function evidence_render_history($variant_id)
{
$html = "<UL>\n";
$thisyear = strftime("%Y", time());
$today = strftime("%b %e %Y", time());
$q = theDb()->query("\nSELECT\n UNIX_TIMESTAMP(edit_timestamp) AS edit_timestamp,\n edit_oid,\n u.fullname AS edit_fullname,\n article_pmid,\n s.genome_id AS genome_id,\n s.disease_id AS disease_id,\n d.disease_name AS disease_name,\n IF(g.name IS NULL OR g.name='',concat('[',global_human_id,']'),g.name) AS genome_name,\n is_delete,\n previous_edit_id,\n edit_id,\n v.*\nFROM edits s\nLEFT JOIN variants v ON v.variant_id=s.variant_id\nLEFT JOIN eb_users u ON u.oid=s.edit_oid\nLEFT JOIN genomes g ON g.genome_id=s.genome_id\nLEFT JOIN diseases d ON d.disease_id=s.disease_id\nWHERE s.variant_id=? AND is_draft=0\nORDER BY edit_timestamp DESC, edit_id DESC, previous_edit_id DESC\n", array($variant_id));
if (theDb()->isError($q)) {
die($q->getMessage());
}
$lastli = "";
while ($row =& $q->fetchRow()) {
$li = "<LI>";
$nicetime = strftime("%b %e %Y %l:%M%P", $row["edit_timestamp"]);
$nicetime = str_replace(" ", " ", $nicetime);
$nicetime = str_replace("{$today} ", "", $nicetime);
$nicetime = str_replace("{$thisyear} ", "", $nicetime);
$nicetime = ereg_replace(" [^ ]+\$", "", $nicetime);
$li .= $nicetime;
$li .= " <A href=\"edits?oid=" . urlencode($row["edit_oid"]) . "\">" . htmlspecialchars($row["edit_fullname"]) . "</A> ";
$summary = "";
if ($row["is_delete"]) {
$li .= "removed ";
} else {
if ($row["previous_edit_id"]) {
$li .= "edited ";
$summary = " summary";
} else {
$li .= "added ";
}
}
if ($row["disease_id"]) {
$li .= "OR figures for " . htmlspecialchars($row["disease_name"]) . " from " . ($row["article_pmid"] ? "article " . $row["article_pmid"] : "unpublished research section");
} else {
if ($row["article_pmid"]) {
$li .= "article " . htmlspecialchars($row["article_pmid"]) . $summary;
} else {
if ($row["genome_id"]) {
$li .= htmlspecialchars($row["genome_name"]) . $summary;
} else {
$li .= "variant{$summary}";
}
}
}
$variant_name = evidence_get_variant_name(&$row, "-");
$li .= " <A href=\"" . $variant_name . ";" . $row["edit_id"] . "\">view</A>";
$li .= "</LI>\n";
// Compress sequences of same type of edit (same person, date, etc.)
