Merge pull request #70 from mobidic/dev

Merge for v1.1.9
mobidic · Feb 21, 2024 · bc13945 · bc13945
2 parents 3fad567 + 48958fa
commit bc13945
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Showing 3 changed files with 60 additions and 38 deletions.
diff --git a/seal/schedulers.py b/seal/schedulers.py
@@ -681,40 +681,44 @@ def check_clinvar(genome="GRCh37"):
     lockFile = open(path_locker, 'x')
     lockFile.close()
 
-    ftp=FTP('ftp.ncbi.nlm.nih.gov')
-    ftp.login()
-    ftp.cwd(f'pub/clinvar/vcf_{genome}')
-
-    ls = ftp.nlst()
-    for i in ls:
-        r = re.compile("clinvar_([0-9]+).vcf.gz$")
-        match = r.search(i)
-        app.logger.info(f"  - file : {i}")
-        if match:
-            app.logger.info(f"    - match : {match.group(1)}")
-            version = match.group(1)
-            file = match.group(0)
-
-            if not Clinvar.query.filter_by(version=version, genome=genome.lower()).one_or_none():
-                app.logger.info(f"    - new clinvar")
-                vcf_path = Path(app.root_path).joinpath(f'static/temp/clinvar/{genome}')
-                vcf_path = vcf_path.joinpath(file)
-                t = 0
-                while t < 10:
-                    try:
-                        app.logger.info(f"    - download attempt : {t}")
-                        with open(f'{vcf_path}', 'wb') as fp:
-                            ftp.retrbinary(f'RETR {file}', fp.write)
-                        Thread(target=update_clinvar_thread, args=(vcf_path, int(version), genome.lower(), )).start()
-                        app.logger.info(f"    - thread launched")
-                        t=10
-                    except Exception as e:
-                        app.logger.info(f"    - download filed retry")
-                        app.logger.error(e)
-                        ftp.close()
-                        ftp=FTP('ftp.ncbi.nlm.nih.gov')
-                        ftp.login()
-                        ftp.cwd(f'pub/clinvar/vcf_{genome}')
-                        t+=1
-    app.logger.info("END CLINVAR UPDATE")
-    path_locker.unlink()
+    try:
+        ftp=FTP('ftp.ncbi.nlm.nih.gov')
+        ftp.login()
+        ftp.cwd(f'pub/clinvar/vcf_{genome}')
+    except Exception as e:
+        app.logger.error(e)
+    else:
+        ls = ftp.nlst()
+        for i in ls:
+            r = re.compile("clinvar_([0-9]+).vcf.gz$")
+            match = r.search(i)
+            app.logger.info(f"  - file : {i}")
+            if match:
+                app.logger.info(f"    - match : {match.group(1)}")
+                version = match.group(1)
+                file = match.group(0)
+
+                if not Clinvar.query.filter_by(version=version, genome=genome.lower()).one_or_none():
+                    app.logger.info(f"    - new clinvar")
+                    vcf_path = Path(app.root_path).joinpath(f'static/temp/clinvar/{genome}')
+                    vcf_path = vcf_path.joinpath(file)
+                    t = 0
+                    while t < 10:
+                        try:
+                            app.logger.info(f"    - download attempt : {t}")
+                            with open(f'{vcf_path}', 'wb') as fp:
+                                ftp.retrbinary(f'RETR {file}', fp.write)
+                            Thread(target=update_clinvar_thread, args=(vcf_path, int(version), genome.lower(), )).start()
+                            app.logger.info(f"    - thread launched")
+                            t=10
+                        except Exception as e:
+                            app.logger.info(f"    - download filed retry")
+                            app.logger.error(e)
+                            ftp.close()
+                            ftp=FTP('ftp.ncbi.nlm.nih.gov')
+                            ftp.login()
+                            ftp.cwd(f'pub/clinvar/vcf_{genome}')
+                            t+=1
+    finally:
+        app.logger.info("END CLINVAR UPDATE")
+        path_locker.unlink()
diff --git a/seal/templates/analysis/sample.html b/seal/templates/analysis/sample.html
@@ -1225,7 +1225,7 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
                             if(data["INTRON"] == null) {
                                 return "NA";
                             }
-                            return "Inton " + data["INTRON"].split("/")[0];
+                            return "Intron " + data["INTRON"].split("/")[0];
                         }
                         return "Exon " + data["EXON"].split("/")[0];
                     },

diff --git a/seal/templates/essentials/about.html b/seal/templates/essentials/about.html
@@ -84,6 +84,24 @@ <h3>License</h3>
             <h2>Releases</h2>
             <div id="releases-notes" class="w3-small">
                 <div class="w3-panel w3-leftbar w3-blue">
+                    <h3>v1.1.9 [February 21, 2024]</h3>
+
+                    <p>This minor version mainly enhances fix some bugs.</p>
+                    <h4>Fixes</h4>
+                        <ul>
+                            <li>Fix some typo</li>
+                            <li>Fix locker when ftp of ncbi not reached</li>
+                            <li>Update Links for GnomAD</li>
+                        </ul>
+
+                    <h4>Known Issues</h4>
+                        <ul>
+                            <li>Initialisation of database</li>
+                        </ul>
+
+                </div>
+
+                <div class="w3-panel w3-leftbar w3-pale-blue w3-text-gray">
                     <h3>v1.1.8 [November 08, 2023]</h3>
 
                     <p>This minor version mainly enhances fix some bugs.</p>