freeze before clean tools/view

cirDraw/static/tools/js/denChrPlot.js

@@ -433,6 +433,7 @@ $("#previous").click(function () {
     index = getIndex();
     if (index > 0) {
         blockRecord[densityFilter[index - 1].chr+densityFilter[index - 1].start].click();
+        currentClickBlock = $chr.text() + $('#js-input-from').text();
         /* preDen = densityFilter[index - 1];
         $('#geneNameSelect').val(preDen.name);
         $("#js-input-from").text(preDen.start);
@@ -450,6 +451,7 @@ $("#next").click(function () {
     // console.log('Next index:', index);
     if (index < densityFilter.length - 1) {
         blockRecord[densityFilter[index + 1].chr+densityFilter[index + 1].start].click();
+        currentClickBlock = $chr.text() + $('#js-input-from').text();
         /*
         $('#geneNameSelect').val(nextDen.name);
         $("#js-input-from").text(nextDen.start);

cirDraw/static/tools/js/drawCirc.js

@@ -973,8 +973,8 @@ function ring(opt) {
         }).click(function () {
             if (links !== undefined & links !== null) {
                 elink = links.split(',')
-                for (var i = 0, up = links.length; i < up; i++) {
-                    openNewTab(links[i]);
+                for (var i = 0, up = elink.length; i < up; i++) {
+                    openNewTab(elink[i]);
                 }
             }
         });
@@ -1004,8 +1004,9 @@ function ring(opt) {
             }
         }).click(function () {
             if (links !== undefined & links !== null) {
-                for (var i = 0, up = links.length; i < up; i++) {
-                    openNewTab(links[i]);
+                elink = links.split(',')
+                for (var i = 0, up = elink.length; i < up; i++) {
+                    openNewTab(elink[i]);
                 }
             }
         });

cirDraw/static/tools/js/upload.js

@@ -31,7 +31,7 @@ $(document).ready(function () {
         $('#uploadlabel').hide();
         document.querySelector('.textarea').innerText = example_content;
         $('#submit').prop('disabled', true);
-        finishProcess('8bd10a77cbda74ed2513d2643a39b0bb');
+        finishProcess('4672896d383d34c10a4561dddece79aa');
     });
 
     function finishProcess(md5, display_time) {
@@ -144,6 +144,7 @@ $(document).ready(function () {
                 data: formdata,
                 processData: false,
                 contentType: false,
+                timeout: 5000000000,
             };
 
              /* else {
@@ -248,7 +249,7 @@ $(document).ready(function () {
                     function () {
                         $('.lds-roller').remove();
                         $('#upload-text').remove();
-                        $('#processtip').html('<p>Failed to upload, please check your connection and <a id="refresher" onclick="location.reload()"><i>refresh</i><i class="fas fa-redo-alt ml-1"></i></a></p>');
+                        $('#processtip').html('<p>Server timeout, please <a id="refresher" onclick="location.reload()"><i>refresh</i><i class="fas fa-redo-alt ml-1"></i></a></p>');
                         $('#refresher').hover(function(){
                             $('#refresher').css({'cursor':'pointer', 'color': '#fed136'});
                         },

cirDraw/templates/base.html

@@ -25,7 +25,7 @@
   <!-- CSS -->
   <link rel="stylesheet" href="https://code.jquery.com/ui/1.9.2/themes/base/jquery-ui.css">
   <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.13.2/css/bootstrap-select.min.css">
-  <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/jquery.dataTables.min.css">
+  <!--<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/jquery.dataTables.min.css">-->
   <link href="https://cdnjs.cloudflare.com/ajax/libs/animate.css/3.7.0/animate.min.css" rel="stylesheet">
   <link href="{% static 'base/css/agency.css' %}" rel="stylesheet">
   <link href="{% static 'base/css/circCirc.css' %}" rel="stylesheet">
@@ -46,7 +46,7 @@
       <div class="collapse navbar-collapse" id="navbarResponsive">
         <ul class="navbar-nav text-uppercase ml-auto">
         <li class="nav-item">
-            <a class="nav-link js-scroll-trigger" href="/tools/display/8bd10a77cbda74ed2513d2643a39b0bb">Example</a>
+            <a class="nav-link js-scroll-trigger" href="/tools/display/4672896d383d34c10a4561dddece79aa">Example</a>
           </li>
           <li class="nav-item">
             <a class="nav-link js-scroll-trigger" href="{% url 'tools' %}">Upload</a>

