From 70059b0d00de150a6ba749ac28ef373b86408982 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 24 Apr 2024 19:18:16 -0500
Subject: Layout

---
 issues/systems/mariadb/move-to-innodb.gmi | 53 ++++++++++++++++---------------
 tasks/pjotrp.gmi                          | 20 +++++-------
 2 files changed, 36 insertions(+), 37 deletions(-)

diff --git a/issues/systems/mariadb/move-to-innodb.gmi b/issues/systems/mariadb/move-to-innodb.gmi
index c6b52c7..924a203 100644
--- a/issues/systems/mariadb/move-to-innodb.gmi
+++ b/issues/systems/mariadb/move-to-innodb.gmi
@@ -664,6 +664,7 @@ CREATE TABLE 'ProbeSetFreeze' (
 
 There is a primary key. Good.
 
+```
 ALTER TABLE ProbeSetSE
   ADD PRIMARY KEY(DataId,StrainId);
 Query OK, 688744613 rows affected (15 min 13.830 sec)
@@ -920,12 +921,14 @@ Or
 
 ```
 SHOW CREATE TABLE ProbeSet;
+```
 
 E.g.
 
-  FULLTEXT KEY `SEARCH_GENE_IDX` (`Symbol`,`alias`),
-  FULLTEXT KEY `SEARCH_FULL_IDX` (`Name`,`description`,`Symbol`,`alias`,`GenbankId`,`UniGeneId`,`Probe_Target_Description`),
-  FULLTEXT KEY `RefSeq_FULL_IDX` (`RefSeq_TranscriptId`)
+```
+FULLTEXT KEY 'SEARCH_GENE_IDX' ('Symbol','alias'),
+  FULLTEXT KEY 'SEARCH_FULL_IDX' ('Name','description','Symbol','alias','GenbankId','UniGeneId','Probe_Target_Description'),
+  FULLTEXT KEY 'RefSeq_FULL_IDX' ('RefSeq_TranscriptId')
 ```
 
 To see all:
@@ -995,10 +998,10 @@ CREATE FULLTEXT INDEX ft_ProbeSet_Symbol ON ProbeSet(Symbol);
 Now we have
 
 ```
-FULLTEXT KEY `SEARCH_GENE_IDX` (`Symbol`,`alias`),
-FULLTEXT KEY `SEARCH_FULL_IDX` (`Name`,`description`,`Symbol`,`alias`,`GenbankId`,`UniGeneId`,`Probe_Target_Description`),
-FULLTEXT KEY `RefSeq_FULL_IDX` (`RefSeq_TranscriptId`),
-FULLTEXT KEY `ft_ProbeSet_Symbol` (`Symbol`)
+FULLTEXT KEY 'SEARCH_GENE_IDX' ('Symbol','alias'),
+FULLTEXT KEY 'SEARCH_FULL_IDX' ('Name','description','Symbol','alias','GenbankId','UniGeneId','Probe_Target_Description'),
+FULLTEXT KEY 'RefSeq_FULL_IDX' ('RefSeq_TranscriptId'),
+FULLTEXT KEY 'ft_ProbeSet_Symbol' ('Symbol')
 ```
 
