Merge pull request #105 from dengzq1234/desktop_v2

Desktop v2

README.md

@@ -106,8 +106,12 @@ TreeProfiler requires
   - webdriver_manager
   - pyvirtualdisplay
 
-### Quick install via pip
+### Quick Install Environment
 ```
+# create environment
+conda create -n treeprofiler python=3.10
+conda activate treeprofiler
+
 # Install ETE Toolkit v4
 pip install --force-reinstall https://github.com/etetoolkit/ete/archive/ete4.zip
 

treeprofiler/app.py

@@ -651,14 +651,19 @@ def explore_tree(treename):
     # Start the ete exploration thread
     start_explore_thread(t, treename, current_layouts, current_props)
 
+    # Before rendering the template, convert to JSON
+    #layouts_json = json.dumps(tree_info['layouts'])
+    #layouts_metadata_json = json.dumps(layouts_metadata)
+
     # Render template
     return template(
         'explore_tree_v2',
         treename=treename,
         tree_info=tree_info,
         selected_props=current_props,
         color_schemes=continuous_colormaps,
-        layouts_metadata=layouts_metadata
+        layouts_metadata=layouts_metadata,
+        #layouts_metadata_json = json.dumps(layouts_metadata)
     )
 
 def get_colormap_hex_colors(colormap_name, num_colors):

treeprofiler/layouts/text_layouts.py

@@ -363,7 +363,7 @@ def set_node_style(self, node):
                     tooltip += f'<br>{self.prop}: {prop_text}<br>'
 
                 if self.color_dict:
-                    color = self.color_dict.get(str(prop_text),"")
+                    color = self.color_dict.get(prop_text,"")
                     prop_face = RectFace(width=self.width, height=self.height, color=color, \
                         padding_x=self.padding_x , padding_y=self.padding_y, tooltip=tooltip)
                     node.add_face(prop_face, column=self.column, position="aligned")
@@ -458,7 +458,7 @@ def set_node_style(self, node):
                 tooltip += f'<br>{self.prop}: {prop_text}<br>'
 
             if self.color_dict:
-                color = self.color_dict.get(str(prop_text), self.absence_color)
+                color = self.color_dict.get(prop_text, self.absence_color)
                 align_link_face = AlignLinkFace(width=self.width*2, height=None,
                     stroke_color=color, stroke_width=2, line_type=0, opacity=0.7)
                 node.sm_style["bgcolor"] = color

treeprofiler/src/utils.py

@@ -13,6 +13,7 @@
 import matplotlib.colors as mcolors
 import numpy as np
 from scipy import stats
+import numbers
 import random
 import colorsys
 import operator
@@ -270,7 +271,23 @@ def get_internal_parser(internal_parser="name"):
         return 1
     elif internal_parser == "support":
         return 0
-
+
+def get_prop2type(node):
+    output = {}
+    prop2value = node.props
+    if '_speciesFunction' in prop2value:
+        del prop2value['_speciesFunction']
+
+    for prop, value in prop2value.items():
+        if value != 'NaN':
+            if isinstance(value, numbers.Number):
+                output[prop] = float
+            elif type(value) == list:
+                output[prop] = list
+            else:
+                output[prop] = str    
+    return output
+
 def ete4_parse(newick, internal_parser="name"):
     tree = PhyloTree(newick, parser=get_internal_parser(internal_parser))
     # Correct 0-dist trees
@@ -349,11 +366,6 @@ def conditional_prune(tree, conditions_input, prop2type):
             #         n.dist = 1
     return tree
 
-
-    #array = [n.props.get(prop) if n.props.get(prop) else 'NaN' for n in nodes] 
-    array = [n.props.get(prop) for n in nodes if n.props.get(prop) ] 
-    return array
-
 # def _tree_prop_array(node, prop, leaf_only=False, numeric=False, list_type=False):
 #     array = []
 #     sep = '||'

treeprofiler/tree_annotate.py

@@ -731,6 +731,14 @@ def run(args):
     # parsing tree
     try:
         tree, eteformat_flag = utils.validate_tree(args.tree, args.input_type, args.internal)
+        # get tree orignal properties
+        for path, node in tree.iter_prepostorder():
+            prop2type.update(utils.get_prop2type(node))
+        del prop2type['name']
+        del prop2type['dist']
+        if 'support' in prop2type:
+            del prop2type['support']
+
     except utils.TreeFormatError as e:
         logger.error(e)
         sys.exit(1)
@@ -750,8 +758,9 @@ def run(args):
     logger.info(f'start parsing...')