cirDraw/tools/handle_file.py

@@ -118,24 +118,36 @@ def find_exon_combo(chr_num: str, circStart: int, circEnd: int, assembly: str, b
     engine.dispose()
     connection = engine.raw_connection()
     try:
-        get_gene_script = f'select id from {assembly}_genome_genes where chr_num="{chr_num}" and start<={circStart+bias} and end>={circEnd-bias};'
+        get_gene_script_1 = f'select id from {assembly}_genome_genes where chr_num="{chr_num}" and start<={circStart+bias} and end>={circStart-bias};'
+        get_gene_script_2 = f'select id from {assembly}_genome_genes where chr_num="{chr_num}" and start<={circEnd+bias} and end>={circEnd-bias};'
         with connection.cursor() as cur:
-            cur.execute(get_gene_script)
-            get_gene = cur.fetchall()
-    except:
+            cur.execute(get_gene_script_1)
+            get_gene_1 = cur.fetchall()
+            cur.execute(get_gene_script_2)
+            get_gene_2 = cur.fetchall()
+        get_gene = get_gene_1 + get_gene_2
+    except Exception as e:
+        print('When get gene', e)
         return None, None, None
 
     transcripts_pool = []
     if len(get_gene) == 0:
             #print(f'circRNA: {chr_num}|{circStart}-{circEnd}: \033[33mGene Not Found\033[0m')
         return None, None, None
     elif len(get_gene) > 0:
-
         for i in get_gene:
-            get_transcripts_script = f'select id from {assembly}_genome_transcripts where gene="{i[0]}" and start<={circStart+bias} and end>={circEnd-bias};'
-            with connection.cursor() as cur:
-                cur.execute(get_transcripts_script)
-                get_transcripts = cur.fetchall()
+            get_transcripts_script_1 = f'select id from {assembly}_genome_transcripts where gene="{i[0]}" and start<={circStart+bias} and end>={circStart-bias};'
+            get_transcripts_script_2 = f'select id from {assembly}_genome_transcripts where gene="{i[0]}" and start<={circEnd+bias} and end>={circEnd-bias};'
+            try:
+                with connection.cursor() as cur:
+                    cur.execute(get_transcripts_script_1)
+                    get_transcripts_1 = cur.fetchall()
+                    cur.execute(get_transcripts_script_2)
+                    get_transcripts_2 = cur.fetchall()
+                get_transcripts = get_transcripts_1 + get_transcripts_2
+                #print(get_transcripts)
+            except Exception as e:
+                print('When get transcripts', e)
             if len(get_transcripts) == 0:
                 pass
             else:
@@ -219,7 +231,7 @@ def process_file(file, assembly: str, file_type, task_id, bias=2):
                         with connection.cursor() as cur:
                             cur.execute(f'select disease from circ_disease where assembly="{assembly}" and chr_num="{chr_num}" and start>={start-bias} and start<={start+bias} and end<={end+bias} and end>={end-bias};')
                             disease = cur.fetchall()
-                        print(disease)
+                        #print(disease)
                         if len(disease) == 0:
                             disease = 'Unknown'
                         else:
@@ -261,8 +273,11 @@ def process_file(file, assembly: str, file_type, task_id, bias=2):
 
     for circ in unmap_circ:
         try:
-            combo, gene, transcript = find_exon_combo(circ[0], int(circ[1]), int(circ[2]), assembly)
-            #print(gene, transcript)
+            try:
+                combo, gene, transcript = find_exon_combo(circ[0], int(circ[1]), int(circ[2]), assembly)
+                #print(gene, transcript)
+            except Exception as e:
+                print('When calculating exon combo', e)
             if combo != None:
                 #print('before components')
                 try:
@@ -274,16 +289,20 @@ def process_file(file, assembly: str, file_type, task_id, bias=2):
                 except Exception as e:
                     print(e)
                 #print('After components')
-                for i in components:
-                    i['mods'] = ujson.loads(i['mods'])
-                #print('alter components')
-                with connection.cursor() as cur:
-                    cur.execute(f'select disease from circ_disease where assembly="{assembly}" and chr_num="{chr_num}" and start>={start-bias} and start<={start+bias} and end<={end+bias} and end>={end-bias};')
-                    disease = cur.fetchall()
-                if len(disease) == 0:
+                try:
                     disease = 'Unknown'
-                else:
-                    disease = disease[0]
+                    for i in components:
+                        if type(i['mods']) == str:
+                            i['mods'] = ujson.loads(i['mods'])
+                    #print('alter components')
+                    with connection.cursor() as cur:
+                        cur.execute(f'select disease from circ_disease where assembly="{assembly}" and chr_num="{chr_num}" and start>={start-bias} and start<={start+bias} and end<={end+bias} and end>={end-bias};')
+                        find_disease = cur.fetchall()
+                        #print(find_disease)
+                    if len(find_disease) > 0:
+                        disease = find_disease[0]
+                except Exception as e:
+                    print('When mapping disease',e)
 
                 try:
                     circ_on_gene[gene][1].append({"start": int(circ[1]),
@@ -311,7 +330,7 @@ def process_file(file, assembly: str, file_type, task_id, bias=2):
                     except Exception as e:
                         print("Add circ error:", e)
         except Exception as e:                
-            print(mp.current_process().name, "Failed to process one unmapped circ:", e)
+            print(mp.current_process().name, "Failed to process one unmapped circ:", circ[0], int(circ[1]), int(circ[2]), e)
 
