function render_row(&$row)
{
global $gDisableEditing;
$html = "";
$this->row_transition($row);
$id_prefix = "v_{$row['variant_id']}__a_{$row['article_pmid']}__g_{$row['genome_id']}__d_{$row['disease_id']}__p_{$row['edit_id']}__";
$title = "";
foreach (array("article_pmid", "genome_id", "disease_id") as $keyfield) {
if (strlen($row[$keyfield]) == 0) {
$row[$keyfield] = 0;
}
}
if ($row["disease_id"] != "0") {
$tr = editable("{$id_prefix}f_summary_short__8x1__oddsratio", $row["summary_short"], $row["disease_name"] . "<BR />", array("rownumber" => $this->rownumber, "tip" => "Indicate the contribution of this article to OR statistics for " . htmlspecialchars($row["disease_name"]) . "."));
if ($tr != "") {
if ($this->rownumber == 0) {
$html .= $this->starttable;
}
$html .= $tr;
++$this->rownumber;
}
} else {
if ($row["article_pmid"] != "0") {
$html .= "<A name=\"a" . htmlentities($row["article_pmid"]) . "\"></A>\n";
$summary = article_get_summary($row["article_pmid"]);
$html .= editable("{$id_prefix}f_summary_short__70x8__textile", $row[summary_short], $summary . "<BR />", array("tip" => "Explain this article's contribution to the conclusions drawn in the variant summary above."));
} else {
if ($row["genome_id"] != "0") {
$html .= "<A name=\"g" . $row["genome_id"] . "\"></A>\n";
// Pick the most human-readable name for this genome/person
if (!($name = $row["name"])) {
if (!($name = $row["global_human_id"])) {
$name = "[" . $row["genome_id"] . "]";
}
}
$name = htmlspecialchars($name);
// Link to the full genome(s)
if ($row["dataset_count"] > 0) {
$name = "<A href=\"{$row['dataset_url']}\">{$name}</A>";
}
if ($row["dataset_count"] > 1) {
$more = $row["dataset_count"] - 1;
$name .= " (";
if ($row["dataset_url_2"]) {
$name .= "<A href=\"{$row['dataset_url_2']}\">alternate</A>, ";
--$more;
}
if ($more > 1) {
$name .= "plus {$more} other data sets";
} else {
if ($more == 1) {
$name .= "plus 1 other data set";
} else {
$name = ereg_replace(", \$", "", $name);
}
}
$name .= ")";
}
// Indicate the SNP that causes the variant
if ($row["chr"]) {
$name .= htmlspecialchars("\n" . substr($row["zygosity"], 0, 3) . " " . $row["allele"] . " @ " . $row["chr"] . ":" . $row["chr_pos"]);
$name = nl2br($name);
}
$html .= editable("{$id_prefix}f_summary_short__70x8__textile", $row[summary_short], $name);
} else {
if ($row["disease_id"] != "0") {
// Disease summary not attached to any particular publication
} else {
$html .= editable("{$id_prefix}f_summary_short__70x8__textile", $row[summary_short], "Short summary", array("tip" => "Provide a one line summary of clinical action to be undertaken given this variant (possibly modified by known phenotypes)."));
$html .= editable("{$id_prefix}f_variant_quality", $row, "Variant quality");
global $gImpactOptions;
$opts =& $gImpactOptions;
$qualified_impact = evidence_qualify_impact($row["variant_quality"], $row["variant_impact"]);
$html .= editable("{$id_prefix}f_variant_impact__", $row["variant_impact"], "Impact", array("select_options" => $opts, "previewtextile" => $qualified_impact, "tip" => "Categorize the expected impact of this variant."));
if (strtolower($qualified_impact) != strtolower($row["variant_impact"])) {
$html .= "<P><I>(The \"" . strtolower(eregi_replace(",? " . $row["variant_impact"], "", $qualified_impact)) . "\" qualifier is assigned automatically based on the above evidence and importance scores.)</I></P>";
}
global $gInheritanceOptions;
$html .= editable("{$id_prefix}f_variant_dominance__", $row[variant_dominance], "Inheritance pattern", array("select_options" => $gInheritanceOptions));
$html .= editable("{$id_prefix}f_summary_long__70x8__textile", $row[summary_long], "Summary of published research, and additional commentary", array("tip" => "Provide a comprehensive review of the variant including youngest age of onset, oldest age of onset and oldest asymptomatic individual."));
}
}
}
}
if ($html == "") {
return;
}
if (ereg('^<(TABLE|TR)', $html)) {
// TODO: handle is_delete and flag_edited_id for table rows
// somehow; for now just don't indicate them at all
if ($row["is_delete"]) {
return;
}
if ($row["flag_edited_id"]) {
$this->html .= $html;
return;
}
} else {
if (!$gDisableEditing && getCurrentUser() || 0 < strlen($row["talk_text"])) {
$show_label = 0 < strlen($row["talk_text"]) ? "<B>show discussion</B>" : "start discussion";
$html .= "<DIV class=\"rectangle-speech-border-hidden\"><DIV>{$show_label}</DIV>";
$html .= editable("{$id_prefix}f_talk_text__70x8__textile", $row[talk_text], "Discussion<BR />", array("tip" => "Comments about this section"));
$html .= "</DIV>";
}
}
if ($row["is_delete"]) {
$html .= "<DIV style=\"outline: 1px dashed #300; background-color: #fdd; color: #300; padding: 20px 20px 0 20px; margin: 0 0 10px 0;\"><P>Deleted in this revision:</P>{$html}</DIV>";
} else {
if ($row["flag_edited_id"]) {
if ($row["previous_edit_id"]) {
$edited = "Edited";
} else {
$edited = "Added";
}
$html = "<DIV style=\"outline: 1px dashed #300; background-color: #dfd; color: #300; padding: 20px 20px 0 20px; margin: 0 0 10px 0;\"><P>{$edited} in this revision:</P>\n{$html}</DIV>";
}
}
$this->html .= $html;
}
function editable_quality_preview(&$rationale)
{
global $gTheTextile;
$html = '';
$html .= $gTheTextile->textileRestricted($rationale["text"]);
if ($rationale["seealso"] && sizeof($rationale["seealso"])) {
$html .= "<P>See ";
foreach ($rationale["seealso"] as $a) {
if ($a == "0") {
$html .= "unpublished research (below)";
continue;
}
$summary = preg_replace('/<.*?>/', '', article_get_summary($a));
if (preg_match('/^(.*?)(\\.|,.*?\\.).*?\\..*?\\.\\s*(\\d\\d\\d\\d)[;\\s]/s', $summary, $regs)) {
$summary = $regs[1] . ($regs[2] == '.' ? '' : ' et al.') . ' ' . $regs[3] . ' (' . $a . ')';
} else {
$summary = $a;
}
$html .= "<SPAN onmouseover=\"evidence_article_citation_tip(this,'{$a}');\" onmouseout=\"UnTip();\">{$summary}</SPAN>";
$html .= ", ";
}
$html = ereg_replace(', $', '', $html);
$html .= ".</P>\n";
}
return $html;
}