if ($li != $lastli) {
$html .= $li;
} else {
// TODO: offer to expand these in case the person wants to
// recover an intermediate edit
}
$lastli = $li;
}
$html .= "</UL>\n";
return $html;
}
function print_content($x)
{
global $report_title, $where_sql, $where_param, $orderby_sql;
if (!$_GET["bareli"]) {
print "<h1>{$report_title}</h1>\n\n";
}
$sql_limit = $_GET["all"] ? "" : "LIMIT 300";
$q = theDb()->query("SELECT *, diseases.disease_name disease_name, edits.genome_id genome_id, UNIX_TIMESTAMP(edit_timestamp) t FROM edits\n\tLEFT JOIN eb_users ON edit_oid=oid\n\tLEFT JOIN variants ON variants.variant_id=edits.variant_id\n\tLEFT JOIN genomes ON edits.genome_id>0 AND edits.genome_id=genomes.genome_id\n\tLEFT JOIN diseases ON diseases.disease_id=edits.disease_id\n\tWHERE {$where_sql} AND is_draft=0\n\tORDER BY {$orderby_sql}\n\t{$sql_limit}", $where_param);
if (theDb()->isError($q)) {
die($q->getMessage());
}
$relevant_fields = array("is_delete", "variant_id", "article_pmid", "genome_id", "disease_id", "edit_oid");
$lastrow = FALSE;
$output_count = 0;
if (!$_GET["bareli"]) {
print "<UL>";
}
while ($row =& $q->fetchRow()) {
if ($lastrow && arrays_partially_equal($lastrow, $row, $relevant_fields) && $lastrow["previous_edit_id"] > 0 == $row["previous_edit_id"] > 0) {
continue;
}
$variant_link = evidence_get_variant_name($row, " ", true);
$version_link = "<A href=\"" . evidence_get_variant_name(&$row, "-") . ";{$row['edit_id']}\">view</A>";
if (!$lastrow || $lastrow[variant_id] != $row[variant_id]) {
$variant_link = "<A href=\"" . evidence_get_variant_name(&$row, "-") . "\">{$variant_link}</A>";
}
$lastrow = $row;
print "<LI>";
print strftime("%b %e ", $row["t"]);
print $variant_link;
if ($row["is_delete"] && !$row["article_pmid"] && !$row["genome_id"] && !$row["disease_id"]) {
print " deleted by ";
} else {
if (!$row["previous_edit_id"] && !$row["article_pmid"] && !$row["genome_id"]) {
print " added by ";
} else {
print " edited by ";
}
}
print "<A href=\"edits?oid=" . urlencode($row["edit_oid"]) . "\">" . htmlspecialchars($row["fullname"] ? $row["fullname"] : $row["nickname"]) . "</A>";
if ($row["genome_id"]) {
if (!($genome_name = $row["name"])) {
if (!($genome_name = $row["global_human_id"])) {
$genome_name = "#" . $row["genome_id"];
}
}
}
$genome_name = htmlspecialchars($genome_name);
if ($row["article_pmid"] && $row["is_delete"]) {
print " (PMID {$row['article_pmid']} removed)";
} else {
if ($row["genome_id"] && $row["is_delete"]) {
print " ({$genome_name} removed)";
} else {
if ($row["article_pmid"] && !$row["previous_edit_id"]) {
print " (PMID {$row['article_pmid']} added)";
} else {
if ($row["genome_id"] && !$row["previous_edit_id"]) {
print " ({$genome_name} added)";
} else {
if ($row["disease_id"]) {
print " (" . htmlspecialchars($row["disease_name"]) . ")";
}
}
}
}
}
print " -- {$version_link}";
print "</LI>\n";
if (!$_GET["all"] && ++$output_count >= 30) {
print "<SPAN> <BR />\n";
foreach (array("", "&all=1") as $all) {
print "<BUTTON onclick=\"\$('busysignal').removeClassName('csshide'); this.disabled = true; new Ajax.Updater (this.parentNode, 'edits?" . htmlentities(ereg_replace('&?(before_edit_id|bareli)=[0-9]+', '', $_SERVER[QUERY_STRING])) . "&before_edit_id={$row[edit_id]}&bareli=1{$all}', { onFailure: function() { this.disabled = false; \$('busysignal').addClassName('csshide'); } }); return false;\">" . ($all == "" ? "Next page" : "Show all") . "</BUTTON> \n";
}
