MG-RAST · teharrison · Sep 7, 2016 · Aug 1, 2016 · Aug 1, 2016 · Aug 2, 2016
diff --git a/bin/api2html.pl b/bin/api2html.pl
@@ -74,6 +74,7 @@ sub usage {
 
 # build the navigation
 $html .= '';
+
 foreach my $res (sort { $a->{name} cmp $b->{name} } @{$structure->{resources}}) {
   $html .= '<li><a href="#'.$res->{name}.'">'.$res->{name}.'</a></li>';
 }
@@ -142,6 +143,9 @@ sub usage {
     foreach my $param (sort keys(%{$req->{attributes}})) {
       my ($att_obj, $att_hash);
       my $att = $param;
+      if (ref($req->{attributes}->{$param}) ne 'ARRAY') {
+	next;
+      }
       my $att_type = $req->{attributes}->{$param}->[0];
       my $att_desc = $req->{attributes}->{$param}->[1];
       if ($att_type eq 'cv') {

diff --git a/bin/download_m5nr_blast.sh b/bin/download_m5nr_blast.sh
@@ -2,7 +2,7 @@
 
 # set a default values
 # m5nr blast files - 2.6 GB & 11.7 GB
-M5NR_VERSIONS="20100309 20131215"
+M5NR_VERSIONS="20100309 20120401 20131215"
 TARGET="/m5nr"
 
 for i in $M5NR_VERSIONS; do

diff --git a/dockerfiles/api/Dockerfile b/dockerfiles/api/Dockerfile
@@ -7,6 +7,7 @@ RUN apt-get update && apt-get install -y \
   libpq-dev \
   make \
   curl \
+  ncbi-blast+ \
   perl-modules \
   liburi-perl \
   libwww-perl \
@@ -36,7 +37,7 @@ RUN mkdir -p /MG-RAST /var/log/httpd/api.metagenomics
 COPY . /MG-RAST
 RUN cd /MG-RAST && \
   make && \
-#  make api-doc && \
+  make api-doc && \
   cp -rv src/MGRAST/bin/* bin/. && \
   cd site/CGI && \
   rm -fv metagenomics.cgi linkin.cgi m5nr.cgi m5nr_rest.cgi
@@ -58,12 +59,6 @@ RUN apt-get install -y python-dev python-pip && \
 ENV PERL_MM_USE_DEFAULT 1
 RUN cpan Inline::Python
 
-# setup sendmail
-RUN DEBIAN_FRONTEND=noninteractive apt-get -y install postfix && \
-  cp /usr/share/postfix/main.cf.debian /etc/postfix/main.cf && \
-  postconf -e relayhost=[smtp.mcs.anl.gov] && \
-  postconf -e myorigin=mcs.anl.gov
-
 RUN mkdir -p /sites/1/ && \
   cd /sites/1/ && \
   ln -s /MG-RAST/
@@ -75,9 +70,7 @@ RUN cd /MG-RAST/conf && ln -s /api-server-conf/Conf.pm
 RUN ln -s /api-server-conf/postgresql/ /usr/sbin/.postgresql
 
 # m5nr blast files in mounted dir
-RUN mkdir -p /m5nr && \
-  ln -s /api-server-data/20100309 /m5nr/20100309 && \
-  ln -s /api-server-data/20131215 /m5nr/20131215
+RUN mkdir -p /m5nr
 
 # Execute:
 # /etc/init.d/postfix start

diff --git a/src/MGRAST/bin/validate_metadata b/src/MGRAST/bin/validate_metadata
@@ -25,6 +25,7 @@ ENVO_VER = None
 LOG_FILE = None
 JSON_FILE = None
 INVALID   = []
+EXCEL_DATE_START = datetime.datetime(1899, 12, 30)
 valid_email    = Email()
 valid_http_url = HttpUrl()
 valid_name_str = string.ascii_letters+string.digits+'+-_()@; :.'
@@ -161,6 +162,12 @@ def validate_type(key, val, atype, name=False):
             except ValueError:
                 return None
             return unicode(dVal.date())
+        elif isinstance(val, float):
+            try:
+                dVal = EXCEL_DATE_START + datetime.timedelta(days=int(val))
+            except ValueError:
+                return None
+            return unicode(dVal.date())
         else:
             return None
     elif atype == 'time':

diff --git a/src/MGRAST/lib/Abundance.pm b/src/MGRAST/lib/Abundance.pm
@@ -12,12 +12,12 @@ use List::MoreUtils qw(natatime);
 1;
 
 sub new {
-    my ($class, $chdl, $version) = @_;
+    my ($class, $chdl, $version, $pghost) = @_;
 
