Move dead code to old/server.py

1 files changed, 141 insertions, 0 deletions

diff --git a/old/server_gene_gene.py b/old/server_gene_gene.py
new file mode 100644
index 0000000..a125699
--- /dev/null
+++ b/old/server_gene_gene.py
@@ -0,0 +1,141 @@
+# Dead code removed from server.py -- gene-gene search routes
+# These routes were not referenced from any template.
+
+@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():
+    if 'path' not in session:
+        if 'email' not in session :
+             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:
+            if 'path_user' in session:
+                session['path'] = session['path_user']
+            else:
+                 return "Error: User session path not found.", 500
+
+
+    tmp_ggPMID=session['path']+"_ggPMID"
+    gg_file=session['path']+"_ggSent"
+    result_file=session['path']+"_ggResult"
+
+    def findWholeWord(w):
+        return re.compile(r'(?<!\w)({})(?!\w)'.format(w), flags=re.IGNORECASE).search
+
+    def generate(query):
+        from nltk.tokenize import sent_tokenize
+        progress=1
+        yield "data:"+str(progress)+"\n\n"
+        safe_query = query.replace("\"", "\\\"")
+        os.system(f"esearch -db pubmed -query \"{safe_query}\" | efetch -format uid |sort > \"{tmp_ggPMID}\"")
+
+        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.")
+            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):
+            os.system(f"rm \"{tmp_ggPMID}\"")
+
+        progress=10
+        yield "data:"+str(progress)+"\n\n"
+        topGenes=dict()
+        out_str=str()
+        hitGenes=dict()
+
+        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
+        rowCnt=0
+
+        for row in allAbstracts:
+            if not row.strip(): continue
+            rowCnt+=1
+            if abstractCnt > 0 and rowCnt % 10 == 0 :
+                progress=10+round(rowCnt/abstractCnt,2)*80
+                yield "data:"+str(progress)+"\n\n"
+
+            tiab_parts=row.split("\t", 1)
+            if len(tiab_parts) < 2: continue
+            pmid = tiab_parts[0]
+            tiab_text_gg = tiab_parts[1]
+
+            sentences_gg = sent_tokenize(tiab_text_gg)
+            for sent_item in sentences_gg:
+                if findWholeWord(query)(sent_item):
+                    sent_item=re.sub(r'\b(%s)\b' % query, r'<strong>\1</strong>', sent_item, flags=re.I)
+                    for symb_item in topGenes:
+                        allNames=symb_item+"|"+topGenes[symb_item]
+                        if findWholeWord(allNames)(sent_item) :
+                            sent_item=sent_item.replace("<b>","").replace("</b>","")
+                            sent_item=re.sub(r'\b(%s)\b' % allNames, r'<b>\1</b>', sent_item, flags=re.I)
+                            out_str+=query+"\t"+"gene\t" + symb_item+"\t"+pmid+"\t"+sent_item+"\n"
+                            if symb_item in hitGenes:
+                                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)
+
+        results_html="<h4>"+query+" vs top addiction genes</h4> Click on the number of sentences will show those sentences. Click on the <span style=\"background-color:#FcF3cf\">top addiction genes</span> will show an archived search for that gene.<hr>"
+        topGeneHits={}
+        for key_gene in hitGenes.keys():
+            url_gg=gg_file+"|"+query+"|"+key_gene
+            sentword="sentence" if hitGenes[key_gene]==1 else "sentences"
+            topGeneHits[ "<li> <a href=/sentences?edgeID=" + url_gg+ " target=_new>" + "Show " + str(hitGenes[key_gene]) + " " + sentword +" </a> about "+query+" and <a href=/showTopGene?topGene="+key_gene+" target=_gene><span style=\"background-color:#FcF3cf\">"+key_gene+"</span></a>" ]=hitGenes[key_gene]
+
+        topSorted = sorted(topGeneHits.items(), key=lambda item: item[1], reverse=True)
+
+        for k_html,v_count in topSorted:
+            results_html+=k_html
+
+        with open(result_file, "w+") as saveResult:
+            saveResult.write(results_html)
+
+        progress=100
+        yield "data:"+str(progress)+"\n\n"
+
+    query_gene_gene=session.get('forTopGene', '')
+    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 = "<p>No results found.</p>"
+    result_file_path = session.get('path', '') + "_ggResult"
+    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+"<p><br>",no_footer=True,version=version())