print " <IMG style=\"vertical-align: middle;\" id=\"busysignal\" class=\"csshide\" src=\"/img/busy.gif\" width=\"16\" height=\"16\" alt=\"\" /></SPAN>\n";
break;
}
}
if (!$_GET["bareli"]) {
print "</UL>\n";
}
}
$history_box .= "<LI>View the <A href=\"{$variant_name}\">latest version";
} else {
$history_box .= "<LI>View <A href=\"{$variant_name}\">this version without highlighted changes";
}
$history_box .= "</A>";
if (getCurrentUser()) {
$history_box .= " and enable editing features";
}
$history_box .= "</LI>\n";
$history_box .= "</UL></DIV>";
$gDisableEditing = TRUE;
}
$report =& evidence_get_report($history_box && $max_edit_id ? 0 + $max_edit_id : "latest", $variant_id);
$row0 =& $report[0];
$variant_name_long = evidence_get_variant_name($row0, " ", false);
$variant_name_short = evidence_get_variant_name($row0, " ", true);
$gOut["title"] = "{$variant_name_short} - GET-Evidence";
$gOut["content"] = "<h1>{$variant_name_short}</h1>\n<!-- {$variant_id} -->\n";
if ($variant_name_long != $variant_name_short) {
$gOut["content"] .= "<p>({$variant_name_long})</p>\n";
}
$gOut["content"] .= seealso_related($row0["variant_gene"], $row0["variant_aa_pos"], $variant_id);
$gOut["content"] .= $history_box;
$renderer = new evidence_row_renderer();
foreach ($report as $row) {
if ($row["article_pmid"] > 0 || $row["genome_id"] > 0) {
break;
}
$renderer->render_row($row);
}
$gOut["content"] .= $renderer->html();
function print_content()
{
global $config;
global $sql_where;
global $sql_having;
global $sql_occur_filter;
global $sql_orderby;
global $sql_right_join;
global $sql_params;
global $min_certainty;
global $max_certainty;
global $snap;
global $gTheTextile;
global $want_column;
$q = theDb()->query($sql = "\nSELECT s.*, v.*, g.*, fs.*,\n-- gs.summary_short AS g_summary_short,\n MAX(o.zygosity) AS max_zygosity,\n d.dataset_id AS d_dataset_id,\n g.genome_id AS g_genome_id,\n y.hitcount AS hitcount,\n vf.f AS variant_frequency\nFROM snap_{$snap} s\n{$sql_right_join}\nLEFT JOIN flat_summary fs ON s.variant_id=fs.variant_id\nLEFT JOIN variants v ON s.variant_id=v.variant_id\nLEFT JOIN variant_frequency vf ON vf.variant_id=v.variant_id\nLEFT JOIN variant_occurs o ON v.variant_id=o.variant_id AND {$sql_occur_filter}\nLEFT JOIN datasets d ON o.dataset_id=d.dataset_id\nLEFT JOIN genomes g ON d.genome_id=g.genome_id\nLEFT JOIN yahoo_boss_cache y ON s.variant_id=y.variant_id\nLEFT JOIN variant_external omim ON omim.variant_id=s.variant_id AND omim.tag='OMIM'\n-- LEFT JOIN snap_{$snap} gs ON gs.variant_id=s.variant_id AND gs.article_pmid=0 AND gs.genome_id=g.genome_id\nWHERE s.article_pmid=0 AND s.genome_id=0 AND s.disease_id=0 AND {$sql_where}\nGROUP BY v.variant_id,g.genome_id\nHAVING {$sql_having}\n{$sql_orderby}\n", $sql_params);
$colcount = 5 + count($want_column);
if (theDb()->isError($q)) {
die("DB Error: " . $q->getMessage() . "<br>" . $sql);
}
print "<TABLE class=\"report_table\" style=\"width: 100%\">\n";
print "<TR><TD colspan=\"{$colcount}\" id=\"reportpage_turner_copy\" style=\"text-align: right;\"> </TD></TR>\n";
print "<TR><TH>" . join("</TH><TH>", array("Variant", "Impact", "Inheritance pattern", "Summary", "Genomes"));
foreach ($want_column as $k => $v) {
print "</TH><TH>{$v}";
}
print "</TH></TR>\n";
$output_row = 0;
$output_page = 0;
$output_cut_off_after = 0;
$tr_attrs = "";
$genome_rows = array();
for ($row =& $q->fetchRow(); $row; $row =& $nextrow) {
$row["name"] = $row["name"] ? $row["name"] : "[" . $row["global_human_id"] . "]";
$genome_rows[$row["genome_id"]] = $row;
$nextrow =& $q->fetchRow();