     print('Mapped circ:', len(circ_on_gene))
     return circ_on_gene
@@ -363,7 +382,7 @@ def handle(config):
                     result[k][1] += v[1]
                 except:
                     result[k] = v
-
+        #print('raw result:', circ_on_gene_all)
         print('Create result file:', path + config['NEW_FILE'])
         with open(path + config['NEW_FILE'], 'w+') as f:
             for _,v in result.items():
@@ -432,6 +451,7 @@ def count_dist(array, step):
                     cord[s[i]] += 1
             return cord
         try:
+            tmp_circ_len = {}
             if len(circRNA_length) > 16:
                 tmp_circ_len = count_dist(np.array(circRNA_length,dtype=np.float64),16)
             else:

cirDraw/tools/templates/tools/tools.html

@@ -181,7 +181,7 @@ <h2 id="BaTable" class="d-inline-block mr-3">Possible modifications on circRNA</
 <!-- Outside js -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/intro.js/2.9.3/intro.min.js" type="text/javascript"></script>
 <script src="https://cdnjs.cloudflare.com/ajax/libs/tabulator/4.2.3/js/tabulator.js"></script>
-<script src="https://cdn.bootcss.com/echarts/4.1.0.rc2/echarts-en.common.js" type="text/javascript"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/echarts/4.2.1/echarts-en.common.js" integrity="sha256-4omDrvG5ELofoBmmZnfzGAe2hzSzjiG2qHBXIZwuDXA=" crossorigin="anonymous"></script>
 <script src="https://cdnjs.cloudflare.com/ajax/libs/snap.svg/0.5.1/snap.svg-min.js" type="text/javascript"></script>
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jspdf/1.5.3/jspdf.debug.js"
     integrity="sha384-NaWTHo/8YCBYJ59830LTz/P4aQZK1sS0SneOgAvhsIl3zBu8r9RevNg5lHCHAuQ/" crossorigin="anonymous">

cirDraw/tools/urls.py

@@ -6,7 +6,7 @@
 urlpatterns = [
 
     # Render pages
-	url(r'^$', views.render_upload_page, name='tools'),
+    url(r'^$', views.render_upload_page, name='tools'),
     url(r'^display/(?P<md5>[0-9a-f-]+)$', views.render_display_page, name="render_display"),
 
     # Upload

load.py

@@ -0,0 +1,24 @@
+import pymysql
+import ujson
+
+connection = pymysql.connect(host='127.0.0.1',
+                             port=6603,
+                             user='root',
+                             db='circDraw',
+                             password='mypassword',
+                             charset='utf8',
+                             local_infile=True)
+
+with connection.cursor() as cur:
+    counter = 0
+    with open('/home/circ/map_circ/server/hg19_circRNA_annotated.txt','r') as f1:
+        for line in f1:
+            i = line.strip().split('\t')
+            cur.execute(f'''INSERT INTO hg19_circRNAs_new (gene,transcript,chr_num,start,end,components) VALUES ("{i[0]}","{i[1]}","{i[2]}","{i[3]}","{i[4]}",{ujson.dumps(i[-1])})''')
+    connection.commit()
+    with open('/home/circ/map_circ/server/hg38_circRNA_annotated.txt','r') as f2:
+        for line in f2:
+            i = line.strip().split('\t')
+            cur.execute(f'''INSERT INTO hg38_circRNAs_new (gene,transcript,chr_num,start,end,components) VALUES ("{i[0]}","{i[1]}","{i[2]}","{i[3]}","{i[4]}",{ujson.dumps(i[-1])})''')
+    connection.commit()
+

process_watchdog/auto-clean.py

@@ -1,21 +1,4 @@
 #!/usr/bin/python3
-#import datetime
-#import time
-#
-#path = "/home/circ/circDraw/process_watchdog/auto-clean.log"
-## reset
-#with open(path, 'w') as f:
-#    f.write(str(datetime.datetime.now()) + ": Restart")
-#    f.write('\n')
-#
-#while True:
-#    time.sleep(2)
-#    a = datetime.datetime.now()
-#    with open(path, 'a') as f:
-#        f.write(str(a))
-#        print(a)
-#        f.write('\n')
-#
 
 import mysqlconnect as mc
 import datetime, time
@@ -61,8 +44,6 @@ def cleanup_once(login_file_name, logfile):
 
 
 
-
-
 def main():
     check_duration = 1800 # as in seconds
     login_file_name = '/home/circ/circDraw/process_watchdog/admin_login.json'

process_watchdog/resetdb.py

@@ -145,7 +145,7 @@ def main(login_file_name, inp):
 
     elif inp == "clean":
         clean_box = ['tools_species_circrnas', 'tools_species_genome_exons_introns', 'tools_species_genome_genes', 'tools_species_genome_transcripts']
-        example_md5 = ''#'8bd10a77cbda74ed2513d2643a39b0bb'
+        example_md5 = '4672896d383d34c10a4561dddece79aa'#'8bd10a77cbda74ed2513d2643a39b0bb'
         path_box = ["../cirDraw/media/md5_data/"]
         empty_db(connector, clean_box)
         empty_dir(path_box)