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[Treebase-guts] SF.net SVN: treebase:[994] trunk/treebase-core/db/cleaning
|
From: <sfr...@us...> - 2011-12-06 19:24:14
|
Revision: 994
http://treebase.svn.sourceforge.net/treebase/?rev=994&view=rev
Author: sfrgpiel
Date: 2011-12-06 19:24:05 +0000 (Tue, 06 Dec 2011)
Log Message:
-----------
PERL script to clean the database of orphaned taxonlabelsets.
Added Paths:
-----------
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/README
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/affected_studies.sql
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/delete_orphaned_taxonlabelsets.pl
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/output.txt
Added: trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/README
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/README (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/README 2011-12-06 19:24:05 UTC (rev 994)
@@ -0,0 +1,18 @@
+The script delete_orphaned_taxonlabelsets.pl is intended to delete orphaned taxonlabelsets.
+
+As of Dec 6 2012, orphans were being generated as a result of a bug. Our delete treeblock
+function inadvertently failed to include a cleanup step to delete related, but now orphaned,
+taxonlabelset records. The result is studies that (sometimes) generate a "yikes" error when
+you try to get a list of taxa.
+
+For example, this page generates a Yikes:
+
+http://treebase.org/treebase-web/search/study/taxa.html?id=12037
+
+While this page (after fixing the data with delete_orphaned_taxonlabelsets.pl) does not:
+
+http://treebase-dev.nescent.org/treebase-web/search/study/taxa.html?id=12037
+
+To run the script, first edit lines 12-15 to point to production, then execute. It takes no
+parameters. Example output is provided with "output.txt".
+
Added: trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/affected_studies.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/affected_studies.sql (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/affected_studies.sql 2011-12-06 19:24:05 UTC (rev 994)
@@ -0,0 +1,361 @@
+
+SELECT DISTINCT ON (tls.study_id) tls.taxonlabelset_id, tls.study_id, ss.description
+FROM
+taxonlabelset tls LEFT JOIN
+matrix mx ON (tls.taxonlabelset_id = mx.taxonlabelset_id) LEFT JOIN
+treeblock tb ON (tls.taxonlabelset_id = tb.taxonlabelset_id) JOIN
+study s ON (tls.study_id = s.study_id) JOIN
+studystatus ss USING (studystatus_id)
+WHERE
+mx.matrix_id IS NULL
+AND
+tb.treeblock_id IS NULL
+
+-- 345 studies are affected
+
+-- 1394 22 In Progress
+-- 4810 23 In Progress
+-- 9450 44 In Progress
+-- 11200 1019 Published
+-- 13335 1919 Published
+-- 14190 2264 In Progress
+-- 16071 10215 In Progress
+-- 16132 10317 Published
+-- 16464 10335 Published
+-- 16188 10339 In Progress
+-- 18753 10347 In Progress
+-- 16228 10356 In Progress
+-- 16280 10367 In Progress
+-- 16399 10399 Published
+-- 16402 10400 Published
+-- 16434 10413 In Progress
+-- 16456 10424 In Progress
+-- 16466 10425 In Progress
+-- 16477 10429 Published
+-- 16567 10431 In Progress
+-- 16484 10433 Published
+-- 16501 10434 In Progress
+-- 16507 10435 Published
+-- 18799 10436 Published
+-- 16514 10438 Published
+-- 16545 10449 In Progress
+-- 16554 10452 In Progress
+-- 16668 10462 In Progress
