diff options
| -rwxr-xr-x | ratspub.py | 10 | ||||
| -rw-r--r-- | ratspub_keywords.py | 12 | ||||
| -rwxr-xr-x | server.py | 30 |
3 files changed, 41 insertions, 11 deletions
@@ -6,7 +6,6 @@ from ratspub_keywords import * global function_d, brain_d, drug_d, addiction_d, brain_query_term, pubmed_path - ## turn dictionary (synonyms) to regular expression def undic(dic): return "|".join(dic.values()) @@ -103,14 +102,15 @@ function=undic(function_d) addiction=undic(addiction_d) drug=undic(drug_d) -nodecolor={'function':"#A9CCE3", 'addiction': "#D7BDE2", 'drug': "#F9E79F", 'brain':"#A3E4D7", 'gwas':"#AEB6BF"} -#https://htmlcolorcodes.com/ +nodecolor={'function':"#A9CCE3", 'addiction': "#D7BDE2", 'drug': "#F9E79F", 'brain':"#A3E4D7", 'gwas':"#AEB6BF", 'stress':"#EDBB99", 'psychiatric':"#F5B7B1"} +#https://htmlcolorcodes.com/ third column down n0=generate_nodes(function_d, 'function') n1=generate_nodes(addiction_d, 'addiction') n2=generate_nodes(drug_d, 'drug') n3=generate_nodes(brain_d, 'brain') -default_nodes=n0+n1+n2+n3 - +n4=generate_nodes(stress_d, 'stress') +n5=generate_nodes(psychiatric_d, 'psychiatric') +default_nodes=n0+n1+n2+n3+n4+n5 host= os.popen('hostname').read().strip() if host=="x1": diff --git a/ratspub_keywords.py b/ratspub_keywords.py index 8a23e73..ade04f6 100644 --- a/ratspub_keywords.py +++ b/ratspub_keywords.py @@ -31,3 +31,15 @@ function_d={"signalling":"signalling|signaling|phosphorylation|glycosylation", "neurotransmission": "neurotransmission|neuropeptides|neuropeptide|glutamate|glutamatergic|GABA|GABAergic|dopamine|dopaminergic|DAergic|cholinergic|nicotinic|muscarinic|serotonergic|serotonin|5 ht|acetylcholine", } #"regulation":"increased|decreased|regulated|inhibited|stimulated", + +stress_d={"stress":"stress|psycological trauma|distress", + "PTSD":"PTSD" + } +psychiatric_d={"anxiety":"anxiety|anxious", + "depression":"depression|depressive", + "bipolar":"bipolar disorder", + "impulsivity":"impulsivity|impulsive", + "compulsive":"compulsive|obssessive", + "schizophrenia": "schizophrenia", + "autism": "autism|autistic" + } @@ -20,7 +20,7 @@ def about(): @app.route('/progress') def progress(): - # only 1-6 terms are allowed + # only 1-100 terms are allowed genes=request.args.get('query') genes=genes.replace(",", " ") genes=genes.replace(";", " ") @@ -42,7 +42,7 @@ def progress(): @app.route("/search") def search(): genes=session['query'] - percent=round(100/(len(genes)*4),1) + percent=round(100/(len(genes)*6),1) # 6 categories snt_file=session['path']+"_snt" cysdata=open(session['path']+"_cy","w+") sntdata=open(snt_file,"w+") @@ -79,16 +79,34 @@ def search(): sent3=gene_category(gene, brain_d, brain_query_term, "brain") progress+=percent e3=generate_edges(sent3, tf_name) + # stress + stress=undic(stress_d) + sent4=gene_category(gene, stress_d, stress, "drug") + progress+=percent + yield "data:"+str(progress)+"\n\n" + e4=generate_edges(sent4, tf_name) + # psychiatric + psychiatric=undic(psychiatric_d) + sent5=gene_category(gene, psychiatric_d, psychiatric, "psychiatric") + progress+=percent + yield "data:"+str(progress)+"\n\n" + e5=generate_edges(sent5, tf_name) # gwas - e4=searchArchived('gwas', gene) - geneEdges=e0+e1+e2+e3+e4 + e6=searchArchived('gwas', gene) + geneEdges=e0+e1+e2+e3+e4+e5+e6 ## there is a bug here. zero link notes are not excluded anymore if len(geneEdges) >1: edges+=geneEdges nodes+="{ data: { id: '" + gene + "', nodecolor:'#E74C3C', fontweight:700, url:'/startGeneGene?forTopGene="+gene+"'} },\n" else: nodesToHide+=gene + " " - sentences+=sent0+sent1+sent2+sent3 + sentences+=sent0+sent1+sent2+sent3+sent4+sent5 + sent0=None + sent1=None + sent2=None + sent3=None + sent4=None + sent5=None #save data before the last yield searchCnt+=1 if (searchCnt==len(genes)): @@ -138,7 +156,7 @@ def showTopGene(): @app.route("/shownode") def shownode(): node=request.args.get('node') - allnodes={**brain_d, **drug_d, **function_d, **addiction_d} + allnodes={**brain_d, **drug_d, **function_d, **addiction_d, **stress_d, **psychiatric_d} out="<p>"+node.upper()+"<hr><li>"+ allnodes[node].replace("|", "<li>") return render_template('sentences.html', sentences=out+"<p>") |