progress working

5 files changed, 95 insertions, 158 deletions

diff --git a/ratspub.py b/ratspub.py
index 70877b6..7916198 100755
--- a/ratspub.py
+++ b/ratspub.py
@@ -106,7 +106,7 @@ drug_d = {"alcohol":"alcohol|alcoholism|alcoholic",
         "nicotine":"smoking|nicotine|tobacco",
         "cocaine":"cocaine",
         "opioid":"opioid|opioids|fentanyl|oxycodone|oxycontin|heroin|morphine|methadone|buprenorphine|vicodin|hydrocodone|hycodan|kadian|percoset|hydromorphone|naloxone|codeine|suboxone|tramadol|kratom",
-        "amphetamine":"methamphetamine|amphetamine|METH",
+        "amphetamine":"methamphetamine|amphetamine|METH|AMPH",
         "cannabinoid":"endocannabinoid|cannabinoids|endocannabinoids|marijuana|cannabidiol|cannabinoid|tetrahydrocannabinol|thc|thc 9|Oleoylethanolamide|palmitoylethanolamide|acylethanolamides"
         }
 drug=undic(drug_d)
@@ -121,11 +121,11 @@ brain_d ={"cortex":"cortex|prefrontal|pfc|mPFC|vmpfc|corticostriatal|cortico lim
 # brain region has too many short acronyms to just use the undic function, so search PubMed using the following 
 brain="cortex|accumbens|striatum|amygadala|hippocampus|tegmental|mesolimbic|infralimbic|prelimbic"
 
-function_d={"neuroplasticity":"neuroplasticity|plasticity|long term potentiation|LTP|long term depression|LTD|synaptic|epsp|epsc|neurite|neurogenesis|boutons|mIPSC|IPSC|IPSP",
-            "signalling":"signalling|signaling|phosphorylation|glycosylation",
-#            "regulation":"increased|decreased|regulated|inhibited|stimulated",
+function_d={"signalling":"signalling|signaling|phosphorylation|glycosylation",
             "transcription":"transcription|methylation|hypomethylation|hypermethylation|histone|ribosome",
+            "neuroplasticity":"neuroplasticity|plasticity|long term potentiation|LTP|long term depression|LTD|synaptic|epsp|epsc|neurite|neurogenesis|boutons|mIPSC|IPSC|IPSP",
             "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",
             }
 function=undic(function_d)
 
diff --git a/s2.py b/s2.py
deleted file mode 100755
index 7e2848b..0000000
--- a/s2.py
+++ /dev/null
@@ -1,112 +0,0 @@
-#!/bin/env  python3
-from flask import Flask, render_template, request, session, Response
-import tempfile
-import random
-import string
-from ratspub import *
-import time
-
-app=Flask(__name__)
-app.config['SECRET_KEY'] = '#DtfrL98G5t1dC*4'
-
-@app.route("/")
-def root():
-    return render_template('index.html')
-
-@app.route('/progress')
-def progress():
-    # only 1-6 terms are allowed
-    genes=request.args.get('query')
-    genes=genes.replace(",", " ")
-    genes=genes.replace(";", " ")
-    genes=genes.split()
-    if len(genes)>=6:
-        message="<span class='text-danger'>Up to five terms can be searched at a time</span>"
-        return render_template('index.html', message=message)
-    elif len(genes)==0:
-        message="<span class='text-danger'>Please enter a search term </span>"
-        return render_template('index.html', message=message)
-    # put the query in session cookie
-    session['query']=genes
-    # generate a unique session ID to track the results 
-    tf_path=tempfile.gettempdir()
-    session['path']=tf_path+"/tmp" + ''.join(random.choice(string.ascii_letters) for x in range(6))
-    return render_template('progress.html')
-
-@app.route("/search")
-def search():
-#    tf_path=tempfile.gettempdir()
-#    tf_name=tf_path+"/tmp"+''.join(random.choice(string.ascii_letters) for x in range(6))
-    genes=session['query']
-    percent=round(100/(len(genes)*3), 2)
-    print ("percent percent --->"+str(percent))
-    cysdata=open(session['path']+"_cy","w+")
-    sntdata=open(session['path']+"_snt","w+")
-    def generate(genes):
-        sentences=str()
-        edges=str()
-        nodes=default_nodes
-        nodes=str()
-        progress=0
-        #ft_name=session['path']
-        ft_name="path"
-        for  gene in genes:
-            nodes+="{ data: { id: '" + gene +  "', nodecolor:'#FADBD8', fontweight:700, url:'https://www.ncbi.nlm.nih.gov/gene/?term="+gene+"'} },\n"
-            print ("xxxxxxxxxxxxxxxxxxxxxx")
-            print (genes)
-            sent0=gene_addiction(gene)
-            progress+=percent
-            print ("yyyyyyyyyyyyyx")
-            print(progress)
-            yield "data:"+str(progress)+"\n\n"
-            e0=generate_edges(sent0, "tf_name")
-            sent1=gene_functional(gene)
-            progress+=percent
-            yield "data:"+str(progress)+"\n\n"
-            e1=generate_edges(sent1, "tf_name")
-            sent2=gene_anatomical(gene)
-            progress+=percent
-            e2=generate_edges(sent2, "tf_name")
-            edges+=e0+e1+e2
-            sentences+=sent0+sent1+sent2
-            #save data before the last yield
-            if (progress>99):
-                progress=100
-                sntdata.write(sentences)
-                sntdata.close()
-                cysdata.write(nodes)
-                cysdata.close()
-            yield "data:"+str(progress)+"\n\n"
-    return Response(generate(genes), mimetype='text/event-stream')
-
-@app.route('/cytoscape')
-def cytoscape():
-    with open(session['path']+"_cy","r") as f:
-        elements=f.read()
-        return render_template('cytoscape.html', elements=elements)
-
-@app.route("/sentences")
-def sentences():
-    edge=request.args.get('edgeID')
-    (tf_name, gene0, cat0)=edge.split("|")
-    out="<h3>"+gene0 + " and " + cat0  + "</h3><hr>\n"
-    print(tf_name)
-    with open(tf_name, "r") as df:
-        all_sents=df.read()
-    for sent in all_sents.split("\n"):
-        if len(sent.strip())!=0:
-           (gene,nouse,cat, pmid, text)=sent.split("\t")
-           if (gene == gene0 and cat == cat0) :
-               out+= "<li> "+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>"
-    return render_template('sentences.html', sentences="<ol>"+out+"</ol><p>")
-
-@app.route("/shownode")
-def shownode():
-    node=request.args.get('node')
-    allnodes={**brain_d, **drug_d, **function_d, **addiction_d}
-    out="<p>"+node.upper()+"<hr><li>"+ allnodes[node].replace("|", "<li>")
-    return render_template('sentences.html', sentences=out+"<p>")
-
-
-if __name__ == '__main__':
-    app.run(debug=True)
diff --git a/server.py b/server.py
index 457a8cd..b171c1e 100755
--- a/server.py
+++ b/server.py
@@ -1,9 +1,10 @@
 #!/bin/env  python3
-from flask import Flask, render_template, request, redirect
+from flask import Flask, render_template, request, session, Response
 import tempfile
 import random
 import string
 from ratspub import *
+import time
 