+-- 16784 10464 Published
+-- 16633 10468 In Progress
+-- 16638 10469 Published
+-- 16643 10470 In Progress
+-- 16653 10474 In Progress
+-- 16749 10485 Published
+-- 16757 10486 In Progress
+-- 16702 10489 Published
+-- 16696 10492 Published
+-- 16700 10493 Published
+-- 16731 10504 Published
+-- 16734 10507 Published
+-- 16738 10508 In Progress
+-- 16772 10511 Published
+-- 21310 10512 Published
+-- 16860 10529 In Progress
+-- 16888 10530 In Progress
+-- 16940 10536 Published
+-- 16972 10541 Published
+-- 16969 10542 Published
+-- 17064 10553 Published
+-- 17057 10569 In Progress
+-- 17076 10570 Published
+-- 17093 10583 In Progress
+-- 17289 10589 In Progress
+-- 17293 10593 Published
+-- 17206 10603 Published
+-- 17138 10604 In Progress
+-- 18665 10605 In Progress
+-- 17671 10608 Published
+-- 17174 10613 Published
+-- 17192 10623 Published
+-- 17237 10635 Published
+-- 17255 10639 In Progress
+-- 17379 10644 Published
+-- 17291 10648 Published
+-- 17338 10652 Published
+-- 22206 10653 Published
+-- 17347 10654 Published
+-- 17355 10658 Published
+-- 17468 10665 Published
+-- 18527 10673 In Progress
+-- 17453 10679 Published
+-- 17568 10680 Published
+-- 17429 10684 Published
+-- 17463 10689 Published
+-- 17471 10692 Published
+-- 17514 10698 In Progress
+-- 17528 10699 In Progress
+-- 17572 10703 Published
+-- 17584 10711 In Progress
+-- 22854 10713 Published
+-- 17605 10714 Published
+-- 18102 10724 Published
+-- 17643 10727 Published
+-- 17659 10732 Published
+-- 17669 10733 In Progress
+-- 17740 10736 Published
+-- 17752 10740 In Progress
+-- 17784 10749 Published
+-- 17821 10759 In Progress
+-- 17836 10766 Published
+-- 17850 10772 Published
+-- 17856 10774 Published
+-- 17895 10786 In Progress
+-- 17950 10795 In Progress
+-- 17992 10797 Published
+-- 17987 10803 Published
+-- 17997 10812 In Progress
+-- 18004 10814 In Progress
+-- 20216 10817 In Progress
+-- 18030 10821 Published
+-- 18044 10828 In Progress
+-- 18748 10830 Published
+-- 18138 10831 In Progress
+-- 18123 10847 Published
+-- 18216 10859 In Progress
+-- 18286 10861 In Progress
+-- 18238 10870 In Progress
+-- 18244 10876 Published
+-- 18346 10888 Published
+-- 18283 10898 Published
+-- 18366 10902 In Progress
+-- 18566 10904 In Progress
+-- 21995 10905 Published
+-- 18410 10908 Published
+-- 18478 10927 Published
+-- 18564 10938 Published
+-- 18580 10940 Published
+-- 18509 10942 Published
+-- 18591 10950 Published
+-- 18593 10951 Published
+-- 18619 10961 In Progress
+-- 18638 10963 Published
+-- 18633 10966 Published
+-- 18657 10971 In Progress
+-- 18673 10977 In Progress
+-- 18683 10983 Published
+-- 18687 10984 Published
+-- 18737 10996 Published
+-- 18726 10999 In Progress
+-- 18760 11009 Published
+-- 18822 11020 Published
+-- 22845 11021 Published
+-- 18826 11022 Published
+-- 18887 11032 Published
+-- 18983 11056 In Progress
+-- 19367 11058 Published
+-- 19007 11061 Published
+-- 19045 11078 In Progress
+-- 19055 11079 Published
+-- 19062 11080 Published
+-- 19077 11083 Published
+-- 19095 11088 Published
+-- 19107 11089 In Progress
+-- 19104 11090 Published
+-- 19429 11091 In Progress
+-- 19127 11093 Published
+-- 19126 11097 Published
+-- 19160 11111 Published
+-- 19173 11112 Published
+-- 19186 11114 Published
+-- 19191 11115 Published
