Merge pull request #294 from AmpliconSuite/project_alias

Feature to access projects via an alias name & redirect

caper/caper/forms.py

@@ -10,6 +10,9 @@
 from crispy_forms.layout import Submit, Layout, Field
 
 
+from django.utils.safestring import mark_safe
+
+
 class RunForm(forms.ModelForm):
     accept_license = forms.BooleanField(
         label=format_html(
@@ -22,7 +25,7 @@ class RunForm(forms.ModelForm):
 
     class Meta:
         model = Run
-        fields = ('project_name','description','publication_link','private','project_members', 'accept_license')
+        fields = ('project_name','description','publication_link','private','project_members', 'accept_license', 'alias')
         labels = {
             'private': 'Visibility'
         }
@@ -36,6 +39,7 @@ def __init__(self, *args, **kwargs):
         self.fields['project_members'].widget.attrs.update({'placeholder': 'Optional: List of additional email addresses or AmpliconRepository usernames separated by spaces or commas'})
 
 class UpdateForm(forms.ModelForm):
+
     accept_license = forms.BooleanField(
         label=format_html(
             "I acknowledge that the uploaded files will be released under a <a href='https://raw.githubusercontent.com/AmpliconSuite/AmpliconRepository/main/licenses/CCv4-BY.txt'>Creative Commons v4 license</a>."),
@@ -47,7 +51,7 @@ class UpdateForm(forms.ModelForm):
 
     class Meta:
         model = Run
-        fields = ('project_name', 'description', 'publication_link', 'private', 'project_members', 'accept_license')
+        fields = ('project_name', 'description', 'publication_link', 'private', 'project_members', 'accept_license', 'alias')
         labels = {
             'private': 'Visibility'
         }

caper/caper/models.py

@@ -11,6 +11,7 @@ class Run(models.Model):
     BOOL_CHOICES = ((True, 'Private'), (False, 'Public'))
     private = models.BooleanField(choices=BOOL_CHOICES,default=True)
     project_members = models.CharField(max_length=1000, blank = True)
+    alias = models.CharField(max_length = 300, blank =True, null = True)
 
 
 class FeaturedProjectUpdate(models.Model):

caper/caper/utils.py

@@ -197,8 +197,22 @@ def sample_data_from_feature_list(features_list):
     # print(f'********** TOOK {datetime.datetime.now() - now}')
     return sample_data
 
+def get_all_alias():
+    """
+    Gets all alias names in the db
+    """
+    return collection_handle.distinct('alias_name')
+
+
 
 def get_one_project(project_name_or_uuid):
+    """
+    Gets one project from name or UUID. 
+    
+    if name, then checks the DB for an "alias" field, then gets that project if it has one 
+    
+    """
+
     try:
         project = collection_handle.find({'_id': ObjectId(project_name_or_uuid), 'delete': False})[0]
         prepare_project_linkid(project)
@@ -209,6 +223,15 @@ def get_one_project(project_name_or_uuid):
 
     # backstop using the name the old way
     if project is None:
+        ## first try finding the alias name
+        try:
+            project = collection_handle.find({'alias_name' : project_name_or_uuid, 'delete':False})[0]
+            prepare_project_linkid(project)
+            return project
+        except:
+            project = None
+
+        ## then find project via project name
         try:
             project = collection_handle.find_one({'project_name': project_name_or_uuid, 'delete': False})
             if project is not None:

caper/caper/views.py

@@ -34,7 +34,7 @@
 from .forms import RunForm, UpdateForm, FeaturedProjectForm, DeletedProjectForm, SendEmailForm, UserPreferencesForm
 from .utils import collection_handle, collection_handle_primary, db_handle, fs_handle, replace_space_to_underscore, \
     preprocess_sample_data, get_one_sample, sample_data_from_feature_list, get_one_project, validate_project, \
-    prepare_project_linkid, replace_underscore_keys, get_projects_close_cursor
+    prepare_project_linkid, replace_underscore_keys, get_projects_close_cursor, get_all_alias
 from django.forms.models import model_to_dict
 
 import subprocess
@@ -166,6 +166,14 @@ def form_to_dict(form):
     # print(form)
     run = form.save(commit=False)
     form_dict = model_to_dict(run)
+
+    if "alias" in form_dict:
+        try:
+            form_dict['alias'] = form_dict['alias'].replace(' ', '_')
+            print(f'alias for this project is: {form_dict["alias"]}')
+        except:
+            print('No alias provided, probably Null')
+            print(type(form_dict['alias']))
     return form_dict
 
 
@@ -1260,7 +1268,7 @@ def edit_project_page(request, project_name):
 
         form = UpdateForm(request.POST, request.FILES)
         form_dict = form_to_dict(form)
-
+        
         form_dict['project_members'] = create_user_list(form_dict['project_members'], get_current_user(request))
 
