diff options
Diffstat (limited to 'server.py')
| -rwxr-xr-x | server.py | 103 |
1 files changed, 55 insertions, 48 deletions
diff --git a/server.py b/server.py index 60b5909..f457e17 100755 --- a/server.py +++ b/server.py @@ -59,7 +59,14 @@ except FileNotFoundError: except Exception as e: print(f"Error loading genecup_synthesis_prompt.txt: {e}. LLM prompts will be affected.") +VERSION=None +def version(): + global VERSION + if VERSION is None: + with open("VERSION", 'r') as file: + VERSION = file.read() + return VERSION app=Flask(__name__) @@ -256,7 +263,7 @@ def root(): onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) @app.route("/login", methods=["POST", "GET"]) @@ -283,8 +290,8 @@ def login(): onto_list = session['onto_list'] else: flash("Invalid username or password!", "inval") - return render_template('signup.html') - return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('signup.html',version=version()) + return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) @app.route("/signup", methods=["POST", "GET"]) @@ -302,7 +309,7 @@ def signup(): if (found_user and (bcrypt.checkpw(password.encode('utf8'), found_user.password)==False)): flash("Already registered, but wrong password!", "inval") - return render_template('signup.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('signup.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) session['email'] = email session['hashed_email'] = hashlib.md5(session['email'] .encode('utf-8')).hexdigest() @@ -328,12 +335,12 @@ def signup(): os.makedirs(session['user_folder']+"/ontology/") flash("Login Succesful!") - return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) else: if 'email' in session: flash("Already Logged In!") - return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) - return render_template('signup.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) + return render_template('signup.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) @app.route("/signin", methods=["POST", "GET"]) @@ -357,11 +364,11 @@ def signin(): onto_len_dir = session['onto_len_dir'] onto_list = session['onto_list'] dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) else: flash("Invalid username or password!", "inval") - return render_template('signup.html') - return render_template('signin.html') + return render_template('signup.html',version=version()) + return render_template('signin.html',version=version()) # change password @app.route("/<nm_passwd>", methods=["POST", "GET"]) @@ -387,7 +394,7 @@ def profile(nm_passwd): onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) # remove reserved characters from the hashed passwords reserved = (";", "/", "?", ":", "@", "=", "&", ".") def replace_reserved(fullstring): @@ -397,7 +404,7 @@ def profile(nm_passwd): replaced_passwd = replace_reserved(str(found_user.password)) if replaced_passwd == user_passwd: - return render_template("/passwd_change.html", name=user_name) + return render_template("/passwd_change.html", name=user_name,version=version()) else: return "This url does not exist" else: @@ -422,12 +429,12 @@ def logout(): flash(f"You have been logged out, {user1}", "inval") # Used f-string for clarity session.pop('email', None) session.clear() - return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) @app.route("/about") def about(): - return render_template('about.html') + return render_template('about.html',version=version()) # Ontology selection @@ -449,7 +456,7 @@ def index_ontology(): dict_onto=ast.literal_eval(onto_cont) onto_len_dir = session['onto_len_dir'] onto_list = session['onto_list'] - return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = session['namecat'], dict_onto=dict_onto ) + return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = session['namecat'], dict_onto=dict_onto ,version=version()) @app.route("/ontology", methods=["POST", "GET"]) @@ -697,7 +704,7 @@ def ontology(): else: onto_len_dir=0 onto_list='' - return render_template('ontology.html',dict_onto=dict_onto, namecat=name_to_html, onto_len_dir=onto_len_dir, onto_list=onto_list) + return