function evidence_get_report($snap, $variant_id)
{
$flag_edited_id = 0;
if ($snap == "latest" || $snap == "release") {
$table = "snap_{$snap}";
$and_max_edit_id = "";
} else {
if (ereg("^[0-9]+\$", $snap)) {
$flag_edited_id = $snap;
$table = "edits";
$variant_id = 0 + $variant_id;
$and_max_edit_id = "AND {$table}.edit_id IN (\n SELECT MAX(edits.edit_id)\n FROM edits\n WHERE variant_id={$variant_id}\n AND edit_id<={$snap}\n AND is_draft=0\n GROUP BY article_pmid, genome_id, disease_id)\n AND ({$table}.edit_id={$snap} OR {$table}.is_delete=0\n )";
}
}
// Get all items relating to the given variant
$v =& theDb()->getAll("SELECT variants.*, {$table}.*, genomes.*, datasets.*, variant_occurs.*,\n\t\t\tvariants.variant_id AS variant_id,\n\t\t\t{$table}.genome_id AS genome_id,\n\t\t\t{$table}.disease_id AS disease_id,\n\t\t\tgenetests.testable AS genetests_testable,\n\t\t\tgenetests.reviewed AS genetests_reviewed,\n\t\t\tdiseases.disease_name AS disease_name,\n\t\t\tvariant_occurs.chr AS chr,\n\t\t\tvariant_occurs.chr_pos AS chr_pos,\n\t\t\tvariant_occurs.allele AS allele,\n\t\t\tvariant_occurs.rsid AS rsid,\n\t\t\tvf.num AS variant_f_num,\n\t\t\tvf.denom AS variant_f_denom,\n\t\t\tvf.f AS variant_f,\n\t\t\tCOUNT(datasets.dataset_id) AS dataset_count,\n\t\t\tMAX(zygosity) AS zygosity,\n\t\t\tMAX(dataset_url) AS dataset_url,\n\t\t\tMIN(dataset_url) AS dataset_url_2,\n\t\t\t{$table}.edit_id=? AS flag_edited_id\n\t\t\tFROM variants\n\t\t\tLEFT JOIN {$table}\n\t\t\t\tON variants.variant_id = {$table}.variant_id\n\t\t\tLEFT JOIN genetests\n\t\t\t\tON {$table}.disease_id=0\n\t\t\t\tAND {$table}.article_pmid=0\n\t\t\t\tAND {$table}.genome_id=0\n\t\t\t\tAND variants.variant_gene = genetests.gene\n\t\t\tLEFT JOIN diseases\n\t\t\t\tON {$table}.disease_id = diseases.disease_id\n\t\t\tLEFT JOIN genomes\n\t\t\t\tON {$table}.genome_id > 0\n\t\t\t\tAND {$table}.genome_id = genomes.genome_id\n\t\t\tLEFT JOIN datasets\n\t\t\t\tON datasets.genome_id = {$table}.genome_id\n\t\t\tLEFT JOIN variant_occurs\n\t\t\t\tON {$table}.variant_id = variant_occurs.variant_id\n\t\t\t\tAND variant_occurs.dataset_id = datasets.dataset_id\n\t\t\tLEFT JOIN variant_frequency vf\n\t\t\t\tON vf.variant_id=variants.variant_id\n\t\t\tWHERE variants.variant_id=?\n\t\t\t\t{$and_max_edit_id}\n\t\t\tGROUP BY\n\t\t\t\t{$table}.genome_id,\n\t\t\t\t{$table}.article_pmid,\n\t\t\t\t{$table}.disease_id\n\t\t\tORDER BY\n\t\t\t\t{$table}.genome_id,\n\t\t\t\t{$table}.article_pmid,\n\t\t\t\tdiseases.disease_name,\n\t\t\t\t{$table}.disease_id,\n\t\t\t\t{$table}.edit_id DESC", array($flag_edited_id, $variant_id));
if (theDb()->isError($v)) {
die($v->getMessage());
}
if (!theDb()->isError($v) && $v && $v[0]) {
foreach (array("article_pmid", "genome_id", "disease_id") as $x) {
if (!$v[0][$x]) {
$v[0][$x] = 0;
}
}
}
// Make sure for every pmid>0 row all of the article=A, disease=D