         # lets notify users (if their preferences request it) if project membership has changed
@@ -1298,10 +1306,11 @@ def edit_project_page(request, project_name):
                 return redirect('project_page', project_name=new_id.inserted_id)
             else:
                 alert_message = "The input file was not a valid aggregation. Please see site documentation."
-                return render(request, 'pages/edit_project.html', {'project': project, 'run': form, 'alert_message': alert_message})
-
-
-
+                return render(request, 'pages/edit_project.html', 
+                              {'project': project, 
+                               'run': form, 
+                               'alert_message': alert_message,
+                               'all_alias' :get_all_alias()})
         # JTL 081823 Not sure what these next 4 lines are about?  An earlier plan to change the project file?
         # leaving them alone for now but they smell like dead code
         if 'file' in form_dict:
@@ -1311,19 +1320,27 @@ def edit_project_page(request, project_name):
 
         if check_project_exists(project_name):
             new_project_name = form_dict['project_name']
+
             logging.info(f"project name: {project_name}  change to {new_project_name}")
             current_runs = project['runs']
             if runs != 0:
                 current_runs.update(runs)
             query = {'_id': ObjectId(project_name)}
-            proj = {'project_name':new_project_name, 'runs' : current_runs, 'description': form_dict['description'], 'date': get_date(),
-                                 'private': form_dict['private'], 'project_members': form_dict['project_members'], 'publication_link': form_dict['publication_link'],
-                                 'Oncogenes': get_project_oncogenes(current_runs)}
+            proj = {'project_name':new_project_name, 
+                    'runs' : current_runs, 
+                    'description': form_dict['description'],
+                    'date': get_date(),
+                    'private': form_dict['private'], 
+                    'project_members': form_dict['project_members'], 
+                    'publication_link': form_dict['publication_link'],
+                    'Oncogenes': get_project_oncogenes(current_runs),
+                    'alias_name':form_dict['alias'],}
             new_val = { "$set": proj }
 
             proj['_id'] = query['_id']
             edit_proj_privacy(proj, old_privacy, new_privacy)
             if form.is_valid():
+                print('im here')
                 collection_handle.update_one(query, new_val)
                 return redirect('project_page', project_name=project_name)
             else:
@@ -1352,8 +1369,11 @@ def edit_project_page(request, project_name):
 
 
 
-
-    return render(request, "pages/edit_project.html", {'project': project, 'run': form})
+    print(project['alias_name'])
+    return render(request, "pages/edit_project.html",
+                  {'project': project, 
+                   'run': form, 
+                   'all_alias' :json.dumps(get_all_alias())})
 
 def create_user_list(string, current_user):
     # user_list = str.split(',')
@@ -1852,11 +1872,15 @@ def create_project(request):
             return redirect('project_page', project_name=new_id.inserted_id)
         else:
             alert_message = "The input file was not a valid aggregation. Please see site documentation."
-            return render(request, 'pages/create_project.html', {'run': form, 'alert_message': alert_message})
+            return render(request, 'pages/create_project.html', 
+                          {'run': form, 
+                           'alert_message': alert_message, 
+                           'all_alias' : json.dumps(get_all_alias())})
 
     else:
         form = RunForm()
-    return render(request, 'pages/create_project.html', {'run' : form})
+    return render(request, 'pages/create_project.html', {'run' : form, 
+                                                         'all_alias' : json.dumps(get_all_alias())})
 
 
 def _create_project(form, request, previous_versions = [], previous_views = [0, 0]):
@@ -2005,6 +2029,7 @@ def create_project_helper(form, user, request_file, save = True, tmp_id = uuid.u
     project['FINISHED?'] = False
     project['views'] = previous_views[0]
     project['downloads'] = previous_views[1]
+    project['alias_name'] = form_dict['alias']
     return project, tmp_id
 
 class FileUploadView(APIView):

caper/templates/pages/create_project.html

@@ -55,7 +55,24 @@ <h1>Create New Project</h1>
     <div id="alert-box"></div>
     <form method="post" enctype="multipart/form-data" id="upload-form">
         {% csrf_token %}
-        {{ run|crispy }}
+        {% for field in run %}
+            {% if field.name == 'alias' %}
+            <p>Enter an unique alias for this project. It can be used to access this project.</p> <p></p>
+                <div style='display:flex; gap:5px; align-items:center;'>
+                    <span> ampliconrepository.org/project/</span>
+                    <div style = 'width:200px; padding:2px; font-size:15px border:1px;'>{{ field }}</div>
+                    <span>/</span>
+                </div>
+                <div id='result'></div>
+                <br>
+                <br>
+
+            {% else %}
+                {{field | as_crispy_field }}
+
+            {% endif %}
+        {% endfor %}
+
 
         <input type="file" name="document" id="fileuploadfield">
         <input type="button" onClick="clearFileInput();" value="Remove Upload" id="remove-upload-btn">
@@ -164,6 +181,29 @@ <h1>Create New Project</h1>
         }
     }
 