 and the query works.
@@ -1061,24 +1064,24 @@ select count(*) from ProbeSetFreeze limit 2;
 |      931 |
 +----------+
 SHOW CREATE TABLE ProbeSetFreeze;
-CREATE TABLE `ProbeSetFreeze` (
-  `Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `ProbeFreezeId` smallint(5) unsigned NOT NULL DEFAULT 0,
-  `AvgID` smallint(5) unsigned NOT NULL DEFAULT 0,
-  `Name` varchar(40) DEFAULT NULL,
-  `Name2` varchar(100) NOT NULL DEFAULT '',
-  `FullName` varchar(100) NOT NULL DEFAULT '',
-  `ShortName` varchar(100) NOT NULL DEFAULT '',
-  `CreateTime` date NOT NULL DEFAULT '0000-00-00',
-  `OrderList` int(5) DEFAULT NULL,
-  `public` tinyint(4) NOT NULL DEFAULT 0,
-  `confidentiality` tinyint(4) NOT NULL DEFAULT 0,
-  `AuthorisedUsers` varchar(300) NOT NULL,
-  `DataScale` varchar(20) NOT NULL DEFAULT 'log2',
-  PRIMARY KEY (`Id`),
-  UNIQUE KEY `FullName` (`FullName`),
-  UNIQUE KEY `Name` (`Name`),
-  KEY `NameIndex` (`Name2`)
+CREATE TABLE 'ProbeSetFreeze' (
+  'Id' smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+  'ProbeFreezeId' smallint(5) unsigned NOT NULL DEFAULT 0,
+  'AvgID' smallint(5) unsigned NOT NULL DEFAULT 0,
+  'Name' varchar(40) DEFAULT NULL,
+  'Name2' varchar(100) NOT NULL DEFAULT '',
+  'FullName' varchar(100) NOT NULL DEFAULT '',
+  'ShortName' varchar(100) NOT NULL DEFAULT '',
+  'CreateTime' date NOT NULL DEFAULT '0000-00-00',
+  'OrderList' int(5) DEFAULT NULL,
+  'public' tinyint(4) NOT NULL DEFAULT 0,
+  'confidentiality' tinyint(4) NOT NULL DEFAULT 0,
+  'AuthorisedUsers' varchar(300) NOT NULL,
+  'DataScale' varchar(20) NOT NULL DEFAULT 'log2',
+  PRIMARY KEY ('Id'),
+  UNIQUE KEY 'FullName' ('FullName'),
+  UNIQUE KEY 'Name' ('Name'),
+  KEY 'NameIndex' ('Name2')
 ) ENGINE=MyISAM AUTO_INCREMENT=1054 DEFAULT CHARSET=latin1
 ```
 
diff --git a/tasks/pjotrp.gmi b/tasks/pjotrp.gmi
index a327f5d..278323b 100644
--- a/tasks/pjotrp.gmi
+++ b/tasks/pjotrp.gmi
@@ -16,7 +16,7 @@ The tasks here should probably be broken out into appropriately tagged issues, w
 
 ## Mempang24
 
-* [+] Invites
+* [X] Invites
 * [+] Payments
 * [+] Rooms
 * [+] Catering
@@ -28,7 +28,6 @@ The tasks here should probably be broken out into appropriately tagged issues, w
 * [+] Julia as part of GN3 deployment
 => /topics/deploy/julia.gmi
 * [+] Shelby's paper+application
-* [+] Debian/free software issues incl. vcflib work in Zig and release
 
 # Tasks
 
@@ -36,8 +35,13 @@ The tasks here should probably be broken out into appropriately tagged issues, w
 
 Now (X=done +=WIP _=kickoff ?=?)
 
+* [ ] ~Test GEMMA/bulklmm speedups & paper
+* [ ] GEMMA batch run and precompute
+=> ../issues/gemma/lmm-precomputed-scores
+* [ ] Genotyping and sparse VCF
+* [ ] GeneNetwork consortium (paper & CTC)
+
 * [+] Build leadership team
-* [+] Build GN consortium
 * [+] gBAM
 * [ ] Audit DB security
 * [ ] p-value global search
@@ -45,12 +49,6 @@ Now (X=done +=WIP _=kickoff ?=?)
 
 => ../issues/systems/octopus
 
-* [ ] GEMMA batch run and precompute
-
-=> ../issues/gemma/lmm-precomputed-scores
-
-* [ ] GEMMA/bulklmm speedups
-* [ ] bulklmm paper
 * [ ] Add R/qtl2 and multi-parent support with Karl (DO and Magic populations)
 * [ ] Fix slow search on Mariadb?
 * [.] GeneNetwork paper
@@ -85,9 +83,6 @@ Later
 
 => ./machine-room.gmi machine room
 
-* [+] move backup dirs on tux01 to a larger partition (from export3 to export2)
-* [.] Check Tony's list and improve search for SNPs and Hs
-* [ ] GeneNetwork consortium (paper & CTC)
 * [ ] Fix issues:
 => https://genenetwork.org/show_trait?trait_id=10441&dataset=HSNIH-PalmerPublish slow mapping
 => http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=2
@@ -108,3 +103,4 @@ Later
 * [X] Set up cgit as a service
 * [X] Fix mariadb index search - need to upgrade mariadb to convert final utf8mb4, see
   => ../issues/slow-sql-query-for-xapian-indexing.gmi
+* [X] Debian/free software issues incl. vcflib work in Zig and release
-- 
cgit v1.2.3