     # connect to database
     my $dbh = undef;
     eval {
-        my $host     = $Conf::mgrast_dbhost;
+        my $host     = $pghost || $Conf::mgrast_dbhost;
         my $database = $Conf::mgrast_db;
         my $user     = $Conf::mgrast_dbuser;
         my $password = $Conf::mgrast_dbpass;
@@ -159,7 +159,6 @@ sub all_job_abundances {
                 }
             }
             if ($org && $set->{organism}) {
-                print STDERR Dumper($set->{organism});
                 foreach my $o (@{$set->{organism}}) {
                     if ($tax) {
                         next if (($tax eq 'domain') && ($tax_map->{$o} =~ /other|unknown|unclassified/));
@@ -181,9 +180,11 @@ sub all_job_abundances {
         }
     };
 
+    my $total_md5 = 0;
     while (my @row = $sth->fetchrow_array()) {
         $md5s->{$row[0]} = $row[1];
         $count++;
+        $total_md5++;
         if ($count == $self->chunk) {
             $add_annotations->();
             $md5s = {};
@@ -195,7 +196,7 @@ sub all_job_abundances {
     }
     $self->end_query($sth);
 
-    return ($org_map, $fun_map, $ont_map);
+    return ($total_md5, $org_map, $fun_map, $ont_map);
 }
 
 sub all_job_md5sums {

diff --git a/src/MGRAST/lib/JobDB/Project.pm b/src/MGRAST/lib/JobDB/Project.pm
@@ -472,8 +472,17 @@ sub metagenomes_summary {
 
   my $project_jobs = $self->_master->ProjectJob->get_objects( {project => $self} );
   my $user = $self->_master->{_user};
-
-  if (@$project_jobs > 0) {    
+
+  if (@$project_jobs > 0) {
+    my $jdbh = $self->_master->db_handle();
+    my $samp_lib_hash = {};
+    my $mdc = $jdbh->selectall_arrayref('select Job.metagenome_id, MetaDataCollection.ID, MetaDataCollection.type from Job, MetaDataCollection where Job.primary_project='.$self->_id.' and (MetaDataCollection._id=Job.library or MetaDataCollection._id=Job.sample)', { Slice => {} });
+    foreach my $row (@$mdc) {
+      unless (exists $samp_lib_hash->{$row->{metagenome_id}}) {
+	$samp_lib_hash->{$row->{metagenome_id}} = {};
+      }
+      $samp_lib_hash->{$row->{metagenome_id}}->{$row->{type}} = $row->{ID};
+    }
     my @pdata = ();
     my $user_jobs = {};
     my $ujr = defined($user) ? $user->has_right_to(undef, 'view', 'metagenome') : [];
@@ -499,11 +508,13 @@ sub metagenomes_summary {
 		     $pj->seq_method,
 		     $pj->viewable,
 		     $pj->created_on,
-		     {}
+		     {},
+		     $samp_lib_hash->{$pj->{metagenome_id}}->{sample} ? "mgs".$samp_lib_hash->{$pj->{metagenome_id}}->{sample} : undef,
+		     $samp_lib_hash->{$pj->{metagenome_id}}->{library} ? "mgl".$samp_lib_hash->{$pj->{metagenome_id}}->{library}: undef
 		  ];
       $i++;
     }
-    my $jdbh  = $self->_master->db_handle();
+    $jdbh = $self->_master->db_handle();
     my $res = $jdbh->selectall_arrayref('SELECT tag, value, job FROM JobAttributes WHERE job IN ('.join(", ", map { $_->{_id} } @pjobs).')', { Slice => {} });
     foreach my $row (@$res) {
       $data[$jindices->{$row->{job}}]->[14]->{$row->{tag}} = $row->{value};

diff --git a/src/MGRAST/lib/Pipeline.pm b/src/MGRAST/lib/Pipeline.pm
@@ -92,7 +92,7 @@ sub template_keywords {
         'ach_annotation_ver' => "1",
 
         # awe clients
-        'clientgroups' => "mgrast_i2_2xlarge,mgrast_i3_xlarge",
+        'clientgroups' => "mgrast_dbload,mgrast_single,mgrast_multi",
         'priority'     => 1,
 
         # urls