diff options
| -rwxr-xr-x | server.py | 40 | ||||
| -rw-r--r-- | templates/create-ontology.html | 27 |
2 files changed, 66 insertions, 1 deletions
diff --git a/server.py b/server.py index a20d388..626179a 100755 --- a/server.py +++ b/server.py @@ -359,6 +359,38 @@ def create_ontology(): "numbering. Add abbreviations and aliases as a list with each term, " "separated by commas") if request.method == "POST": + action = request.form.get("action", "generate") + + if action == "search": + # Build a temporary .onto file from the result terms and redirect to /progress + result_text = request.form.get("result", "") + query = request.form.get("query", "") + search_types = request.form.getlist("type") + # Build onto dict: each term is its own category with aliases as pipe-separated keywords + dict_onto = {} + for line in result_text.strip().split("\n"): + line = line.strip() + if not line: + continue + parts = [p.strip() for p in line.split(",")] + category = parts[0] + keywords = "|".join(parts) + dict_onto[category] = {category: {keywords}} + # Save to a temp .onto file + onto_path = os.path.join(tempfile.gettempdir(), "gemini_ontology") + with open(onto_path + ".onto", "w") as f: + f.write(repr(dict_onto)) + session['namecat'] = onto_path + print(f" Created ontology: {onto_path}.onto with {len(dict_onto)} categories") + print(f" Gene query: '{query}', search_types: {search_types}") + # Build the redirect URL with type and query params + from urllib.parse import urlencode + params = [("query", query)] + for t in search_types: + params.append(("type", t)) + return redirect("/progress?" + urlencode(params)) + + # action == "generate" prompt = request.form.get("prompt", default_prompt) try: result = gemini_query(prompt) @@ -830,6 +862,11 @@ def progress(): if (search_type == []): search_type = ['GWAS', 'function', 'addiction', 'drug', 'brain', 'stress', 'psychiatric', 'cell'] session['search_type'] = search_type + # Use default addiction ontology unless redirected from /create-ontology + if request.referrer and '/create-ontology' in request.referrer: + pass # keep session['namecat'] set by /create-ontology + elif 'namecat' in session: + del session['namecat'] genes_session = '' for gen in genes: @@ -873,8 +910,10 @@ def search(): if 'namecat' in session: namecat_flag=1 ses_namecat = session['namecat'] + print(f" /search: namecat={ses_namecat}, search_type={search_type}") onto_cont = open(session['namecat']+".onto","r").read() dict_onto=ast.literal_eval(onto_cont) + print(f" /search: onto categories={list(dict_onto.keys())[:10]}") for ky in dict_onto.keys(): nodecolor[ky] = "hsl("+str((n_num+1)*int(360/len(dict_onto.keys())))+", 70%, 80%)" @@ -935,6 +974,7 @@ def search(): all_d = all_d+'|'+all_d_ls if all_d: # Check if all_d is not empty all_d=all_d[1:] + print(f" /search generate: all_d={all_d[:200] if all_d else '(empty)'}, search_type={search_type}") if ("GWAS" in search_type): datf = pd.read_csv('./utility/gwas_used.csv',sep='\t') diff --git a/templates/create-ontology.html b/templates/create-ontology.html index 44d8ef1..627bc86 100644 --- a/templates/create-ontology.html +++ b/templates/create-ontology.html @@ -5,6 +5,7 @@ <h3>Create Ontology with Gemini AI</h3> <form method="POST" action="/create-ontology"> + <input type="hidden" name="action" value="generate"> <div class="form-group"> <label for="prompt">Prompt:</label> <textarea class="form-control" id="prompt" name="prompt" rows="6">{{ prompt }}</textarea> @@ -15,8 +16,32 @@ {% if result %} <div class="form-group mt-4"> <label for="result">Result ({{ count }} terms):</label> - <textarea class="form-control" id="result" rows="20" readonly>{{ result }}</textarea> + <textarea class="form-control" id="result" name="result" rows="20" form="search-form">{{ result }}</textarea> </div> + + <form id="search-form" method="POST" action="/create-ontology" class="mt-3"> + <input type="hidden" name="action" value="search"> + <div class="form-group"> + <label for="query">Gene symbols (space or comma separated):</label> + <textarea class="form-control" id="query" name="query" rows="2"></textarea> + </div> + <div id="check_selection_onto"></div> + <button type="submit" class="btn btn-primary">Search</button> + </form> + + <script> + var lines = document.getElementById('result').value.split('\n'); + var checkbox = ''; + for (var i = 0; i < lines.length; i++) { + var term = lines[i].trim(); + if (term) { + var label = term.split(',')[0].trim(); + checkbox += '<strong><input type="checkbox" name="type" value="' + label + '" checked form="search-form"> ' + label + ' </strong>'; + } + } + checkbox += '<br><strong><input type="checkbox" onClick="var c=document.querySelectorAll(\'input[name=type]\');for(var i=0;i<c.length;i++)c[i].checked=this.checked;"/> (Un)select all</strong>'; + document.getElementById('check_selection_onto').innerHTML = checkbox; + </script> {% endif %} </div> |