+-- 19199 11116 Ready
+-- 19394 11117 In Progress
+-- 19205 11118 Published
+-- 19213 11122 Published
+-- 19260 11126 Published
+-- 19274 11128 Published
+-- 19318 11132 Published
+-- 19337 11136 In Progress
+-- 19359 11140 Published
+-- 21258 11159 In Progress
+-- 19424 11161 Published
+-- 19454 11174 Published
+-- 19462 11177 In Progress
+-- 19494 11181 In Progress
+-- 19497 11183 Published
+-- 19503 11184 Published
+-- 19513 11192 Published
+-- 19523 11197 Published
+-- 19540 11200 Published
+-- 20145 11204 Published
+-- 19682 11210 Published
+-- 19576 11211 Published
+-- 19601 11216 Published
+-- 19662 11219 In Progress
+-- 19654 11226 Published
+-- 19793 11252 In Progress
+-- 19828 11260 Published
+-- 19829 11261 In Progress
+-- 19844 11267 Published
+-- 19854 11269 Published
+-- 19883 11273 In Progress
+-- 19893 11276 In Progress
+-- 19918 11284 Published
+-- 19942 11289 Published
+-- 19962 11294 In Progress
+-- 19979 11296 In Progress
+-- 20000 11298 Published
+-- 20317 11303 Published
+-- 20140 11312 Published
+-- 20142 11313 Published
+-- 20177 11327 In Progress
+-- 20207 11331 Published
+-- 20190 11333 In Progress
+-- 20222 11336 Published
+-- 20252 11346 In Progress
+-- 20258 11348 In Progress
+-- 20284 11352 In Progress
+-- 20283 11355 Published
+-- 22141 11367 In Progress
+-- 20338 11369 In Progress
+-- 20802 11378 Published
+-- 20375 11380 In Progress
+-- 20520 11383 In Progress
+-- 20424 11391 Published
+-- 20419 11392 Published
+-- 20468 11397 In Progress
+-- 22095 11398 In Progress
+-- 20503 11404 Published
+-- 22263 11409 In Progress
+-- 20610 11415 Published
+-- 23182 11416 Published
+-- 20628 11417 In Progress
+-- 20631 11418 Published
+-- 20670 11439 Published
+-- 20719 11448 In Progress
+-- 21327 11461 In Progress
+-- 20964 11465 In Progress
+-- 21181 11468 Published
+-- 21278 11472 Published
+-- 21062 11476 Published
+-- 20901 11480 Published
+-- 21036 11487 In Progress
+-- 20941 11489 Published
+-- 20962 11499 In Progress
+-- 20976 11504 In Progress
+-- 21067 11512 Published
+-- 21052 11517 Published
+-- 21141 11524 In Progress
+-- 21513 11527 In Progress
+-- 21106 11535 Published
+-- 21112 11536 In Progress
+-- 21135 11537 In Progress
+-- 21188 11552 Published
+-- 22436 11557 Published
+-- 21216 11561 In Progress
+-- 21673 11563 Published
+-- 21343 11568 In Progress
+-- 21243 11570 Published
+-- 21246 11571 In Progress
+-- 21264 11575 Published
+-- 21273 11586 Published
+-- 21305 11593 Published
+-- 21320 11596 Published
+-- 21413 11600 In Progress
+-- 21349 11601 In Progress
+-- 21340 11607 In Progress
+-- 21345 11608 In Progress
+-- 21369 11616 Published
+-- 21380 11619 In Progress
+-- 21390 11623 Published
+-- 21387 11625 In Progress
+-- 22145 11644 Published
+-- 21461 11651 Published
+-- 21568 11652 In Progress
+-- 21520 11654 In Progress
+-- 21485 11659 In Progress
+-- 21750 11662 Published
+-- 21611 11670 In Progress
+-- 21696 11681 In Progress
+-- 21712 11683 In Progress
+-- 22040 11687 In Progress
+-- 21762 11689 Published
+-- 21774 11692 In Progress
+-- 21999 11695 Published
+-- 22004 11705 In Progress
+-- 22019 11711 In Progress
+-- 22027 11713 Published
+-- 22052 11719 In Progress
+-- 22089 11729 In Progress
+-- 22153 11747 Published
+-- 22170 11756 In Progress
+-- 22183 11759 Published