// rows are there too (and ditto for article=0, genome=0)
$have_a_d = array();
// will contain one array per article
// id (incl. "0" for the main variant
// summary section)
foreach ($v as $row) {
if (!$row["genome_id"]) {
$have_a_d[$row["article_pmid"]][$row["disease_id"]] = 1;
}
}
// Get a list of all the diseases that should be listed in each disease table
$v_d = theDb()->getAll("SELECT diseases.* FROM diseases\n WHERE disease_id IN\n (SELECT disease_id\n FROM variant_disease\n WHERE variant_id=?\n UNION\n SELECT disease_id\n FROM gene_disease\n WHERE gene = ?)", array($variant_id, $v[0]["variant_gene"]));
// Look for article=A, disease=D rows that should be there but
// aren't... and add them
foreach ($v_d as $row) {
// for each disease...
foreach ($have_a_d as $a => $have_d) {
// for each article...
$d = $row["disease_id"];
if (isset($have_d[$d])) {
// already have a result row for this {article, disease}
continue;
}
// add a row after all of the existing rows pertaining to the
// target article
for ($i = 0; $i < sizeof($v); $i++) {
// skip until we reach the target article's row
if ($v[$i]["article_pmid"] != $a) {
continue;
}
// skip until we reach the last row for the target article
if ($i < sizeof($v) - 1 && $a != 0 && $v[$i + 1]["article_pmid"] == $a) {
continue;
}
// found the last row for this article. copy the existing row
// (minus the editable stuff) and insert after.
array_splice($v, $i + 1, 0, array($v[$i]));
$v[$i + 1]["disease_id"] = $row["disease_id"];
$v[$i + 1]["disease_name"] = $row["disease_name"];
$v[$i + 1]["summary_short"] = "";
$v[$i + 1]["summary_long"] = "";
$v[$i + 1]["talk_text"] = "";
$v[$i + 1]["edit_id"] = "";
$v[$i + 1]["previous_edit_id"] = "";
break;
}
}
}
if ($v && is_array($v[0])) {
if (1) {
// fix up obsolete impacts (until they get fixed in the db, at which
// point this section can be removed)
if ($v[0]["variant_impact"] == "unknown" || $v[0]["variant_impact"] == "none") {
$v[0]["variant_impact"] = "not reviewed";
}
}
$v[0]["certainty"] = evidence_compute_certainty($v[0]["variant_quality"], $v[0]["variant_impact"]);
$v[0]["qualified_impact"] = evidence_qualify_impact($v[0]["variant_quality"], $v[0]["variant_impact"]);
list($v[0]["variant_evidence"], $v[0]["clinical_importance"]) = str_split($v[0]["certainty"]);
}
if ($v && is_array($v[0])) {
$row =& $v[0];
$row["nblosum100"] = 0 - blosum100($row["variant_aa_from"], $row["variant_aa_to"]);
$tags = array();
foreach (theDb()->getAll("SELECT distinct tag FROM variant_external WHERE variant_id=?", array($variant_id)) as $tagrow) {
$tags[] = $tagrow["tag"];
}
$row["in_omim"] = in_array("OMIM", $tags) ? 'Y' : '-';
$row["in_gwas"] = in_array("GWAS", $tags) ? 'Y' : '-';
$row["in_pharmgkb"] = in_array("PharmGKB", $tags) ? 'Y' : '-';
$autoscore = 0;
$why = array();
// Computational (max of 2 points):