     # parsing metadata
     if args.metadata: # make a series of metadatas
-        metadata_dict, node_props, columns, prop2type = parse_csv(args.metadata, delimiter=args.metadata_sep, \
+        metadata_dict, node_props, columns, metadata_prop2type = parse_csv(args.metadata, delimiter=args.metadata_sep, \
         no_headers=args.no_headers, duplicate=args.duplicate)
+        prop2type.update(metadata_prop2type)
     else: # annotated_tree
         node_props=[]
         columns = {}
@@ -919,16 +928,23 @@ def run(args):
                     list2str = list_sep.join(node.props.get(key))
                     node.add_prop(key, list2str)
         avail_props = list(prop2type.keys())
-        del avail_props[avail_props.index('name')]
+
+        #del avail_props[avail_props.index('name')]
         del avail_props[avail_props.index('dist')]
         if 'support' in avail_props:
             del avail_props[avail_props.index('support')]
-        
+
         annotated_tree.write(outfile=os.path.join(args.outdir, out_newick), props=avail_props, 
                     parser=utils.get_internal_parser(args.internal), format_root_node=True)
 
     if args.stdout:
-        print(annotated_tree.write(props=avail_props, parser=utils.get_internal_parser(args.internal), format_root_node=True))
+        avail_props = list(prop2type.keys())
+        #del avail_props[avail_props.index('name')]
+        del avail_props[avail_props.index('dist')]
+        if 'support' in avail_props:
+            del avail_props[avail_props.index('support')]
+        print(annotated_tree.write(props=avail_props, parser=utils.get_internal_parser(args.internal), 
+        format_root_node=True))
 
     # if args.outtsv:
     #     tree2table(annotated_tree, internal_node=True, outfile=args.outtsv)
@@ -1656,10 +1672,11 @@ def merge_dictionaries(dict_ranks, dict_names):
         if n.props.get('rank') and n.props.get('rank') != 'Unknown':
             rank2values[n.props.get('rank')].append(n.props.get('sci_name',''))
 
-        # if n.name:
-        #     pass
-        # else:
-        #     n.name = n.props.get("sci_name", "")
+        # TODO assign internal node as sci_name, ATTENTION of potential bug
+        if n.name:
+            pass
+        else:
+            n.name = n.props.get("sci_name", "")
 
     return tree, rank2values
 

treeprofiler/tree_plot.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-import numbers
 import math
 import sys
 import os
@@ -393,7 +392,7 @@ def run(args):
 
         if eteformat_flag:
             for path, node in tree.iter_prepostorder():
-                prop2type.update(get_prop2type(node))
+                prop2type.update(utils.get_prop2type(node))
 
     if args.collapsed_by: # need to be wrap with quotes
         condition_strings = args.collapsed_by
@@ -1549,7 +1548,6 @@ def process_prop_values(tree, prop):
 
         #minval, maxval = all_prop_values.min(), all_prop_values.max()
         if bubble_range:
-            print(bubble_range)
             abs_maxval = np.abs(bubble_range).max()
             max_val = bubble_range[1]
             min_val = bubble_range[0]
@@ -1771,22 +1769,6 @@ def get_heatmap_matrix_layouts(layout_name, numerical_props, norm_method, intern
             layouts.append(matrix_layout)
     return layouts, level
 
-def get_prop2type(node):
-    output = {}
-    prop2value = node.props
-    if '_speciesFunction' in prop2value:
-        del prop2value['_speciesFunction']
-
-    for prop, value in prop2value.items():
-        if value != 'NaN':
-            if isinstance(value, numbers.Number):
-                output[prop] = float
-            elif type(value) == list:
-                output[prop] = list
-            else:
-                output[prop] = str    
-    return output
-
 def categorical2matrix(tree, profiling_props, dtype=str, color_config=None):
     """
     Input:

treeprofiler/views/explore_tree_v2.html

@@ -562,7 +562,7 @@ <h6 class="mb-0 fw-bold">Manage Loaded Layouts</h6>
                                                     <button class="btn btn-sm btn-outline-primary">
                                                         <i class="bi bi-pencil-square me-1"></i>Edit
                                                     </button>
-                                                    <button class="btn btn-sm btn-outline-danger">
+                                                    <button class="btn btn-sm btn-outline-danger delete-layout-btn">
                                                         <i class="bi bi-trash-fill me-1"></i>Delete
                                                     </button>
                                                 </div>
@@ -571,10 +571,12 @@ <h6 class="mb-0 fw-bold">Manage Loaded Layouts</h6>
                                         % end
                                     </tbody>
                                 </table>
+                                <!-- Hidden input to store the current layouts_metadata -->
+                                <input id="layoutsMetadataInput" value="{{ layouts_metadata }}">
                             </div>
                             <!-- Apply Changes Button -->
                             <div class="text-center mt-4">
