From 2ed7960d1db5480c53c770cb9a6dcfc5f9ca5f8a Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 28 Mar 2026 09:17:07 +0100
Subject: Move dead code to old/server.py
---
server.py | 161 --------------------------------------------------------------
1 file changed, 161 deletions(-)
(limited to 'server.py')
diff --git a/server.py b/server.py
index b1a7404..4ea4891 100755
--- a/server.py
+++ b/server.py
@@ -1900,167 +1900,6 @@ def synonyms():
return f"An error occurred while processing your request for {node}.", 500
-@app.route("/startGeneGene")
-def startGeneGene():
- session['forTopGene']=request.args.get('forTopGene')
- return render_template('progress.html', url_in="searchGeneGene", url_out="showGeneTopGene",version=version())
-
-
-@app.route("/searchGeneGene")
-def gene_gene():
- # Ensure session['path'] is set (e.g. from /progress by non-logged-in user)
- if 'path' not in session:
- # Handle error: session path not set, perhaps redirect or show error
- # For now, let's assume it's set by a previous step like /progress
- # If it can be called directly, this needs robust handling.
- # Quick fix: if not set, create a temporary one, but this might indicate flow issue
- if 'email' not in session : # Only create temp path if not logged in and path is missing
- tf_path_gg=tempfile.gettempdir()
- rnd_gg = "tmp_gg" + ''.join(random.choice(string.ascii_letters) for x in range(6))
- session['path'] = tf_path_gg + "/" + rnd_gg
- os.makedirs(session['path'], exist_ok=True)
- else: # Logged in user should have path_user from /progress
- if 'path_user' in session:
- session['path'] = session['path_user'] # Unify to use session['path']
- else: # Critical error if logged in and no path_user
- return "Error: User session path not found.", 500
-
-
- tmp_ggPMID=session['path']+"_ggPMID"
- gg_file=session['path']+"_ggSent" # Gene_gene
- result_file=session['path']+"_ggResult"
-
- # pubmed_path needs to be defined, assuming it's a global or config
- # For this example, let's assume it's a pre-configured path.
- # If not, this os.system call will fail or use current dir.
- # pubmed_path = "/path/to/local/pubmed/mirror" # Example, should be configured
- pubmed_path = "./pubmed_data/" # Placeholder, ensure this path exists or is correctly set
- os.makedirs(pubmed_path, exist_ok=True) # Ensure it exists if it's a local relative path
-
- def findWholeWord(w): # Helper function, should be defined if not in more_functions
- return re.compile(r'(? \"{tmp_ggPMID}\"")
-
- # 'topGene_uniq.pmid' file needs to exist
- # For robustness, check if it exists
- top_gene_pmid_file = "topGene_uniq.pmid"
- if not os.path.exists(top_gene_pmid_file):
- print(f"Warning: {top_gene_pmid_file} not found. Gene-gene search might be affected.")
- # Create an empty file to prevent comm command error, or handle differently
- open(top_gene_pmid_file, 'a').close()
-
- abstracts_cmd = f"comm -1 -2 \"{top_gene_pmid_file}\" \"{tmp_ggPMID}\" | fetch-pubmed -path \"{pubmed_path}\" | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText | sed \"s/-/ /g\""
- try:
- abstracts_process = os.popen(abstracts_cmd)
- abstracts = abstracts_process.read()
- abstracts_process.close()
- except Exception as e_abs:
- print(f"Error getting abstracts for gene-gene search: {e_abs}")
- abstracts = ""
-
- if os.path.exists(tmp_ggPMID): # Clean up temp file
- os.system(f"rm \"{tmp_ggPMID}\"")
-
- progress=10
- yield "data:"+str(progress)+"\n\n"
- topGenes=dict()
- out_str=str() # Renamed from out
- hitGenes=dict()
-
- # 'topGene_symb_alias.txt' file needs to exist
- top_gene_alias_file = "topGene_symb_alias.txt"
- if os.path.exists(top_gene_alias_file):
- with open(top_gene_alias_file, "r") as top_f:
- for line in top_f:
- parts = line.strip().split("\t")
- if len(parts) == 2:
- symb, alias = parts
- topGenes[symb]=alias.replace("; ","|")
- else:
- print(f"Warning: {top_gene_alias_file} not found. Top gene list will be empty.")
