New 2012 Curation Status

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Curation Status & Statistics Form (2012)

The sandbox/testing form can be found here

Precanned Comments

The keys stored in postgres for the hashes of these values are only numbers, so the descriptions/titles can change or be updated and still apply retroactively.


sub populatePremadeComments {
  $premadeComments{"1"} = "SVM Positive, Curation Negative";
  $premadeComments{"2"} = "pre-made comment #2";
  $premadeComments{"3"} = "pre-made comment #3";}

So, as of now:

| Key | Comment |
| 1 | "SVM Positive, Curation Negative" |
| 2 | "pre-made comment #2" |
| 3 | "pre-made comment #3" |

Hence, if a completely new comment is desired, a new key will need to be made and there after associated with that new comment. Also, old keys should never be recycled and documentation describing what each key refers to should be maintained in this Wiki.

New Result

Each paper-data-type pair can be assigned a 'New Result' indicating its status as curated (or not) or validated (or not), and if validated, positive or negative for the particular paper-data-type pair. These results can be entered via the "Add Results Page" or directly in the "<Get Results Page>" via the "New Results" column. The code is below:


sub populateDonPosNegOptions {
  $donPosNegOptions{""}             = "";
  $donPosNegOptions{"curated"}      = "curated and positive";
  $donPosNegOptions{"positive"}     = "validated positive";
  $donPosNegOptions{"negative"}     = "validated negative";
  $donPosNegOptions{"notvalidated"} = "not validated";}

where "curated", "positive", "negative", and "notvalidated" are the keys (for the %donPosNegOptions hash table in the form code) that will be stored in postgres and the corresponding values (e.g. "curated and positive") are what will be displayed on the form.

Note that "" and "not validated" represent no data for that paper-data-type pair, but "not validated" is present as an option to overwrite accidental validations (it is impossible to go back to a blank "" field via the form).

Data Types

The form determines which data types exist via a 'populateDatatypes' subroutine in the form code. As of 12-5-2012, the form first collects all data types used in SVM from the 'cur_svmdata' postgres table (which, as of 12-5-2012, all also are identically named in the Author First Pass (AFP) and Curator First Pass (CFP) tables) and then supplements with other data types not in SVM but in AFP and CFP (as of 12-5-2012, all anatomy curation related data types) plus one additional data type ("geneticablation") not in SVM, AFP, or CFP.

Here is the code:

sub populateDatatypes {
  $result = $dbh->prepare( "SELECT DISTINCT(cur_datatype) FROM cur_svmdata " );
  $result->execute() or die "Cannot prepare statement: $DBI::errstr\n";
  while (my @row = $result->fetchrow) { $datatypesAfpCfp{$row[0]} = $row[0]; }
  $datatypesAfpCfp{'blastomere'}    = 'cellfunc';
  $datatypesAfpCfp{'exprmosaic'}    = 'siteaction';
  $datatypesAfpCfp{'geneticmosaic'} = 'mosaic';
  $datatypesAfpCfp{'laserablation'} = 'ablationdata';
  foreach my $datatype (keys %datatypesAfpCfp) { $datatypes{$datatype}++; }
} # sub populateDatatypes

As for the data types currently (12-5-2012) NOT in SVM but IN AFP and CFP, the data type name is different between the Curation Status form and the AFP and CFP forms. So, the data types named "cellfunc", "siteaction", "mosaic", and "ablationdata" in the AFP and CFP tables are respectively named "blastomere", "exprmosaic", "geneticmosaic", "laserablation" in the Curation Status form.

The IMPORTANT thing here is: if, at some point, the data types are changed (added, renamed, etc.), and the code is not updated in kind, the form will likely break. Curators should tell Juancarlos/Chris/Daniela to update the code.

new datatypes should be accounted in this code :

  • - no svm, no afp/cfp : add to %datatypes hash like 'geneticablation'.
  • - no svm, yes afp/cfp : add to %datatypesAfpCfp + %datatypes hashes like 'blastomere'
  • - yes svm, yes afp/cfp : add to code to populate cur_svmdata, which will populate in the SELECT query
  • - yes svm, no afp/cfp : add to code to populate cur_svmdata, which will populate in the SELECT query, but also subsequently delete from %datatypesAfpCfp (to prevent a postgres query to a non-existing table which will crash the form)

Creating PDF links to papers

In the <"Get Results Page"> each paper ID is linked to its corresponding PDF document using the code below:


sub populatePdf {
  $result = $dbh->prepare( "SELECT * FROM pap_electronic_path WHERE pap_electronic_path IS NOT NULL");
  $result->execute() or die "Cannot prepare statement: $DBI::errstr\n";
  my %temp;
  while (my @row = $result->fetchrow) {
    my ($data, $isPdf) = &makePdfLinkFromPath($row[1]);
    $temp{$row[0]}{$isPdf}{$data}++; }
  foreach my $joinkey (sort keys %temp) {
    my @pdfs;
    foreach my $isPdf (reverse sort keys %{ $temp{$joinkey} }) {
      foreach my $pdfLink (sort keys %{ $temp{$joinkey}{$isPdf} }) {
        push @pdfs, $pdfLink; } }
    my ($pdfs) = join"<br/>", @pdfs;
    $pdf{$joinkey} = $pdfs;
  } # foreach my $joinkey (sort keys %temp)
} # sub populatePdf

sub makePdfLinkFromPath {
  my ($path) = shift;
  my ($pdf) = $path =~ m/\/([^\/]*)$/;
  my $isPdf = 0; if ($pdf =~ m/\.pdf$/) { $isPdf++; }           # kimberly wants .pdf files on top, so need to flag to sort
  my $link = '' . $pdf;
  my $data = "<a href=\"$link\" target=\"new\">$pdf</a>"; return ($data, $isPdf); }