Merge branch 'release-1.1'

gotrack/etc/scripts/update/resources.py

@@ -42,7 +42,6 @@ def __init__(self, directory, database_state, check_ftp=True):
         self.missing_go = {}
         self.missing_goa = defaultdict(dict)
         self.ftp_checked = False
-        self.missing_data = False
 
         if check_ftp:
             self.populate_missing_data()
@@ -80,7 +79,6 @@ def populate_missing_data(self):
         self.missing_go = {}
         self.missing_goa = defaultdict(dict)
         self.ftp_checked = False
-        self.missing_data = False
 
         go = self.fetch_go_dates()
         self.missing_go = {d: f for d, f in go.iteritems() if d not in self.go and d not in self.db_go}
@@ -91,11 +89,11 @@ def populate_missing_data(self):
             missing = {ed: f for ed, f in goa.iteritems() if ed not in self.goa[sp] and ed not in self.db_goa[sp_id]}
             self.missing_goa[sp] = missing
 
-        if self.missing_go or sum([len(goa_sp) for goa_sp in self.missing_goa.values()]) or not self.sec_ac:
-            self.missing_data = True
-
         self.ftp_checked = True
 
+    def is_missing_data(self):
+        return self.missing_go or sum([len(goa_sp) for goa_sp in self.missing_goa.values()]) or not self.sec_ac
+
     @staticmethod
     def match_file_patterns(files, pattern):
         matches = []
@@ -168,7 +166,7 @@ def ftp_list(host, directory):
             if ftp is not None:
                 ftp.close()
 
-    def ftp_files(self, host, directory, files):
+    def ftp_files(self, host, directory, files, skip_if_exists=True):
         ftp = None
         fname_list = []
         if files:
@@ -188,7 +186,7 @@ def ftp_files(self, host, directory, files):
                         ftp.login()
                         ftp.cwd(directory)
                     full_path = os.path.join(self.directory, fname)
-                    if os.path.isfile(full_path):
+                    if skip_if_exists and os.path.isfile(full_path):
                         log.warn('%s already exists, skipping...', full_path)
                         continue
 
@@ -223,20 +221,23 @@ def fetch_go_dates(self):
         files = Resources.ftp_list(Resources.go_ftp_host, Resources.go_ftp_directory)
         return self.search_files_for_go(files)
 
-    def download_missing_goa_data(self):
+    def download_missing_goa_data(self, skip_if_exists=True):
         for sp, goa_eds in self.missing_goa.iteritems():
             files = goa_eds.values()
-            self.ftp_files(Resources.goa_ftp_host, Resources.goa_ftp_directory_template.format(sp.upper()), files)
+            self.ftp_files(Resources.goa_ftp_host, Resources.goa_ftp_directory_template.format(sp.upper()), files,
+                           skip_if_exists)
 
             # GPI Files
             gpi_files = [Resources.goa_gpi_template.format(sp, ed) for ed in goa_eds]
-            self.ftp_files(Resources.goa_ftp_host, Resources.goa_ftp_directory_template.format(sp.upper()), gpi_files)
+            self.ftp_files(Resources.goa_ftp_host, Resources.goa_ftp_directory_template.format(sp.upper()), gpi_files,
+                           skip_if_exists)
 
-    def download_missing_go_data(self):
-        self.ftp_files(Resources.go_ftp_host, Resources.go_ftp_directory, self.missing_go.values())
+    def download_missing_go_data(self, skip_if_exists=True):
+        self.ftp_files(Resources.go_ftp_host, Resources.go_ftp_directory, self.missing_go.values(), skip_if_exists)
 
-    def download_accession_history(self):
-        return self.ftp_files(Resources.uniprot_ftp_host, Resources.uniprot_ftp_directory, ['sec_ac.txt'])
+    def download_accession_history(self, skip_if_exists=True):
+        return self.ftp_files(Resources.uniprot_ftp_host, Resources.uniprot_ftp_directory, ['sec_ac.txt'],
+                              skip_if_exists)
 
     def get_new_go(self):
         return {d: f for d, f in self.go.iteritems() if d not in self.db_go}

gotrack/etc/scripts/update/update.py

@@ -47,8 +47,11 @@ def main(resource_directory=None, cron=False, no_download=False):
     # Display current state of resource directory, database, and ftp site
     LOG.info(res)
 
+    # if cron, force download of accession history file
+    res.sec_ac = None if cron else res.sec_ac
+
     # Deal with missing data
-    if res.ftp_checked and res.missing_data:
+    if res.ftp_checked and res.is_missing_data():
         missing_cnt = len(res.missing_go)
         if missing_cnt:
             LOG.warn("Missing %s GO Versions from FTP", missing_cnt)
@@ -64,14 +67,14 @@ def main(resource_directory=None, cron=False, no_download=False):
         if not res.sec_ac:
             LOG.warn("Missing secondary accession file (sec_ac.txt)")
             if cron or query_yes_no("Download missing secondary accession file?"):
-                res.download_accession_history()
+                res.download_accession_history(skip_if_exists=not cron)
 