+-- 22225 11768 In Progress
+-- 22636 11779 Published
+-- 22256 11780 In Progress
+-- 22293 11798 Published
+-- 22348 11815 Published
+-- 22362 11822 Published
+-- 22390 11823 In Progress
+-- 22374 11825 In Progress
+-- 22387 11829 In Progress
+-- 22405 11832 In Progress
+-- 22450 11848 In Progress
+-- 22480 11849 Published
+-- 22706 11852 In Progress
+-- 22494 11863 In Progress
+-- 22489 11864 In Progress
+-- 22519 11865 Published
+-- 22496 11866 In Progress
+-- 22514 11868 Published
+-- 22529 11872 Published
+-- 22600 11876 Published
+-- 22551 11878 Published
+-- 22574 11891 Published
+-- 22581 11892 Published
+-- 22661 11893 In Progress
+-- 22608 11906 Published
+-- 23365 11908 Published
+-- 22632 11911 In Progress
+-- 22638 11914 In Progress
+-- 22652 11917 In Progress
+-- 22723 11918 Published
+-- 22727 11936 In Progress
+-- 22883 11943 In Progress
+-- 22872 11949 Published
+-- 22828 11950 Published
+-- 22876 11956 In Progress
+-- 23160 11959 In Progress
+-- 22895 11960 In Progress
+-- 23072 11963 In Progress
+-- 22914 11975 Published
+-- 22930 11980 In Progress
+-- 23021 11985 Published
+-- 23399 11988 Published
+-- 23539 11991 Published
+-- 22979 11995 In Progress
+-- 22996 12003 Published
+-- 23012 12006 In Progress
+-- 23061 12009 Published
+-- 23080 12029 In Progress
+-- 23095 12034 In Progress
+-- 23146 12036 Published
+-- 23102 12037 Published
+-- 23203 12043 In Progress
+-- 23158 12048 In Progress
+-- 23174 12050 In Progress
+-- 23200 12055 In Progress
+-- 23211 12057 Published
+-- 23226 12065 In Progress
+-- 23247 12072 In Progress
+-- 23274 12079 Published
+-- 23290 12087 In Progress
+-- 23292 12088 In Progress
+-- 23342 12096 In Progress
+-- 23357 12101 In Progress
+-- 23401 12120 In Progress
+-- 23408 12121 In Progress
+-- 23428 12128 In Progress
+-- 23491 12145 In Progress
+-- 23509 12149 In Progress
+-- 23606 12153 In Progress
+-- 23532 12160 Published
+-- 23590 12162 Published
+-- 23608 12167 In Progress
+
Added: trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/delete_orphaned_taxonlabelsets.pl
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/delete_orphaned_taxonlabelsets.pl (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/delete_orphaned_taxonlabelsets.pl 2011-12-06 19:24:05 UTC (rev 994)
@@ -0,0 +1,97 @@
+#!/usr/bin/perl
+
+use strict;
+use DBI;
+
+# This script is intended to delete orphaned taxonlabelsets. As of Dec 6 2012, orphans
+# were being generated as a result of a bug. When our delete-treeblock function inadvertently
+# failed to include a cleanup step to delete related, but now orphaned, taxonlabelset records.
+# The result are studies that generate a "yikes" error when you try to get a list of taxa.
+
+
+my $database = "treebasedev";
+my $username = "treebase_app";
+my $password = "";
+my $host = "treebasedb-dev.nescent.org";
+
+
+my $dbh = &ConnectToPg($database, $username, $password, $host);
+
+# start by asking how many taxonlabelset records are orphaned
+
+my $recs = "SELECT count(*) FROM
+taxonlabelset tls LEFT JOIN
+matrix mx ON (tls.taxonlabelset_id = mx.taxonlabelset_id) LEFT JOIN
+treeblock tb ON (tls.taxonlabelset_id = tb.taxonlabelset_id) JOIN
+study s ON (tls.study_id = s.study_id) JOIN
+studystatus ss USING (studystatus_id)
+WHERE mx.matrix_id IS NULL