render_template('ontology.html',dict_onto=dict_onto, namecat=name_to_html, onto_len_dir=onto_len_dir, onto_list=onto_list,no_footer=True,version=version()) @app.route("/ontoarchive") @@ -711,7 +718,7 @@ def ontoarchive(): onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) else: session['user_folder'] = datadir+"/user/"+str(session['hashed_email']) else: @@ -720,7 +727,7 @@ def ontoarchive(): onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) session_id=session['id'] def sorted_alphanumeric(data): @@ -746,7 +753,7 @@ def ontoarchive(): session['onto_len_dir'] = onto_len_dir session['onto_list'] = onto_list message3="<ul><li> Click on the Date/Time to view archived results. <li>The Date/Time are based on US Central time zone.</ul> " - return render_template('ontoarchive.html', onto_len_dir=onto_len_dir, onto_list = onto_list, onto_folder_list=onto_folder_list, onto_directory_list=onto_directory_list, session_id=session_id, message3=message3) + return render_template('ontoarchive.html', onto_len_dir=onto_len_dir, onto_list = onto_list, onto_folder_list=onto_folder_list, onto_directory_list=onto_directory_list, session_id=session_id, message3=message3,version=version()) # Remove an ontology folder @@ -762,7 +769,7 @@ def removeonto(): onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) @app.route('/progress') @@ -792,7 +799,7 @@ def progress(): onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) message="<span class='text-danger'>Up to 200 terms can be searched at a time</span>" - return render_template('index.html' ,onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto, message=message) + return render_template('index.html' ,onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto, message=message,version=version()) if len(genes)==0: if ('email' in session): @@ -804,7 +811,7 @@ def progress(): onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) message="<span class='text-danger'>Please enter a search term </span>" - return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto, message=message) + return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto, message=message,version=version()) tf_path=tempfile.gettempdir() genes_for_folder_name ="" @@ -892,7 +899,7 @@ def progress(): genes_session += str(gen) + "_" genes_session = genes_session[:-1] session['query']=genes - return render_template('progress.html', url_in="search", url_out="cytoscape/?rnd="+rnd+"&genequery="+genes_session) + return render_template('progress.html', url_in="search", url_out="cytoscape/?rnd="+rnd+"&genequery="+genes_session,version=version()) @app.route("/search") @@ -1159,7 +1166,7 @@ def tableview(): onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) jedges ='' nodata_temp = 1 # Default to no data @@ -1194,7 +1201,7 @@ def tableview(): onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) jedges ='' nodata_temp = 1 # Default to no data @@ -1227,7 +1234,7 @@ def tableview(): num_gene = gene_name.count(',')+1 message3="<ul><li> <font color=\"#E74C3C\">Click on the abstract count to read sentences linking the keyword and the gene</font> <li> Click on a keyword to see the terms included in the search. <li>View the results in <a href='\\cytoscape/?rnd={}&genequery={}'\ ><b> a graph.</b></a> </ul> Links will be preserved when the table is copy-n-pasted into a spreadsheet.".format(rnd_url,genes_url) - return render_template('tableview.html', genes_session_tmp = genes_session_tmp, nodata_temp=nodata_temp, num_gene=num_gene, jedges=jedges, jnodes=jnodes,gene_name=gene_name, message3=message3, rnd_url=rnd_url, genes_url=genes_url) + return render_template('tableview.html', genes_session_tmp = genes_session_tmp, nodata_temp=nodata_temp, num_gene=num_gene, jedges=jedges, jnodes=jnodes,gene_name=gene_name, message3=message3, rnd_url=rnd_url, genes_url=genes_url,no_footer=True,version=version()) # Table for the zero abstract counts @@ -1250,7 +1257,7 @@ def tableview0(): onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) jedges ='' nodata_temp = 1 # Default to no data @@ -1282,7 +1289,7 @@ def tableview0(): onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) jedges ='' nodata_temp = 1 # Default to no data @@ -1316,7 +1323,7 @@ def tableview0(): gene_name = gene_name+added num_gene = gene_name.count(',')+1 message4="<b> Notes: </b><li> These are the keywords that have <b>zero</b> abstract counts. <li>View all the results in <a href='\\cytoscape/?rnd={}&genequery={}'><b> a graph.