Merge branch 'dev'

Changelog.md

@@ -1,5 +1,10 @@
 ### Changelog ###
 
+#### v0.4.1 31.05.2016 ####
+* Add function to change download urls from direct file paths to file serving function
+* Add function to remove attachments
+* Fixing multiple minor bugs
+
 #### v0.4 22.05.2016 ####
 * Fixing multiple minor bugs
 * Improving code quality with perlcritic

README.md

@@ -1,5 +1,7 @@
 # README #
 
+BibSpace is an Online Bibtex Publications Management Software for Authors and Research Groups. Read about its features on the [BibSpace @ the Error Blog](https://blog.hex64.com/bibspace-online-bibtex-publications-management-software-for-authors-and-research-groups/).
+
 ## Build status ##
 
 Branch | Status | Test coverage
@@ -26,4 +28,4 @@ Visit [hex64.com](http://www.hex64.com/) and click backend/frontend demo to have
 - [] Describe nginx and apache2 configuration
 - [] Describe cron setup
 - [] ``perlcritic -4 `find ./lib -iname *.pm```
-- [] Upload local list of known bugs
+- [] Upload local list of known bugs

install-bibtex2html.sh

@@ -1,5 +1,5 @@
 #!/bin/sh
 set -e
-wget http://www.lri.fr/~filliatr/ftp/bibtex2html/bibtex2html-1.98.tar.gz
+wget --no-check-certificate http://www.lri.fr/~filliatr/ftp/bibtex2html/bibtex2html-1.98.tar.gz
 tar -xzvf bibtex2html-1.98.tar.gz
 cd bibtex2html-1.98 && ./configure --prefix=$HOME/bibtex2html && make && make install

lib/BibSpace.pm

@@ -21,7 +21,7 @@ use Try::Tiny;
 use Path::Tiny;  # for creating directories
 
 # for Makemake. Needs to be removed for Dist::Zilla
-# our $VERSION = '0.4';
+# our $VERSION = '0.4.1';
 
 # 0 4,12,20 * * * curl http://localhost:8081/cron/day
 # 0 2 * * * curl http://localhost:8081/cron/night
@@ -57,7 +57,7 @@ has db => sub {
 
 has version => sub {
   my $self = shift;
-  return $BibSpace::VERSION // "0.4";
+  return $BibSpace::VERSION // "0.4.1";
 };
 
 
@@ -72,18 +72,28 @@ sub startup {
     push @{$self->app->static->paths}, $self->app->home->rel_dir('public');
     # push @{$self->app->static->paths}, $self->config->{backups_dir};
 
+    say "Using config: ".$self->app->config_file;
+    say "App version: ".$self->app->version;
+    $config = $self->plugin('Config' => {file => $self->app->config_file});
+
     $self->hook(before_dispatch => sub {
       my $c = shift;
       $c->req->url->base->scheme('https') if $c->req->headers->header('X-Forwarded-HTTPS');
 
       # TODO!!
       # only for directory deployment!!
       # push @{$c->req->url->base->path->trailing_slash(1)}, shift @{$c->req->url->path->leading_slash(0)};
+
+      # dirty fix for production deployment in a directory
+      my $proxy_prefix = $self->config->{proxy_prefix};
+      if($proxy_prefix ne ""){
+        # we remove the leading slash
+        $proxy_prefix =~ s|^/||;
+        push @{$c->req->url->base->path->trailing_slash(1)}, $proxy_prefix;  
+      }
     });
 
-    say "Using config: ".$self->app->config_file;
-    say "App version: ".$self->app->version;
-    $config = $self->plugin('Config' => {file => $self->app->config_file});
+
 
     say "Creating directories.";
 
@@ -313,8 +323,9 @@ sub startup {
   # EXPERIMENTAL
   $logged_user->get('/publications-set')->to('publications#all_defined_by_set'); 
   # description of this function is included with the code
-  # $anyone->get('/publications/special/:id')->to('publications#special_map_pdf_to_local_file'); # use with extreeme caution!
-  $superadmin->get('/publications/fix_urls')->to('publications#replace_urls_to_file_serving_function');
+  # $anyone->get('/publications/special/:id')->to('publications#special_map_pdf_to_local_file'); # use with extreme caution!
+  $logged_user->get('/publications/sdqpdf')->to('publications#all_with_pdf_on_sdq'); 
+  $superadmin->get('/publications/fix_urls')->to('publications#replace_urls_to_file_serving_function')->name('fix_attachment_urls');
   # EXPERIMENTAL END
 
