last copy of front before merge into master

cirDraw/restart_uwsgi.sh

@@ -6,4 +6,4 @@ sudo uwsgi --ini /home/circ/circDraw/cirDraw/uwsgi.ini --uid circ --enable-threa
 cd /home/circ/circDraw/process_watchdog/
 python3 resetdb.py admin_login.json clean
 
-> /var/log/uwsgi/circDraw.log
+#> /var/log/uwsgi/circDraw.log

cirDraw/static/tools/js/denChrPlot.js

@@ -194,13 +194,13 @@ function gradientLegend(x, y) {
             stroke: 'none'
         });
     }
-    den.paper.text(x - 10, y + 5, '1').attr({
+    den.paper.text(x - 10, y + 5, denBlockMIN).attr({
         fill: palette[0],
         stroke: 'none',
         'font-size': 8,
         //'font-family': 'arial'
     });
-    den.paper.text(x + 203, y + 5, '100').attr({
+    den.paper.text(x + 203, y + 5, denBlockMAX).attr({
         fill: palette[99],
         stroke: 'none',
         'font-size': 8,

cirDraw/static/tools/js/drawCirc.js

@@ -110,7 +110,7 @@ $scale.ionRangeSlider({
 });
 
 var table = new Tabulator("#table", {
-    layout:"fitDataFill",
+    layout:"fitColumns",
     height:"350px",
     headerFilterPlaceholder:"Search",
     placeholder:"No Data Available",
@@ -814,6 +814,7 @@ function drawArc(data) {
             //console.log(tableData)
 
             table.replaceData(tableData);
+            table.redraw();
 
             $("#download-csv").click(function(){
                 table.download("csv", name + ".csv");

cirDraw/templates/base.html

@@ -45,6 +45,9 @@
       </button>
       <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>
+          </li>
           <li class="nav-item">
             <a class="nav-link js-scroll-trigger" href="{% url 'tools' %}">Upload</a>
           </li>

cirDraw/tools/templates/tools/tools.html

@@ -20,9 +20,9 @@
                 <a id='origin-data' style='font-size: 7pt; color: #fed136; cursor: pointer;'><u>Result data</u></a>
                 <h2 id="report">Basic Report</h2>
                 <div class="row justify-content-center mt-3">
-                    <div class="col-12">
-                    <h3 id="len">circRNA length distribution</h3>
-                <div data-intro="Statistic of circRNA length in the file." data-step="1" id="lenChart" style="width: 100%; min-height: 400px"></div>
+                    <div class="col-10">
+                    <h3 id="len">Distrubution of circRNA splicing sites span</h3>
+                <div data-intro="Statistic of the span of all circRNA backsplicing sites in the file." data-step="1" id="lenChart" style="width: 100%; min-height: 400px"></div>
                 <h3 id="top">Top 20 genes with most circRNA isoforms</h3>
                 <div id="topChart" style="width: 100%; min-height: 400px"></div>
                     </div>
@@ -35,7 +35,7 @@ <h3 id="iso">circRNA length</h3>
                 <h2 id="density" data-toc-text="Density plot">circRNA density distribution on chromosome
                 </h2>
 
-                <svg id="svg2" width="800" height="500" class="svg" data-intro="Interactive plot of circRNA density on chromosome. Try to click on the color block."
+                <svg id="svg2" width="800" height="500" class="svg" data-intro="Interactive plot of circRNA counts on chromosome. Try to click on the color block. Darker block means the gene has more circRNAs. The block surrounded by red squre is the gene currently displaying below."
                 data-step="2">
                     <image id="load" x="360" y="220" width="80" height="80" xlink:href="../../../media/dna.gif"/>
                 </svg>
@@ -74,7 +74,7 @@ <h2 id="density" data-toc-text="Density plot">circRNA density distribution on ch
                     <a class="btn btn-primary btn-sm text-center" id="denDownload" download="circDraw.svg">Download</a>
                 </div>-->
 
-                <h2 id="isoform" data-toc-text="Isoform plot">circRNA isoforms on chromosome region</h2>
+                <h2 id="isoform" data-toc-text="Isoform plot">circRNA isoforms on gene</h2>
                 <svg id="svg" width="800" height="500" class="svg" data-intro="Interactive plot of circRNAs back-splicing events on gene, Select a block from above plot, the detail of that block will be displayed here. Click the curve to view the predicted internal structure of circRNAs." data-step="5">
                     <foreignObject width="800" height="500" id="svg-tip">
                         <p style="padding-top: 240px; font-size: 20px; color: grey;"><strong>Please select a region from
@@ -101,10 +101,10 @@ <h2 id="isoform" data-toc-text="Isoform plot">circRNA isoforms on chromosome reg
                 </div>
 
                 <div class="row justify-content-center pt-3">
-                    <div class="col-8">
+                    <div class="col-10">
                         <div class="extra-controls den-select-info">
                             <button id="previous" class="btn btn-light btn-sm"><i
-                                    class="fas fa-angle-double-left"></i><strong> Last Gene</strong></button>
+                                    class="fas fa-angle-double-left"></i><strong> Last</strong></button>
                             <p class="ml-1 mr-1 mb-1 d-inline-block">Name:</p>
                             <!--<p id="geneNameSelect" class="ml-1 mr-1 mb-1 d-inline-block">Unknown</p>-->
                             <input data-step="6" data-intro="type in gene name to search for interested gene." list="genename-list" id="geneNameSelect" style="width: 5em" />
@@ -117,7 +117,7 @@ <h2 id="isoform" data-toc-text="Isoform plot">circRNA isoforms on chromosome reg
                             <p id="js-input-from" class="ml-1 mr-1 mb-1 d-inline-block">0</p>
                             <p class="ml-1 mr-1 mb-1 d-inline-block">End:</p>
                             <p id="js-input-to" class="ml-1 mr-1 mb-1 d-inline-block">0</p>
-                            <button id="next" class="btn btn-light btn-sm"><strong>Next Gene </strong><i
+                            <button id="next" class="btn btn-light btn-sm"><strong>Next </strong><i
                                     class="fas fa-angle-double-right"></i></button>
                         </div>
                     </div>
@@ -161,7 +161,7 @@ <h2 id="BaTable" class="d-inline-block mr-3">Possible modifications on circRNA</
 