+AND tb.treeblock_id IS NULL ";
+my $totRec = $dbh->selectrow_array ($recs);
+
+print "$totRec orphaned taxonlabelset records need to be deleted\n\n";
+
+# get a list of all these taxonlabelset IDs
+
+my $statement = "SELECT tls.taxonlabelset_id FROM
+taxonlabelset tls LEFT JOIN
+matrix mx ON (tls.taxonlabelset_id = mx.taxonlabelset_id) LEFT JOIN
+treeblock tb ON (tls.taxonlabelset_id = tb.taxonlabelset_id) JOIN
+study s ON (tls.study_id = s.study_id) JOIN
+studystatus ss USING (studystatus_id)
+WHERE mx.matrix_id IS NULL
+AND tb.treeblock_id IS NULL ";
+
+my @orphaned;
+my $orphanedlist = $dbh->prepare($statement) or die "Can't prepare $statement: $dbh->errstr\n";
+$orphanedlist->execute;
+while(my @row = $orphanedlist->fetchrow_array) {
+ push(@orphaned, $row[0]);
+}
+
+foreach my $orph ( @orphaned ) {
+ print "preparing to delete $orph\n";
+
+ # run the whole thing in a single transaction
+ eval {
+
+ # First delete the records that reference this taxonlabelset
+ $dbh->do( "DELETE FROM taxonlabelset_taxonlabel WHERE taxonlabelset_id = ?", undef, $orph );
+
+ # Next delete the taxonlabelset
+ $dbh->do( "DELETE FROM taxonlabelset WHERE taxonlabelset_id = ?", undef, $orph );
+
+ # If no errors so far, let's commit
+ $dbh->commit();
+ };
+
+ if ($@) {
+ warn "Failed to delete taxonlabelset_id $orph: $@\n";
+ $dbh->rollback();
+ print "rollback!!\n";
+ }
+
+}
+
+$totRec = $dbh->selectrow_array ($recs);
+
+print "\n$totRec orphaned taxonlabelset records need to be deleted\n";
+
+exit;
+
+
+
+# Connect to Postgres using DBI
+#==============================================================
+sub ConnectToPg {
+
+ my ($cstr, $user, $pass, $host) = @_;
+
+ $cstr = "DBI:Pg:dbname="."$cstr";
+ $cstr .= ";host=$host" if ($host);
+
+ my $dbh = DBI->connect($cstr, $user, $pass, {AutoCommit => 0, PrintError => 1, RaiseError => 1});
+ $dbh || &error("DBI connect failed : ",$dbh->errstr);
+
+ return($dbh);
+}
Added: trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql 2011-12-06 19:24:05 UTC (rev 994)
@@ -0,0 +1,405 @@
+-- psql -U treebase_app -d treebasedev -h treebasedb-dev.nescent.org
+-- qLoMjwRz
+
+
+12037
+
+SELECT tls.taxonlabelset_id, count(tt.*)
+FROM
+taxonlabelset tls JOIN
+taxonlabelset_taxonlabel tt USING (taxonlabelset_id) JOIN
+taxonlabel tl USING (taxonlabel_id)
+WHERE tls.study_id = 12037
+GROUP BY tls.taxonlabelset_id
+
+23165 55
+23161 100
+23102 94
+
+Set 23102 is probably orphaned
+
+SELECT tls.*, mx.matrix_id, tb.treeblock_id
+FROM
+taxonlabelset tls LEFT JOIN
+matrix mx ON (tls.taxonlabelset_id = mx.taxonlabelset_id) LEFT JOIN
+treeblock tb ON (tls.taxonlabelset_id = tb.taxonlabelset_id)
+WHERE
+tls.taxonlabelset_id IN (23165, 23161, 23102)
+
+SELECT DISTINCT ON (tls.study_id) tls.taxonlabelset_id, tls.study_id, ss.description
+FROM
+taxonlabelset tls LEFT JOIN
+matrix mx ON (tls.taxonlabelset_id = mx.taxonlabelset_id) LEFT JOIN
+treeblock tb ON (tls.taxonlabelset_id = tb.taxonlabelset_id) JOIN
+study s ON (tls.study_id = s.study_id) JOIN
+studystatus ss USING (studystatus_id)
+WHERE
+mx.matrix_id IS NULL
+AND
+tb.treeblock_id IS NULL
+
+-- 345 studies are affected
+
+-- 1394 22 In Progress
+-- 4810 23 In Progress
+-- 9450 44 In Progress
+-- 11200 1019 Published
+-- 13335 1919 Published
+-- 14190 2264 In Progress