if ($row["nblosum100"] > 9) {
$autoscore += 2;
$why[] = "nblosum100>9";
} else {
if ($row["nblosum100"] > 3) {
$autoscore++;
$why[] = "nblosum100>3";
}
}
// TODO: ++$autoscore if within 1 base of a splice site
// TODO: ++$autoscore if indel in coding region
// TODO: ++$autoscore if indel in coding region and causes frameshift
if ($autoscore > 2) {
$autoscore = 2;
}
// Variant-specific lists (max of 2 points):
$autoscore_db = 0;
if ($row["in_omim"] == 'Y') {
$autoscore_db += 2;
$why[] = "omim";
}
if ($row["in_gwas"] == 'Y') {
$autoscore_db++;
$why[] = "gwas";
if ($row["gwas_max_or"] >= 1.5) {
$autoscore_db++;
$why[] = "gwas_or";
}
}
if ($row["in_pharmgkb"] == 'Y') {
++$autoscore_db;
$why[] = "PharmGKB";
}
if ($autoscore_db > 2) {
$autoscore_db = 2;
}
$autoscore += $autoscore_db;
// Gene-specific lists (max of 2 points):
if ($row["genetests_testable"]) {
$autoscore++;
$why[] = "genetest";
}
if ($row["genetests_reviewed"]) {
$autoscore++;
$why[] = "genereview";
}
$row["autoscore"] = $autoscore;
$row["autoscore_flags"] = implode(", ", $why);
// Summarize relevant/not-relevant votes as one of { null, 0, 1 }
$row["webscore"] = "N";
$urlscores =& evidence_get_web_votes($variant_id);
foreach (evidence_extract_urls(theDb()->getOne("SELECT content FROM variant_external WHERE variant_id=? AND tag=?", array($variant_id, "Yahoo!"))) as $url) {
if ($urlscores[$url] == 1) {
$row["webscore"] = "Y";
break;
}
if (!strlen($urlscores[$url])) {
$row["webscore"] = "-";
}
}
}
return $v;
}
}
$html .= "<BR /><SPAN class=\"searchurl\">" . htmlspecialchars($url_abbrev) . "</SPAN>";
} else {
$html .= $content;
}
$html . "</LI>";
$lasttag = $r["tag"];
}
if ($lasttag !== FALSE) {
$html .= "</UL>\n";
}
$html .= "</DIV>\n";
}
$html .= "<H2>Other <I>in silico</I> analyses<BR /> </H2>\n<DIV id=\"in_silico\">\n<UL>\n";
if ($aa) {
$html .= "<LI>NBLOSUM100 score = <STRONG>" . ereg_replace("-", "–", 0 - blosum100($row0["variant_aa_from"], $row0["variant_aa_to"])) . "</STRONG></LI>\n";
}
$autoscore_html = $row0["autoscore"];
if ($autoscore_html > 0) {
$autoscore_html = "<SPAN onmouseover=\"Tip('" . htmlspecialchars($row0["autoscore_flags"]) . "',BALLOON,true,FIX,[this,-18,0],FOLLOWMOUSE,false,ABOVE,true,WIDTH,-400);\" onmouseout=\"UnTip();\">" . $autoscore_html . "</SPAN>";
}
$html .= "<LI>GET-Evidence autoscore = <STRONG>" . $autoscore_html . "</STRONG>";
$html .= "</LI>\n";
$html .= "</UL>\n";
$html .= "</DIV>";
$html .= "<H2>Edit history<BR /> </H2>\n<DIV id=\"edit_history\">";
$html .= evidence_render_history($variant_id);
$html .= "</DIV>";
$gOut["content"] .= $html;
// $gOut["content"] .= "<!--\n" . ereg_replace ("-->", "\\-\\-\\>", json_encode ($report)) . "-->\n";
$gOut["content"] .= "<!--\n" . ereg_replace("-->", "\\-\\-\\>", json_encode(evidence_get_assoc_flat_summary("latest", $variant_id))) . "-->\n";