+    document.addEventListener('DOMContentLoaded', function() {
+        // Pass the alias names from Django context to JavaScript
+        var aliasNames = JSON.parse("{{ all_alias | escapejs}}");
+        console.log(aliasNames);
+
+        var inputField = document.getElementById('id_alias');
+        var result = document.getElementById('result');
+
+        inputField.addEventListener('input', function() {
+            var userInput = inputField.value;
+
+            if (aliasNames.includes(userInput) ) {
+                result.textContent = 'Alias already taken ...';
+                result.style.color = 'red';
+            } else {
+                result.textContent = 'This alias works!';
+                result.style.color = 'green';
+            }
+        });
+    });
+
+
+
 </script>
 
 {% endblock %}

caper/templates/pages/edit_project.html

@@ -54,10 +54,33 @@ <h1>Editing project: '{{ project.project_name }}'</h1>
     <div id="alert-box"></div>
     <form method="post" enctype="multipart/form-data" id="upload-form">
         {% csrf_token %}
-        {{ run|crispy }}
+        {% for field in run %}
+
+            {% if field.name == 'alias' %}
+            <p>Enter an unique alias for this project. It can be used to access this project.</p>
+
+                {% if project.alias_name != None %}
+                    <p> Current alias name is: <b>{{ project.alias_name }}</b>. The project can be accessed at <a href="">ampliconrepository.org/project/{{project.alias_name}}</a></p>
+                {% endif %}
+
+
+                <div style='display:flex; gap:5px; align-items:center;'>
+                    <span> ampliconrepository.org/project/</span>
+                    <div style = 'width:200px; padding:2px; font-size:15px border:1px;'>{{ field }}</div>
+                    <span>/</span>
+                </div>
+                <div id='result'></div>
+                <br>
+            {% else %}
+                {{field | as_crispy_field }}
+
+            {% endif %}
+        {% endfor %}
+
         <label for="document">
             Replace AmpliconAggregator output file with: &nbsp;&nbsp;
         </label>
+
         <input type="file" name="document" id="fileuploadfield">
         <input type="button" onClick="clearFileInput();" value="Remove Upload" id="remove-upload-btn">
         <br> <br>
@@ -147,6 +170,29 @@ <h1>Please sign in to edit projects</h1>
         }
     }
 
+    document.addEventListener('DOMContentLoaded', function() {
+        // Pass the alias names from Django context to JavaScript
+        var aliasNames = JSON.parse("{{ all_alias | escapejs}}");
+        console.log(aliasNames);
+
+        var inputField = document.getElementById('id_alias');
+        var result = document.getElementById('result');
+
+        inputField.addEventListener('input', function() {
+            var userInput = inputField.value;
+
+            if (aliasNames.includes(userInput) ) {
+                result.textContent = 'Alias already taken ...';
+                result.style.color = 'red';
+            } else {
+                result.textContent = 'This alias works!';
+                result.style.color = 'green';
+            }
+        });
+    });
+
+
+
 </script>
 
 {% endblock %}

caper/templates/pages/project.html

@@ -4,7 +4,7 @@
 {% load static %}
 
 {% block extra_js %}
-
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0-beta3/css/all.min.css">
 <script>
     $(document).ready( function () {
         $('#myTable1').DataTable({
@@ -98,6 +98,41 @@
     }
 
 
+    function copyToClipboard() {
+        // Get the anchor element with the URL
+        var copyText = document.getElementById("aliaslink");
+
+        // Create a range and select the text
+        var range = document.createRange();
+        range.selectNode(copyText);
+
+        // Get the selection object and add the range to it
+        var selection = window.getSelection();
+        selection.removeAllRanges(); // Clear any existing selections
+        selection.addRange(range);
+
+        // Copy the selected text to the clipboard
+        try {
+            var successful = document.execCommand('copy');
+            var message = successful ? 'Copied to clipboard!' : 'Unable to copy.';
+            document.getElementById("message").innerHTML = message;
+            // Remove the message after 5 seconds (5000 milliseconds)
+            setTimeout(function() {
+                document.getElementById("message").innerHTML = '';
+            }, 3000);
+
+
+        } catch (err) {
+            console.error('Failed to copy:', err);
+        }
+
+        // Clear the selection for better user experience
+        selection.removeAllRanges();
+    }
+
+
+
+
 </script>
 
 {% endblock %}
@@ -129,6 +164,13 @@ <h2>Project: <span style="font-weight: 200">{{ project.project_name }}</span>
         <h5>Description: <span style="font-weight: 200">{{ project.description }}</span></h5>
         <h5>Publication link: <span style="font-weight: 200">{{ project.publication_link|escape|replace_urls|safe }}</span></h5>
         <h5>Reference build: <span style="font-weight: 200">{{ reference_genome }}</span></h5>
+
+        {% if project.alias_name %}
+            <h5>Project Link: <a id='aliaslink' href="">ampliconrepository.org/project/{{project.alias_name}}  </a><i class="fas fa-link chain-icon" style = 'cursor:pointer;'onclick="copyToClipboard()"></i></h5>
+            <p id="message"></p>
+        {% endif %}
+
+
     </div>
 
     <div class="col-md-3">