+-- 16071 10215 In Progress
+-- 16132 10317 Published
+-- 16464 10335 Published
+-- 16188 10339 In Progress
+-- 18753 10347 In Progress
+-- 16228 10356 In Progress
+-- 16280 10367 In Progress
+-- 16399 10399 Published
+-- 16402 10400 Published
+-- 16434 10413 In Progress
+-- 16456 10424 In Progress
+-- 16466 10425 In Progress
+-- 16477 10429 Published
+-- 16567 10431 In Progress
+-- 16484 10433 Published
+-- 16501 10434 In Progress
+-- 16507 10435 Published
+-- 18799 10436 Published
+-- 16514 10438 Published
+-- 16545 10449 In Progress
+-- 16554 10452 In Progress
+-- 16668 10462 In Progress
+-- 16784 10464 Published
+-- 16633 10468 In Progress
+-- 16638 10469 Published
+-- 16643 10470 In Progress
+-- 16653 10474 In Progress
+-- 16749 10485 Published
+-- 16757 10486 In Progress
+-- 16702 10489 Published
+-- 16696 10492 Published
+-- 16700 10493 Published
+-- 16731 10504 Published
+-- 16734 10507 Published
+-- 16738 10508 In Progress
+-- 16772 10511 Published
+-- 21310 10512 Published
+-- 16860 10529 In Progress
+-- 16888 10530 In Progress
+-- 16940 10536 Published
+-- 16972 10541 Published
+-- 16969 10542 Published
+-- 17064 10553 Published
+-- 17057 10569 In Progress
+-- 17076 10570 Published
+-- 17093 10583 In Progress
+-- 17289 10589 In Progress
+-- 17293 10593 Published
+-- 17206 10603 Published
+-- 17138 10604 In Progress
+-- 18665 10605 In Progress
+-- 17671 10608 Published
+-- 17174 10613 Published
+-- 17192 10623 Published
+-- 17237 10635 Published
+-- 17255 10639 In Progress
+-- 17379 10644 Published
+-- 17291 10648 Published
+-- 17338 10652 Published
+-- 22206 10653 Published
+-- 17347 10654 Published
+-- 17355 10658 Published
+-- 17468 10665 Published
+-- 18527 10673 In Progress
+-- 17453 10679 Published
+-- 17568 10680 Published
+-- 17429 10684 Published
+-- 17463 10689 Published
+-- 17471 10692 Published
+-- 17514 10698 In Progress
+-- 17528 10699 In Progress
+-- 17572 10703 Published
+-- 17584 10711 In Progress
+-- 22854 10713 Published
+-- 17605 10714 Published
+-- 18102 10724 Published
+-- 17643 10727 Published
+-- 17659 10732 Published
+-- 17669 10733 In Progress
+-- 17740 10736 Published
+-- 17752 10740 In Progress
+-- 17784 10749 Published
+-- 17821 10759 In Progress
+-- 17836 10766 Published
+-- 17850 10772 Published
+-- 17856 10774 Published
+-- 17895 10786 In Progress
+-- 17950 10795 In Progress
+-- 17992 10797 Published
+-- 17987 10803 Published
+-- 17997 10812 In Progress
+-- 18004 10814 In Progress
+-- 20216 10817 In Progress
+-- 18030 10821 Published
+-- 18044 10828 In Progress
+-- 18748 10830 Published
+-- 18138 10831 In Progress
+-- 18123 10847 Published
+-- 18216 10859 In Progress
+-- 18286 10861 In Progress
+-- 18238 10870 In Progress
+-- 18244 10876 Published
+-- 18346 10888 Published
+-- 18283 10898 Published
+-- 18366 10902 In Progress
+-- 18566 10904 In Progress
+-- 21995 10905 Published
+-- 18410 10908 Published
+-- 18478 10927 Published
+-- 18564 10938 Published
+-- 18580 10940 Published
+-- 18509 10942 Published
+-- 18591 10950 Published
+-- 18593 10951 Published
+-- 18619 10961 In Progress
+-- 18638 10963 Published
+-- 18633 10966 Published
+-- 18657 10971 In Progress
+-- 18673 10977 In Progress
+-- 18683 10983 Published
+-- 18687 10984 Published
+-- 18737 10996 Published