                 </div>
                 <span class="help-block" style="color:grey;" id="circ-name"></span>
-                <div class="row justify-content-center" id="BaTable2" data-step="7" data-intro="When you select a circRNA, related modification info will be displayed here.">
+                <div class="row justify-content-center" id="BaTable2" data-step="7" data-intro="When you select a circRNA, related modification info will be displayed here. If the table content is not displayed, please enlarge your windows.">
                     <div class="col-9">
                         <div id="table" class="table-sm bd-bottom"></div>
                     </div>

process_watchdog/resetdb.py

@@ -87,7 +87,13 @@ def delete_file(file_path, r=False):
 
 
 
-
+def cleandb_except(connector, exception_box, exceptions):
+    # delete from table where exceptions won't be deleted.
+    operator = mc.Operator(connector)
+    for t in exception_box:
+        operator.clean_table(t, {'md5': ['!=', exceptions]})
+        print('Exception drop Success in ', t)
+    operator.terminate()
 
 
 
@@ -132,22 +138,28 @@ def main(login_file_name, inp):
     connector = mc.Connector(login_file_name)
     if inp == "migration":
         remigrations(connector)
+        connector.commit_close_db()
 
     elif inp == "clean":
         clean_box = ['tools_species_circrnas', 'tools_species_genome_exons_introns', 'tools_species_genome_genes', 'tools_species_genome_transcripts']
         example_md5 = '8bd10a77cbda74ed2513d2643a39b0bb'
         path_box = ["../cirDraw/media/md5_data/"]
         empty_db(connector, clean_box)
         empty_dir(path_box)
-        cursor_ob = mc.Cursor(connector)
-        cursor = cursor_ob.cursor
-        cursor.execute(f'''delete from UserTable where md5 != '{example_md5}';''')
-        cursor.execute(f'''delete from tools_uploadmd5 where md5 != '{example_md5}';''')
-        cursor.execute(f'''delete from StatisticTable where md5 != '{example_md5}';''')
-        cursor.execute(f'''delete from UserDensity where md5 != '{example_md5}';''')
-        print(f"Success: Empty table UserTable,tools_uploadmd5,StatisticTable,UserDensity except md5 == '{example_md5}'")
-        cursor_ob.terminate()
-    connector.commit_close_db()
+
+        exception_box = ['UserTable', 'tools_uploadmd5', 'StatisticTable', 'UserDensity']
+        cleandb_except(connector, exception_box, example_md5)
+        connector.commit_close_db()
+
+
+        #cursor_ob = mc.Cursor(login_file_name)
+        #cursor = cursor_ob.origin_cursor
+        #cursor.execute(f'''delete from UserTable where md5 != '{example_md5}';''')
+        #cursor.execute(f'''delete from tools_uploadmd5 where md5 != '{example_md5}';''')
+        #cursor.execute(f'''delete from StatisticTable where md5 != '{example_md5}';''')
+        #cursor.execute(f'''delete from UserDensity where md5 != '{example_md5}';''')
+        #print(f"Success: Empty table UserTable,tools_uploadmd5,StatisticTable,UserDensity except md5 == '{example_md5}'")
+        #cursor_ob.terminate()
 
 if __name__ == '__main__':
     login_file_name = sys.argv[1]

related_genome_info/process_pkg/mysqlconnect.py

@@ -99,7 +99,7 @@ def drop_table(self, table_name):
     def clean_table(self, table_name, conditions=None):
         """empty an existed table
         >>> conditions = None
-        >>> conditions = {'colname1': 'colvalue'}
+        >>> conditions = {'colname1': ['=', 'colvalue']}
         """
         try:
             delete_sql_base = """delete from """ + str(table_name)
@@ -114,12 +114,13 @@ def clean_table(self, table_name, conditions=None):
                     colname = i
                     value = conditions[colname]
                     if num == 0:
-                        adds = """ """ + str(colname) + """ = """ + value.__repr__()
+                        adds = """ """ + str(colname) + """ """ + value[0] + """ """ + value[1].__repr__()
                     else:
-                        adds = """ AND """ + str(colname) + """ = """ + value.__repr__()
+                        adds = """ AND """ + str(colname) + """ """ + value[0] + """ """ + value[1].__repr__()
                     delete_sql_base += adds
                     num += 1
                 delete_sql = delete_sql_base + """;"""
+                print("This is deletesql: ", delete_sql)
             # execute
             if self.connector.checkpoint.is_exist_table(table_name):
                 cursor_ob = Cursor(self.connector)
@@ -146,10 +147,13 @@ def clean_table(self, table_name, conditions=None):
 
         except Exception as e:
             print("Failed: Empty table {} failed, raise Expections:")
+
             print("Error: ", e)
 
 
 
+
+
     ## =====================================================================
     # Create table in database:
     def create_table(self, table_name, table_columns, data):