 app=Flask(__name__)
 app.config['SECRET_KEY'] = '#DtfrL98G5t1dC*4'
@@ -12,11 +13,9 @@ app.config['SECRET_KEY'] = '#DtfrL98G5t1dC*4'
 def root():
     return render_template('index.html')
 
-@app.route("/search")
-def search():
-    tf_path=tempfile.gettempdir()
-    tf_name=tf_path+"/tmp"+''.join(random.choice(string.ascii_letters) for x in range(6))
-    all_sentences=str()
+@app.route('/progress')
+def progress():
+    # only 1-6 terms are allowed
     genes=request.args.get('query')
     genes=genes.replace(",", " ")
     genes=genes.replace(";", " ")
@@ -24,30 +23,64 @@ def search():
     if len(genes)>=6:
         message="<span class='text-danger'>Up to five terms can be searched at a time</span>"
         return render_template('index.html', message=message)
-    nodes=default_nodes
-    edges=str()
-    for  gene in genes:
-        nodes+="{ data: { id: '" + gene +  "', nodecolor:'#FADBD8', fontweight:700, url:'https://www.ncbi.nlm.nih.gov/gene/?term="+gene+"'} },\n"
-        sent0=gene_addiction(gene)
-        e0=generate_edges(sent0, tf_name)
-        sent1=gene_functional(gene)
-        e1=generate_edges(sent1, tf_name)
-        sent2=gene_anatomical(gene)
-        e2=generate_edges(sent2, tf_name)
-        edges+=e0+e1+e2
-        all_sentences+=sent0+sent1+sent2
-    #session['tmpfile']={'filename':tf_name}
-    with open(tf_name,"w") as f:
-        f.write(all_sentences)
-        f.close()
-    return render_template('cytoscape.html', elements=nodes+edges)
+    elif len(genes)==0:
+        message="<span class='text-danger'>Please enter a search term </span>"
+        return render_template('index.html', message=message)
+    # put the query in session cookie
+    session['query']=genes
+    # generate a unique session ID to track the results 
+    tf_path=tempfile.gettempdir()
+    session['path']=tf_path+"/tmp" + ''.join(random.choice(string.ascii_letters) for x in range(6))
+    return render_template('progress.html')
+
+@app.route("/search")
+def search():
+    genes=session['query']
+    percent=round(100/(len(genes)*3),1)
+    snt_file=session['path']+"_snt"
+    cysdata=open(session['path']+"_cy","w+")
+    sntdata=open(snt_file,"w+")
+    def generate(genes, tf_name):
+        sentences=str()
+        edges=str()
+        nodes=default_nodes
+        progress=0
+        for  gene in genes:
+            nodes+="{ data: { id: '" + gene +  "', nodecolor:'#FADBD8', fontweight:700, url:'https://www.ncbi.nlm.nih.gov/gene/?term="+gene+"'} },\n"
+            sent0=gene_addiction(gene)
+            progress+=percent
+            yield "data:"+str(progress)+"\n\n"
+            e0=generate_edges(sent0, tf_name)
+            sent1=gene_functional(gene)
+            progress+=percent
+            yield "data:"+str(progress)+"\n\n"
+            e1=generate_edges(sent1, tf_name)
+            sent2=gene_anatomical(gene)
+            progress+=percent
+            e2=generate_edges(sent2, tf_name)
+            edges+=e0+e1+e2
+            sentences+=sent0+sent1+sent2
+            #save data before the last yield
+            if (progress>99):
+                progress=100
+                sntdata.write(sentences)
+                sntdata.close()
+                cysdata.write(nodes+edges)
+                cysdata.close()
+            yield "data:"+str(progress)+"\n\n"
+    return Response(generate(genes, snt_file), mimetype='text/event-stream')
+
+@app.route('/cytoscape')
+def cytoscape():
+    with open(session['path']+"_cy","r") as f:
+        elements=f.read()
+        return render_template('cytoscape.html', elements=elements)
 