         LOG.info("Re-checking state of resource directory")
         res.populate_existing_files()
         res.populate_missing_data()
         LOG.info(res)
 
-        if res.missing_data or not (cron or query_yes_no("Continue with updates?")):
+        if res.is_missing_data() or not (cron or query_yes_no("Continue with updates?")):
             return
 
     # Insert new GO data

gotrack/pom.xml

@@ -4,7 +4,7 @@
 	<groupId>ubc.pavlab</groupId>
 	<artifactId>gotrack</artifactId>
 	<packaging>war</packaging>
-	<version>1.0</version>
+	<version>1.1</version>
 	<name>gotrack</name>
 	<url>http://maven.apache.org</url>
 
@@ -321,7 +321,7 @@
             <plugin>
                 <groupId>com.amashchenko.maven.plugin</groupId>
                 <artifactId>gitflow-maven-plugin</artifactId>
-                <version>1.6.0</version>
+                <version>1.9.0</version>
                 <configuration>
                     <!-- Do not push to remote -->
                     <pushRemote>false</pushRemote>

gotrack/src/main/java/ubc/pavlab/gotrack/beans/Cache.java

@@ -112,7 +112,7 @@ public class Cache implements Serializable {
     private Map<String, Gene> accessionToGene = new ConcurrentHashMap<>();
 
     // Useful derived constants
-    private ImmutableSet<Integer> availableYears;
+    private ImmutableList<Integer> availableYears;
 
     // These are used for autocompletion
     // *********************************
@@ -218,7 +218,7 @@ public AnnotationType[] getAnnotationTypes() {
         return AnnotationType.values();
     }
 
-    public ImmutableSet<Integer> getAvailableYears() {
+    public ImmutableList<Integer> getAvailableYears() {
         return availableYears;
     }
 
@@ -293,7 +293,7 @@ private void createEditions( CacheDAO cacheDAO ) {
         }
 
         // Populate derived constants
-        ImmutableSet.Builder<Integer> availableYearsBuilder = ImmutableSet.builder();
+        Set<Integer> availableYearsBuilder = Sets.newHashSet();
 
         // Create Edition objects
         for ( EditionDTO dto : cacheDAO.getAllEditions( speciesRestrictions ) ) {
@@ -349,7 +349,12 @@ private void createEditions( CacheDAO cacheDAO ) {
             }
         }
 
-        availableYears = availableYearsBuilder.build();
+        List<Integer> sortedYears = Lists.newArrayList(availableYearsBuilder);
+        Collections.sort(sortedYears);
+
+        availableYears = ImmutableList.copyOf( sortedYears );
+
+        //  ImmutableSet.Builder<Integer> availableYearsBuilder = ImmutableSet.builder();
 
         currentGOEdition = Collections.max( allGOEditions.values() );
 

gotrack/src/main/java/ubc/pavlab/gotrack/beans/EnrichmentView.java

@@ -110,6 +110,9 @@ public String getLabel() {
     @Inject
     private EnrichmentService enrichmentService;
 
+    @Inject
+    private SessionManager session;
+
     // View parameters
     private Gene queryGene;
     // LEE_LIVER_CANCER
@@ -217,7 +220,7 @@ public EnrichmentView() {
     @PostConstruct
     public void postConstruct() {
         log.info( "postConstruct" );
-        currentSpecies = cache.getSpecies( 7 );
+        currentSpecies = session.getSpecies();
 
         for ( Species species : cache.getSpeciesList() ) {
             speciesToSelectedGenes.put( currentSpecies, Lists.<Gene>newArrayList() );

gotrack/src/main/java/ubc/pavlab/gotrack/beans/SessionManager.java

@@ -63,6 +63,9 @@ public void init() {
         // You can do here your initialization thing based on managed properties, if necessary.
         log.info( "SessionManager init" );
         species = cache.getSpecies( 7 );
+        if ( species == null) {
+            species = cache.getSpeciesList().iterator().next();
+        }
     }
 
     @PreDestroy

gotrack/src/main/java/ubc/pavlab/gotrack/beans/Trends.java

@@ -130,6 +130,7 @@ public void postConstruct() {
     }
 
     public void loadCharts( Species species ) {
+        RequestContext.getCurrentInstance().addCallbackParam( "species", species );
         RequestContext.getCurrentInstance().addCallbackParam( "HC_map", allChartsJSON.get( species ) );
     }