   $logged_user->get('/publications')->to('publications#all'); # logged_user icons!
@@ -327,9 +338,12 @@ sub startup {
   $logged_user->get('/publications/candidates_to_delete')->to('publications#all_candidates_to_delete');
   $logged_user->get('/publications/missing_month')->to('publications#all_without_missing_month');
 
-  $logged_user->get('/publications/sdqpdf')->to('publications#all_with_pdf_on_sdq'); 
   $logged_user->get('/publications/get/:id')->to('publications#single'); 
-  $logged_user->get('/publications/download/:filetype/:id')->to('publications#download')->name('download_publication'); 
+  #
+  $anyone->get('/publications/download/:filetype/:id')->to('publications#download')->name('download_publication'); 
+  $anyone->get('/publications/download/:filetype/(:id).pdf')->to('publications#download')->name('download_publication_pdf'); 
+  #
+  $logged_user->get('/publications/remove_attachment/:filetype/:id')->to('publications#remove_attachment')->name('publications_remove_attachment'); 
 
   $logged_user->get('/publications/hide/:id')->to('publications#hide'); 
   $logged_user->get('/publications/unhide/:id')->to('publications#unhide'); 

lib/BibSpace/Controller/BackupFunctions.pm

@@ -118,19 +118,24 @@ sub do_delete_backup{   # added 22.08.14
 
     say "call BackupFunctions::do_delete_backup";
 
-
+    my $backup_dir_absolute = $self->config->{backups_dir};
+    $backup_dir_absolute =~ s!/*$!/!;
+
 
     my $sth = $dbh->prepare("SELECT filename FROM Backup WHERE id = ?");
     $sth->execute($id);
     my $row = $sth->fetchrow_hashref();
     my $fname = $row->{filename};
 
-    my $sth2 = $dbh->prepare("DELETE FROM Backup WHERE id=?");
-    $sth2->execute($id);
+    my $file_path = $backup_dir_absolute.$fname;
+    my $exists = 1 if -e $file_path;
+    say "do_delete_backup deletes file: $file_path exists $exists";
 
     $self->write_log("destroying backup id $id");
 
-    unlink $fname; 
+    my $sth2 = $dbh->prepare("DELETE FROM Backup WHERE id=?");
+    $sth2->execute($id);
+    unlink $file_path; 
 }
 ####################################################################################
 sub do_delete_broken_or_old_backup {   # added 22.08.14

lib/BibSpace/Controller/Core.pm

@@ -79,8 +79,8 @@ our @EXPORT = qw(
     get_html_for_entry_id
     get_exceptions_for_entry_id
     get_year_for_entry_id
-    clean_ugly_bibtex_fileds
-    clean_ugly_bibtex_fileds_for_all_entries
+    clean_ugly_bibtex_fields
+    clean_ugly_bibtex_fields_for_all_entries
     prepare_backup_table
     get_month_numeric
     get_current_year
@@ -149,7 +149,6 @@ sub get_publications_core_from_set{
 ####################################################################################
 
 sub get_publications_core{
-  # say "CALL: get_publications_core";
     my $self = shift;
     my $author = shift;
     my $year = shift;
@@ -161,9 +160,13 @@ sub get_publications_core{
     my $permalink = shift;
     my $hidden = shift;
 
+    # say "CALL: get_publications_core author $author tag $tag";
+
     my $dbh = $self->app->db;
 
-    my $teamid = get_team_id($dbh, $team) || undef;
+    my $teamid = get_team_id($dbh, $team) || undef; # gives -1 if $team contains id
+    $teamid = $team if defined $teamid and $teamid eq -1; # so team = teamid
+
     my $master_id = get_master_id_for_master($dbh, $author) || undef;
     if($master_id == -1){
       $master_id = $author; # it means that author was given as master_id and not as master name
@@ -177,8 +180,7 @@ sub get_publications_core{
 
     $teamid = undef unless defined $team;
     $master_id = undef unless defined $author;
-    $tagid = undef unless defined $tag;
-
+    $tagid = undef unless defined $tag;    
 
     my @objs = BibSpace::Functions::EntryObj->getByFilter($dbh, $master_id, $year, $bibtex_type, $entry_type, $tagid, $teamid, $visible, $permalink, $hidden);
     return @objs;
@@ -276,7 +278,7 @@ sub nohtml{
 sub postprocess_all_entries_after_author_uids_change{  # assigns papers to their authors ONLY. No tags, no regeneration.
     my $self = shift;
 