-
- allAbstracts= abstracts.split("\n")
- abstractCnt=len(allAbstracts) if abstracts else 0 # Handle empty abstracts
- rowCnt=0
-
- for row in allAbstracts:
- if not row.strip(): continue
- rowCnt+=1
- if abstractCnt > 0 and rowCnt % 10 == 0 : # Check abstractCnt > 0
- progress=10+round(rowCnt/abstractCnt,2)*80
- yield "data:"+str(progress)+"\n\n"
-
- tiab_parts=row.split("\t", 1) # Split only on first tab
- if len(tiab_parts) < 2: continue # Skip malformed lines
- pmid = tiab_parts[0]
- tiab_text_gg = tiab_parts[1] # Renamed
-
- sentences_gg = sent_tokenize(tiab_text_gg) # Renamed
- ## keep the sentence only if it contains the gene
- for sent_item in sentences_gg: # Renamed
- if findWholeWord(query)(sent_item):
- sent_item=re.sub(r'\b(%s)\b' % query, r'\1', sent_item, flags=re.I)
- for symb_item in topGenes: # Renamed
- allNames=symb_item+"|"+topGenes[symb_item]
- if findWholeWord(allNames)(sent_item) :
- sent_item=sent_item.replace("","").replace("","") # Clean previous bolds
- sent_item=re.sub(r'\b(%s)\b' % allNames, r'\1', sent_item, flags=re.I) # Bold current match
- out_str+=query+"\t"+"gene\t" + symb_item+"\t"+pmid+"\t"+sent_item+"\n"
- if symb_item in hitGenes: # Check if key exists
- hitGenes[symb_item]+=1
- else:
- hitGenes[symb_item]=1
- progress=95
- yield "data:"+str(progress)+"\n\n"
- with open(gg_file, "w+") as gg:
- gg.write(out_str)
- # gg.close() # Not needed with 'with open'
-
- results_html=""+query+" vs top addiction genes
Click on the number of sentences will show those sentences. Click on the top addiction genes will show an archived search for that gene.
" # Renamed
- topGeneHits={}
- for key_gene in hitGenes.keys(): # Renamed
- url_gg=gg_file+"|"+query+"|"+key_gene # Renamed
- sentword="sentence" if hitGenes[key_gene]==1 else "sentences"
- topGeneHits[ " " + "Show " + str(hitGenes[key_gene]) + " " + sentword +" about "+query+" and "+key_gene+"" ]=hitGenes[key_gene]
-
- topSorted = sorted(topGeneHits.items(), key=lambda item: item[1], reverse=True) # Correct way to sort dict by value
-
- for k_html,v_count in topSorted: # Renamed
- results_html+=k_html
-
- with open(result_file, "w+") as saveResult: # Ensure it's opened in write mode
- saveResult.write(results_html)
- # saveResult.close() # Not needed
-
- progress=100
- yield "data:"+str(progress)+"\n\n"
-
- # Start the run
- query_gene_gene=session.get('forTopGene', '') # Get from session, default to empty
- if not query_gene_gene:
- return Response("Error: No gene query found for gene-gene search.", mimetype='text/event-stream')
- return Response(generate(query_gene_gene), mimetype='text/event-stream')
-
-
-@app.route('/showGeneTopGene')
-def showGeneTopGene ():
- results_content = "No results found.
" # Default content
- result_file_path = session.get('path', '') + "_ggResult" # Get path from session
- if result_file_path and os.path.exists(result_file_path):
- with open(result_file_path, "r") as result_f:
- 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+"
",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():
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