 @app.route("/sentences")
 def sentences():
     edge=request.args.get('edgeID')
     (tf_name, gene0, cat0)=edge.split("|")
     out="<h3>"+gene0 + " and " + cat0  + "</h3><hr>\n"
-    print(tf_name)
     with open(tf_name, "r") as df:
         all_sents=df.read()
     for sent in all_sents.split("\n"):
diff --git a/templates/index.html b/templates/index.html
index 6d50a63..0771787 100644
--- a/templates/index.html
+++ b/templates/index.html
@@ -3,7 +3,7 @@
 <p>
 <br>
 {{ message | safe }}
-    <form action="/search">
+    <form action="/progress">
       <input name="query" class="form-control form-control-lg" type="search" placeholder="Rgma Nrxn3" aria-label="search" value="">
       <button class="btn btn-outline-success my-2 my-sm-0" type="submit">Search</button>
     </form>
@@ -13,6 +13,12 @@
 <br> 
 Searches are conducted through PubMed to get relevant PMIDs, which are then used to retrieve the abstracts from a <a href="https://dataguide.nlm.nih.gov/edirect/archive.html">local archive</a>. The gene-keyword relationships are presented as an interactive <a href="https://js.cytoscape.org" >cytoscape</a> graph. The nodes can be moved to better reveal the connections.  Tap on the links will bring up the corresponding sentences in a new browser window. 
 <p>
+
+    <form action="/gene_gene">
+      <input name="gene" class="form-control form-control-lg" type="search" placeholder="Rgma Nrxn3" aria-label="search" value="Nrxn1">
+      <button class="btn btn-outline-success my-2 my-sm-0" type="submit">Search</button>
+    </form>
+	
 <hr>
 <a href="https://github.com/chen42/ratspub"> Source code </a>
 
diff --git a/templates/progress.html b/templates/progress.html
index 322604d..7b4a9d0 100644
--- a/templates/progress.html
+++ b/templates/progress.html
@@ -3,25 +3,35 @@
 
 <script src="//ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
 
-	<script>
-	var source = new EventSource("/search");
-	source.onmessage = function(event) {
-		$('.progress-bar').css('width', event.data+'%').attr('aria-valuenow', event.data);
-		$('.progress-bar-label').text(event.data+'%');
-
-		if(event.data == 100){
-			window.location.replace("/cytoscape")
-			source.close()
-		}
-	}
-	</script>
+<script>
+
+
+var r =  Math.floor(Math.random() * Math.floor(125));
+var g =  Math.floor(Math.random() * Math.floor(125));
+var b =  Math.floor(Math.random() * Math.floor(125));
+document.body.style.backgroundColor = 'rgba('+r+','+g+','+b+',0.1)'
 
-	<div id="progs" class="progress" style="width: 50%; margin: 50px;">
-		<div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 0%">
-			<span class="progress-bar-label">0%</span>
-		</div>
+var source = new EventSource("/search");
+source.onmessage = function(event) {
+	$('.progress-bar').css('width', event.data+'%').attr('aria-valuenow', event.data);
+	$('.progress-bar-label').text(event.data+'%');
+	var alpha = event.data/150
+	document.body.style.backgroundColor = 'rgba('+r+','+g+','+b+',0.3)'.replace(/[^,]+(?=\))/, alpha)
+
+	if(event.data == 100){
+		window.location.replace("/cytoscape")
+		source.close()
+	}
+}
+</script>
+<br>
+<b> We hope this won't take too long ... </b>
+<div id="progs" class="progress" style="width: 50%; margin: 50px;">
+	<div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 0%">
+		<span class="progress-bar-label">0%</span>
 	</div>
-	
+</div>
+
  
 {% endblock %}