+-- 18726 10999 In Progress
+-- 18760 11009 Published
+-- 18822 11020 Published
+-- 22845 11021 Published
+-- 18826 11022 Published
+-- 18887 11032 Published
+-- 18983 11056 In Progress
+-- 19367 11058 Published
+-- 19007 11061 Published
+-- 19045 11078 In Progress
+-- 19055 11079 Published
+-- 19062 11080 Published
+-- 19077 11083 Published
+-- 19095 11088 Published
+-- 19107 11089 In Progress
+-- 19104 11090 Published
+-- 19429 11091 In Progress
+-- 19127 11093 Published
+-- 19126 11097 Published
+-- 19160 11111 Published
+-- 19173 11112 Published
+-- 19186 11114 Published
+-- 19191 11115 Published
+-- 19199 11116 Ready
+-- 19394 11117 In Progress
+-- 19205 11118 Published
+-- 19213 11122 Published
+-- 19260 11126 Published
+-- 19274 11128 Published
+-- 19318 11132 Published
+-- 19337 11136 In Progress
+-- 19359 11140 Published
+-- 21258 11159 In Progress
+-- 19424 11161 Published
+-- 19454 11174 Published
+-- 19462 11177 In Progress
+-- 19494 11181 In Progress
+-- 19497 11183 Published
+-- 19503 11184 Published
+-- 19513 11192 Published
+-- 19523 11197 Published
+-- 19540 11200 Published
+-- 20145 11204 Published
+-- 19682 11210 Published
+-- 19576 11211 Published
+-- 19601 11216 Published
+-- 19662 11219 In Progress
+-- 19654 11226 Published
+-- 19793 11252 In Progress
+-- 19828 11260 Published
+-- 19829 11261 In Progress
+-- 19844 11267 Published
+-- 19854 11269 Published
+-- 19883 11273 In Progress
+-- 19893 11276 In Progress
+-- 19918 11284 Published
+-- 19942 11289 Published
+-- 19962 11294 In Progress
+-- 19979 11296 In Progress
+-- 20000 11298 Published
+-- 20317 11303 Published
+-- 20140 11312 Published
+-- 20142 11313 Published
+-- 20177 11327 In Progress
+-- 20207 11331 Published
+-- 20190 11333 In Progress
+-- 20222 11336 Published
+-- 20252 11346 In Progress
+-- 20258 11348 In Progress
+-- 20284 11352 In Progress
+-- 20283 11355 Published
+-- 22141 11367 In Progress
+-- 20338 11369 In Progress
+-- 20802 11378 Published
+-- 20375 11380 In Progress
+-- 20520 11383 In Progress
+-- 20424 11391 Published
+-- 20419 11392 Published
+-- 20468 11397 In Progress
+-- 22095 11398 In Progress
+-- 20503 11404 Published
+-- 22263 11409 In Progress
+-- 20610 11415 Published
+-- 23182 11416 Published
+-- 20628 11417 In Progress
+-- 20631 11418 Published
+-- 20670 11439 Published
+-- 20719 11448 In Progress
+-- 21327 11461 In Progress
+-- 20964 11465 In Progress
+-- 21181 11468 Published
+-- 21278 11472 Published
+-- 21062 11476 Published
+-- 20901 11480 Published
+-- 21036 11487 In Progress
+-- 20941 11489 Published
+-- 20962 11499 In Progress
+-- 20976 11504 In Progress
+-- 21067 11512 Published
+-- 21052 11517 Published
+-- 21141 11524 In Progress
+-- 21513 11527 In Progress
+-- 21106 11535 Published
+-- 21112 11536 In Progress
+-- 21135 11537 In Progress
+-- 21188 11552 Published
+-- 22436 11557 Published
+-- 21216 11561 In Progress
+-- 21673 11563 Published
+-- 21343 11568 In Progress
+-- 21243 11570 Published
+-- 21246 11571 In Progress
+-- 21264 11575 Published
+-- 21273 11586 Published
+-- 21305 11593 Published
+-- 21320 11596 Published
+-- 21413 11600 In Progress
+-- 21349 11601 In Progress
+-- 21340 11607 In Progress
+-- 21345 11608 In Progress
+-- 21369 11616 Published
+-- 21380 11619 In Progress
+-- 21390 11623 Published