</b></a> ".format(rnd_url,genes_url) - return render_template('tableview0.html',nodata_temp=nodata_temp, num_gene=num_gene, jedges=jedges, jnodes=jnodes,gene_name=gene_name, message4=message4) + return render_template('tableview0.html',nodata_temp=nodata_temp, num_gene=num_gene, jedges=jedges, jnodes=jnodes,gene_name=gene_name, message4=message4,version=version()) @app.route("/userarchive") @@ -1329,7 +1336,7 @@ def userarchive(): if ('email' in session): if os.path.exists(datadir+"/user/"+str(session['hashed_email'])) == False: flash("Search history doesn't exist!") - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) else: session['user_folder'] = datadir+"/user/"+str(session['hashed_email']) else: @@ -1339,7 +1346,7 @@ def userarchive(): onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) session_id=session['id'] def sorted_alphanumeric(data): @@ -1377,7 +1384,7 @@ def userarchive(): len_dir = len(directory_list) message3="<ul><li> Click on the Date/Time to view archived results. <li>The Date/Time are based on US Central time zone.</ul> " - return render_template('userarchive.html', len_dir=len_dir, gene_list = gene_list, onto_list = onto_list_archive, folder_list=folder_list, directory_list=directory_list, session_id=session_id, message3=message3) + return render_template('userarchive.html', len_dir=len_dir, gene_list = gene_list, onto_list = onto_list_archive, folder_list=folder_list, directory_list=directory_list, session_id=session_id, message3=message3,version=version()) # Remove the search directory @@ -1393,7 +1400,7 @@ def remove(): onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version()) @app.route('/date', methods=['GET', 'POST']) @@ -1475,10 +1482,10 @@ def date(): onto_list_session = '' # Renamed to avoid conflict onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list_session, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list_session, ontol = 'addiction', dict_onto = dict_onto,version=version()) message3="<ul><li> <font color=\"#E74C3C\">Click on the abstract count to read sentences linking the keyword and the gene</font> <li> Click on a keyword to see the terms included in the search. <li>View the results in <a href='\\cytoscape/?rnd={}&genequery={}'\ ><b> a graph.</b></a> </ul> Links will be preserved when the table is copy-n-pasted into a spreadsheet.".format(select_date,genes_session_str) - return render_template('tableview.html',nodata_temp=nodata_temp, num_gene=num_gene,genes_session_tmp = genes_session_tmp, rnd_url=select_date ,jedges=jedges, jnodes=jnodes,gene_name=gene_name, genes_url=genes_session_str, message3=message3) + return render_template('tableview.html',nodata_temp=nodata_temp, num_gene=num_gene,genes_session_tmp = genes_session_tmp, rnd_url=select_date ,jedges=jedges, jnodes=jnodes,gene_name=gene_name, genes_url=genes_session_str, message3=message3,no_footer=True,version=version()) @app.route('/cytoscape/') def cytoscape(): @@ -1504,7 +1511,7 @@ def cytoscape(): onto_list_session = '' # Renamed onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list_session, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list_session, ontol = 'addiction', dict_onto = dict_onto,version=version()) try: with open(rnd_url_path+"_0link","r") as z: @@ -1524,7 +1531,7 @@ def cytoscape(): onto_list_session = '' # Renamed onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list_session, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list_session, ontol = 'addiction', dict_onto = dict_onto,version=version()) try: with open(rnd_url_path+"_0link","r") as z: @@ -1535,7 +1542,7 @@ def cytoscape(): if (len(zeroLink.strip())>0): # Check if zeroLink has content after stripping whitespace message2+="<span style=\"color:darkred;\">No result was found for these genes: " + zeroLink + "</span>" - return render_template('cytoscape.html', elements=elements, message2=message2) + return render_template('cytoscape.html', elements=elements, message2=message2,version=version()) @app.route("/sentences") @@ -1558,7 +1565,7 @@ def sentences(): matching_sents = get_sentences_from_file(tf_name, gene0, cat0) if not matching_sents: # It's possible the file was found but no sentences matched the criteria. - return render_template('sentences.html', sentences=f"<p>No sentences found for {gene0} and {cat0}.