * @param new_name str the new artifact name
+   *
+   * This function executes an AJAX call to update the artifact name
+   * and updates the interface accordingly
+   *
+   */
+  function change_artifact_name(artifact_id, new_name) {
+    $.ajax({
+      url: '/artifact/',
+      type: 'PATCH',
+      data: {'op': 'replace', 'path': '/' + artifact_id + '/name/', 'value': new_name, 'artifact_id': artifact_id},
+      success: function(data) {
+        $("#update-artifact-name").modal('hide');
+        if(data.status == 'error') {
+          bootstrapAlert(data.message, "danger");
+        }
+        else {
+          $("#summary-title").text('Summary: ' + new_name + ' (ID: ' + artifact_id + ')');
+          load_template_graph();
+        }
+      }
+    });
+      console.log('clicked ' + artifact_id + ' ' + new_name);
+  }
+
+  /*
+   *
+   * Allows updating the artifact name if the new artifact name is not empty
+   *
+   */
+  function validate_new_name() {
+    $("#update-name-btn").prop('disabled', $("#new-artifact-name").val() === "");
+  }
 </script>
 <div class='row'>
   <div class='col-md-12'>
     <h4>
-      <i>Summary: {{name}} (ID: {{artifact_id}})</i>
+      <i id='summary-title'>Summary: {{name}} (ID: {{artifact_id}})</i>
       {% if editable %}
+        <a class="btn btn-default btn-sm" data-toggle="modal" data-target="#update-artifact-name"><span class="glyphicon glyphicon-pencil"></span> Edit</a>
         <a class="btn btn-default btn-sm" onclick="populate_main_div('/study/process/', {artifact_id: {{artifact_id}} });"><span class="glyphicon glyphicon-play"></span> Process</a>
       {% end %}
     </h4>
@@ -104,3 +144,22 @@ <h4>
     {% end %}
   </div>
 </div>
+
+<!-- Modal to update the artifact name -->
+<div class="modal fade update-artifact-name" tabindex="-1" role="dialog" id="update-artifact-name">
+  <div class="modal-dialog modal-md">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" class="close" data-dismiss="modal" aria-hidden="true">&times;</button>
+        <h3>Updating artifact {{artifact_id}} name</h3>
+      </div>
+      <div class="modal-body">
+        Introduce the new name:<br/>
+        <input type="text" name="new-artifact-name" id="new-artifact-name" size="35" maxlength="35" onkeyup="validate_new_name();">
+        <button id="update-name-btn" class="btn btn-default" onclick="change_artifact_name({{artifact_id}}, $('#new-artifact-name').val());" disabled>Update</button>
+      </div>
+      <div class="modal-footer">
+      </div>
+    </div>
+  </div>
+</div>

qiita_pet/templates/study_base.html

@@ -215,12 +215,12 @@
 {% block content %}
 <div class="row">
   <div class="col-md-3">
-    <button class="btn btn-info btn-block" onclick="populate_main_div('/study/description/baseinfo/', { study_id: {{study_info['study_id']}} })"><span class="glyphicon glyphicon-info-sign"></span> Study Information</button>
-    <button class="btn btn-info btn-block" onclick="populate_main_div('/study/description/sample_template/', { study_id: {{study_info['study_id']}} })"><span class="glyphicon glyphicon-info-sign"></span> Sample Template</button>
-    <button class="btn btn-info btn-block" onclick="populate_main_div('/study/description/sample_summary/', { study_id: {{study_info['study_id']}} })" id="sample-summary-btn"><span class="glyphicon glyphicon-th-list"></span> Sample Summary</button>
+    <button class="btn btn-default btn-block" onclick="populate_main_div('/study/description/baseinfo/', { study_id: {{study_info['study_id']}} })"><span class="glyphicon glyphicon-info-sign"></span> Study Information</button>
+    <button class="btn btn-default btn-block" onclick="populate_main_div('/study/description/sample_template/', { study_id: {{study_info['study_id']}} })"><span class="glyphicon glyphicon-info-sign"></span> Sample Template</button>
+    <button class="btn btn-default btn-block" onclick="populate_main_div('/study/description/sample_summary/', { study_id: {{study_info['study_id']}} })" id="sample-summary-btn"><span class="glyphicon glyphicon-th-list"></span> Sample Summary</button>
     {% if editable %}
-      <a class="btn btn-info btn-block" href="/study/upload/{{study_info['study_id']}}"><span class="glyphicon glyphicon-upload"></span> Upload Files</a>
-      <button class="btn btn-info btn-block" onclick="populate_main_div('/study/new_prep_template/', { study_id: {{study_info['study_id']}} })"><span class="glyphicon glyphicon-plus-sign"></span> Add New Preparation</button>
+      <a class="btn btn-default btn-block" href="/study/upload/{{study_info['study_id']}}"><span class="glyphicon glyphicon-upload"></span> Upload Files</a>
+      <button class="btn btn-default btn-block" onclick="populate_main_div('/study/new_prep_template/', { study_id: {{study_info['study_id']}} })"><span class="glyphicon glyphicon-plus-sign"></span> Add New Preparation</button>
     {% end %}
 
     <div id="data-types-menu"></div>