-                                <button class="btn btn-success w-100 py-2 fw-bold">
+                                <button id="applyChangesBtn" class="btn btn-success w-100 py-2 fw-bold">
                                     <i class="bi bi-check-circle-fill me-2"></i>Apply Changes
                                 </button>
                             </div>
@@ -849,8 +851,106 @@ <h1>Explore Tree: {{treename}}</h1>
             })
             .catch(error => console.error('Error:', error));
         });
-
+
+        // update changes
+        // document.addEventListener('DOMContentLoaded', () => {
+        //     // Event delegation for the delete button
+        //     document.getElementById('activeLayoutsTable').addEventListener('click', function(event) {
+        //         const deleteBtn = event.target.closest('.delete-layout-btn');
+        //         if (deleteBtn) {
+        //             const row = deleteBtn.closest('tr');
+
+        //             // Clear all cells' content except the row structure
+        //             row.querySelectorAll('td').forEach(cell => {
+        //                 cell.innerHTML = '';
+        //             });
+        //         }
+        //     });
+
+        //     // Handle Apply Changes
+        //     document.getElementById('applyChangesBtn').addEventListener('click', function() {
+        //         const remainingLayouts = [];
+        //         console.log('Applying changes...', remainingLayouts)
+        //         // Collect rows with content
+        //         document.querySelectorAll('#activeLayoutsTable tr').forEach(row => {
+        //             const layoutName = row.querySelector('td:nth-child(1)').innerText.trim();
+        //             const appliedProps = Array.from(row.querySelectorAll('td:nth-child(2) li'))
+        //                                     .map(prop => prop.innerText.trim());
+
+        //             if (layoutName) {  // Only include rows that are not cleared
+        //                 remainingLayouts.push({
+        //                     layout_name: layoutName,
+        //                     applied_props: appliedProps
+        //                 });
+        //             }
+        //         });
+
+        //         // Send the remaining layouts back to the backend
+        //         fetch('', {
+        //             method: 'POST',
+        //             headers: { 'Content-Type': 'application/json' },
+        //             body: JSON.stringify({ action: 'apply_changes', layouts: remainingLayouts })
+        //         })
+        //         .then(response => response.text())
+        //         .then(data => {
+        //             alert('Changes applied successfully!');
+        //             location.reload(); // Optionally reload the page
+        //         })
+        //         .catch(error => console.error('Error:', error));
+        //     });
+        // });
+    </script>
+    <script>
+        document.addEventListener('DOMContentLoaded', () => {
+            const tableBody = document.getElementById('activeLayoutsTable');
+            const layoutsMetadata = document.getElementById('layoutsMetadataInput');
+
+            // Function to update the hidden input field
+            function updateHiddenInput() {
+                layoutsMetadataInput.value = JSON.stringify(layoutsMetadata);
+            }
+
+            // Function to find and remove layout metadata by name
+            function removeLayoutMetadata(layoutName) {
+                layoutsMetadata = layoutsMetadata.filter(layout => layout.layout_name !== layoutName);
+                updateHiddenInput();
+            }
+
+            // Handle Delete Button Click
+            tableBody.addEventListener('click', function (e) {
+                if (e.target.closest('.delete-layout-btn')) {
+                    const row = e.target.closest('tr'); // Find the table row
+                    const layoutName = row.querySelector('td:nth-child(1)').innerText.trim(); // Get layout name
+
+                    // Remove the row from the table
+                    row.remove();
+
+                    // Remove the corresponding layout from the metadata
+                    removeLayoutMetadata(layoutName);
+                }
+            });
+
+            // Handle Apply Changes Button
+            document.getElementById('applyChangesBtn').addEventListener('click', function () {
+                // Send the updated layoutsMetadata back to the backend
+                fetch(window.location.pathname, {
+                    method: 'POST',
+                    headers: { 'Content-Type': 'application/x-www-form-urlencoded' },
+                    body: new URLSearchParams({
+                        updated_metadata: layoutsMetadataInput.value
+                    })
+                })
+                .then(response => response.text())
+                .then(data => {
+                    alert("Layouts updated successfully!");
+                    location.reload();
+                })
+                .catch(error => console.error('Error:', error));
+            });
+        });
     </script>
+
+
     <script>
         // this is for layout toggle settings
         $(document).ready(function (){