</p>") + return render_template('sentences.html', sentences=f"<p>No sentences found for {gene0} and {cat0}.</p>",no_footer=True,version=version()) all_stress_sentences = [] num_abstract = len(matching_sents) @@ -1643,7 +1650,7 @@ Here are the sentences to classify: out= out1+ out2 + "<ol>" + out3 # K.clear_session() # Removed - return render_template('sentences.html', sentences=out+"</ol><p>") + return render_template('sentences.html', sentences=out+"</ol><p>",no_footer=True,version=version()) # Show the cytoscape graph for one gene from the top gene list @@ -1659,7 +1666,7 @@ def showTopGene(): print(f"Warning: searchArchived did not return expected data for {query}") message2="<li><strong>"+query + "</strong> is one of the top addiction genes. <li> An archived search is shown. Click on the blue circle to update the results and include keywords for brain region and gene function. <strong> The update may take a long time to finish.</strong> " - return render_template("cytoscape.html", elements=nodesEdges, message="Top addiction genes", message2=message2) + return render_template("cytoscape.html", elements=nodesEdges, message="Top addiction genes", message2=message2,version=version()) ''' @app.route("/shownode") @@ -1695,7 +1702,7 @@ def shownode(): if not out: # If node not found or details are empty out = f"<p>Details for node '{node.upper()}' not found in the current ontology.</p>" - return render_template('sentences.html', sentences=out+"<p>") + return render_template('sentences.html', sentences=out+"<p>",no_footer=True,version=version()) ''' @app.route("/shownode") def shownode(): @@ -1711,7 +1718,7 @@ def shownode(): for ky in dictionary.keys(): if node in dictionary[ky].keys(): out="<p>"+node.upper()+"<hr><li>"+ next(iter(dictionary[ky][node])).replace("|", "<li>") - return render_template('sentences.html', sentences=out+"<p>") + return render_template('sentences.html', sentences=out+"<p>",no_footer=True,version=version()) @@ -1873,11 +1880,11 @@ def synonyms(): prompt_string = GENECUP_PROMPT_TEMPLATE.replace("{{gene}}", node) prompt_string += formatted_sentences - return render_template('genenames.html', case=case, gene=node.upper(), synonym_list=synonym_list, synonym_list_str=synonym_list_str, prompt=prompt_string) + return render_template('genenames.html', case=case, gene=node.upper(), synonym_list=synonym_list, synonym_list_str=synonym_list_str, prompt=prompt_string,version=version()) except KeyError: case = 2 - return render_template('genenames.html', gene=node, case=case) + return render_template('genenames.html', gene=node, case=case,version=version()) except Exception as e: print(f"An unexpected error occurred in /synonyms for node {node}: {e}") return f"An error occurred while processing your request for {node}.", 500 @@ -1886,7 +1893,7 @@ def synonyms(): @app.route("/startGeneGene") def startGeneGene(): session['forTopGene']=request.args.get('forTopGene') - return render_template('progress.html', url_in="searchGeneGene", url_out="showGeneTopGene") + return render_template('progress.html', url_in="searchGeneGene", url_out="showGeneTopGene",version=version()) @app.route("/searchGeneGene") @@ -2041,13 +2048,13 @@ def showGeneTopGene (): results_content=result_f.read() else: print(f"Warning: Result file {result_file_path} not found for showGeneTopGene.") - return render_template('sentences.html', sentences=results_content+"<p><br>") + return render_template('sentences.html', sentences=results_content+"<p><br>",no_footer=True,version=version()) # Generate a page that lists all the top 150 addiction genes with links to cytoscape graph. @app.route("/allTopGenes") def top150genes(): - return render_template("topAddictionGene.html") + return render_template("topAddictionGene.html",no_footer=True,version=version()) if __name__ == '__main__': |