-    $self->write_log("reassing papers to authors started");
+    $self->write_log("reassign papers to authors started");
 
     my $qry = "SELECT DISTINCT bibtex_key, id, bib FROM Entry";
     my $sth = $self->app->db->prepare( $qry );  
@@ -299,7 +301,7 @@ sub postprocess_all_entries_after_author_uids_change{  # assigns papers to their
         assign_entry_to_existing_authors_no_add($self, $entry_obj);
     }
 
-    $self->write_log("reassing papers to authors finished");
+    $self->write_log("reassign papers to authors finished");
 };
 
 ##################################################################
@@ -338,25 +340,24 @@ sub postprocess_all_entries_after_author_uids_change_w_creating_authors{  # assi
 };
 
 ####################################################################################
-sub clean_ugly_bibtex_fileds_for_all_entries {
+# clean_ugly_bibtex_fileds_for_all_entries
+sub clean_ugly_bibtex_fields_for_all_entries {
     my $self = shift;
     my $dbh = $self->app->db;
-    $self->write_log("clean_ugly_bibtex_fileds_for_all_entries started");
+    $self->write_log("clean_ugly_bibtex_fields_for_all_entries started");
 
 
     my @ids = get_all_entry_ids($dbh);
     for my $id (@ids){
-      clean_ugly_bibtex_fileds($dbh, $id);
+      clean_ugly_bibtex_fields($dbh, $id);
     }
-    $self->write_log("clean_ugly_bibtex_fileds_for_all_entries finished");
+    $self->write_log("clean_ugly_bibtex_fields_for_all_entries finished");
 };
 ####################################################################################
-sub clean_ugly_bibtex_fileds {
+sub clean_ugly_bibtex_fields {
     my $dbh = shift;
     my $eid = shift;
-
-    # TODO: move this into config
-    our @bib_fields_to_delete = qw(bdsk-url-1 bdsk-url-2 bdsk-url-3 date-added date-modified owner tags);
+    my @bib_fields_to_delete = shift || qw(bdsk-url-1 bdsk-url-2 bdsk-url-3 date-added date-modified owner tags);
 
     my @ary = $dbh->selectrow_array("SELECT bib FROM Entry WHERE id = ?", undef, $eid);  
     my $entry_str = $ary[0];
@@ -377,7 +378,7 @@ sub clean_ugly_bibtex_fileds {
         my $new_bib = $entry->print_s;
 
 
-        # celaning errors caused by sqlite - mysql import
+        # cleaning errors caused by sqlite - mysql import
 
         $new_bib =~ s/''\{(.)\}/"\{$1\}/g;
         $new_bib =~ s/"\{(.)\}/\\"\{$1\}/g;
@@ -394,6 +395,7 @@ sub clean_ugly_bibtex_fileds {
     }
 };
 
+
 ##################################################################
 
 sub assign_entry_to_existing_authors_no_add{
@@ -562,8 +564,6 @@ sub delete_entry_by_id{
 
     my $sth3 = $dbh->prepare( "DELETE FROM Entry_to_Author WHERE entry_id = ?" );  
     $sth3->execute($id);
-
-    warn "FIXME: delete_entry_by_id. Pdf file should be deleted from file system as well"; 
 };
 ################################################################################
 sub get_all_non_hidden_entry_ids{

lib/BibSpace/Controller/Cron.pm

@@ -102,7 +102,7 @@ sub cron_week {
 
     ############ Cron ACTIONS 
     # $self->helper_reassign_papers_to_authors();  #can be anbled later
-    # $self->helper_clean_ugly_bibtex_fileds_for_all_entries(); #can be enabled later
+    # $self->helper_$self->helper_clean_ugly_bibtex_fields_for_all_entries(); #can be enabled later
     $self->helper_do_delete_broken_or_old_backup();
     ############ Cron ACTIONS STOP
 

lib/BibSpace/Controller/CronHelpers.pm

@@ -70,9 +70,9 @@ sub register {
 
 
 
-    $app->helper(helper_clean_ugly_bibtex_fileds_for_all_entries => sub {
+    $app->helper(helper_clean_ugly_bibtex_fields_for_all_entries => sub {
         my $self = shift;
-        clean_ugly_bibtex_fileds_for_all_entries($self);
+        clean_ugly_bibtex_fields_for_all_entries($self);
     });