+-- 21387 11625 In Progress
+-- 22145 11644 Published
+-- 21461 11651 Published
+-- 21568 11652 In Progress
+-- 21520 11654 In Progress
+-- 21485 11659 In Progress
+-- 21750 11662 Published
+-- 21611 11670 In Progress
+-- 21696 11681 In Progress
+-- 21712 11683 In Progress
+-- 22040 11687 In Progress
+-- 21762 11689 Published
+-- 21774 11692 In Progress
+-- 21999 11695 Published
+-- 22004 11705 In Progress
+-- 22019 11711 In Progress
+-- 22027 11713 Published
+-- 22052 11719 In Progress
+-- 22089 11729 In Progress
+-- 22153 11747 Published
+-- 22170 11756 In Progress
+-- 22183 11759 Published
+-- 22225 11768 In Progress
+-- 22636 11779 Published
+-- 22256 11780 In Progress
+-- 22293 11798 Published
+-- 22348 11815 Published
+-- 22362 11822 Published
+-- 22390 11823 In Progress
+-- 22374 11825 In Progress
+-- 22387 11829 In Progress
+-- 22405 11832 In Progress
+-- 22450 11848 In Progress
+-- 22480 11849 Published
+-- 22706 11852 In Progress
+-- 22494 11863 In Progress
+-- 22489 11864 In Progress
+-- 22519 11865 Published
+-- 22496 11866 In Progress
+-- 22514 11868 Published
+-- 22529 11872 Published
+-- 22600 11876 Published
+-- 22551 11878 Published
+-- 22574 11891 Published
+-- 22581 11892 Published
+-- 22661 11893 In Progress
+-- 22608 11906 Published
+-- 23365 11908 Published
+-- 22632 11911 In Progress
+-- 22638 11914 In Progress
+-- 22652 11917 In Progress
+-- 22723 11918 Published
+-- 22727 11936 In Progress
+-- 22883 11943 In Progress
+-- 22872 11949 Published
+-- 22828 11950 Published
+-- 22876 11956 In Progress
+-- 23160 11959 In Progress
+-- 22895 11960 In Progress
+-- 23072 11963 In Progress
+-- 22914 11975 Published
+-- 22930 11980 In Progress
+-- 23021 11985 Published
+-- 23399 11988 Published
+-- 23539 11991 Published
+-- 22979 11995 In Progress
+-- 22996 12003 Published
+-- 23012 12006 In Progress
+-- 23061 12009 Published
+-- 23080 12029 In Progress
+-- 23095 12034 In Progress
+-- 23146 12036 Published
+-- 23102 12037 Published
+-- 23203 12043 In Progress
+-- 23158 12048 In Progress
+-- 23174 12050 In Progress
+-- 23200 12055 In Progress
+-- 23211 12057 Published
+-- 23226 12065 In Progress
+-- 23247 12072 In Progress
+-- 23274 12079 Published
+-- 23290 12087 In Progress
+-- 23292 12088 In Progress
+-- 23342 12096 In Progress
+-- 23357 12101 In Progress
+-- 23401 12120 In Progress
+-- 23408 12121 In Progress
+-- 23428 12128 In Progress
+-- 23491 12145 In Progress
+-- 23509 12149 In Progress
+-- 23606 12153 In Progress
+-- 23532 12160 Published
+-- 23590 12162 Published
+-- 23608 12167 In Progress
+
+
+SELECT tb.treeblock_id, stb.submission_id, pt.study_id
+FROM treeblock tb LEFT JOIN
+sub_treeblock stb USING (treeblock_id) LEFT JOIN
+phylotree pt ON (tb.treeblock_id = pt.treeblock_id)
+WHERE tb.taxonlabelset_id IS NULL
+
+-- 4781 66
+-- 4782 67
+-- 4783 68
+-- 4784 69
+-- 4785 70
+-- 4786 71
+-- 4787 72
+-- 4788 73
+
+
Added: trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/output.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/output.txt (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/output.txt 2011-12-06 19:24:05 UTC (rev 994)
@@ -0,0 +1,5102 @@
+5098 orphaned taxonlabelset records need to be deleted
+
+preparing to delete 81
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