if ($nextrow && $row["variant_id"] == $nextrow["variant_id"]) {
continue;
}
$certainty = evidence_compute_certainty($row["variant_quality"], $row["variant_impact"]);
$certainty = substr($certainty, 0, 1);
if ($certainty == 0 && ($min_certainty == 0 || $max_certainty == -1)) {
// need to distinguish between "insufficiently evaluated" and "uncertain"
$have_2or3 = 0;
$have_4or5 = 0;
$nonempty_scores = 0;
$category_index = -1;
$scores = str_split(str_pad($row["variant_quality"], 6, "-"));
foreach ($scores as $score) {
if ($score != "-") {
++$nonempty_scores;
}
}
if ($nonempty_scores < 4 || $scores[2] == "-" && $scores[3] == "-" || $scores[4] == "-" && $scores[5] == "-") {
$certainty = -1;
}
}
if ($min_certainty > $certainty || $max_certainty < $certainty) {
$genome_rows = array();
continue;
}
++$output_row;
if ($output_row % $config["ROWSPERPAGE"] == 1) {
++$output_page;
$tr_attrs = " class=\"reportpage reportpage_{$output_page}\"";
if ($output_page > 1) {
$tr_attrs = " class=\"reportpage reportpage_{$output_page} csshide\"";
}
}
if ($output_page > $config["MAXPAGES"]) {
if (!$output_cut_off_after) {
$output_cut_off_after = $output_row - 1;
}
$genome_rows = array();
continue;
}
$variant_name_display = evidence_get_variant_name($row, " ", true);
$variant_name_link = evidence_get_variant_name($row, "-", true);
$rowspan = count($genome_rows);
if ($rowspan < 1) {
$rowspan = 1;
}
$rowspan = "rowspan=\"{$rowspan}\"";
$impact = ereg_replace("^likely ", "l.", $row["variant_impact"]);
if ($certainty == -1) {
$impact = "insufficiently evaluated / uncertain {$impact}";
} else {
if ($certainty == 1) {
$impact = "likely {$impact}";
} else {
if ($certainty <= 0) {
$impact = "uncertain {$impact}";
}
}
}
if (strlen($row["variant_frequency"])) {
$impact .= sprintf(", f=%.3f", $row["variant_frequency"]);
}
$summary_short = $gTheTextile->textileRestricted($row["summary_short"]);
if ($row["hitcount"] > 0) {
$s = $row["hitcount"] == 1 ? "" : "s";
$summary_short .= "<P>({$row['hitcount']} web hit{$s})</P>";
}
printf("<TR{$tr_attrs}><TD {$rowspan}>%s</TD><TD {$rowspan}>%s</TD><TD {$rowspan}>%s</TD><TD {$rowspan}>%s</TD>", "<A href=\"{$variant_name_link}\">{$variant_name_display}</A>", $impact, $row["variant_dominance"], $summary_short);
$rownum = 0;
foreach ($genome_rows as $id => $row) {
if (++$rownum > 1) {
print "</TR>\n<TR{$tr_attrs}>";
}
if (!$row["g_genome_id"]) {
print "<TD></TD>";
} else {
print "<TD width=\"15%\"><A href=\"{$variant_name_link}#g{$id}\">" . htmlspecialchars($row["name"]) . "</A>";
if ($row["max_zygosity"] == 'homozygous') {
print " (hom)";
}
print "</TD>";
}
if ($rownum == 1) {
foreach ($want_column as $k => $v) {
printf("<TD {$rowspan}>%s</TD>", $row[$k]);
}
}
}
print "</TR>\n";
$genome_rows = array();
}
if ($output_page > 1) {
print "<TR><TD colspan=\"{$colcount}\" id=\"reportpage_turner\" style=\"text-align: right;\">Page: ";
for ($p = 1; $p <= $output_page && $p <= $config["MAXPAGES"]; $p++) {
print "<A class=\"reportpage_turnbutton\" href=\"#\" onclick=\"reportpage_goto({$p});\">{$p}</A> ";
}
print "<BR /><STRONG>Total results: {$output_row}</STRONG>";
if ($output_cut_off_after) {
print "<BR />(Only displaying first {$output_cut_off_after} results)";
}
print "</TD></TR>\n";
print "<SCRIPT type=\"text/javascript\"><!--\n";
print "reportpage_init();\n";
print "\n// -->\n</SCRIPT>";
} else {
print "<TR><TD colspan=\"{$colcount}\" style=\"text-align: right;\"><STRONG>Total results: {$output_row}</STRONG></TD></TR>";
}
print "</TABLE>\n";
}
