sql: Remove database mapping code.

These tools have been greatly improved and moved to a new home at
https://git.genenetwork.org/arunisaac/dump-genenetwork-database

* sql/map-database.sh, sql/schema-from-in-db-documentation.org,
sql/schema-original.sql, sql/schema.png, sql/schema.sql, sql/schema.svg: New
files.

1 files changed, 0 insertions, 2406 deletions

diff --git a/sql/schema.sql b/sql/schema.sql
deleted file mode 100644
index c37754b..0000000
--- a/sql/schema.sql
+++ /dev/null
@@ -1,2406 +0,0 @@
--- This is a work-in-progress schema for the GeneNetwork database. The
--- GeneNetwork database has no foreign key constraint information. This schema
--- has them manually added. But, the work is not complete, and there may be
--- errors. A visualization of this schema can be found in schema.png and
--- schema.svg.
-
--- MySQL dump 10.16  Distrib 10.1.41-MariaDB, for debian-linux-gnu (x86_64)
---
--- Host: localhost    Database: db_webqtl
--- ------------------------------------------------------
--- Server version	10.5.8-MariaDB-log
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8mb4 */;
-/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
-/*!40103 SET TIME_ZONE='+00:00' */;
-/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
-/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
-/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
-/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
-
---
--- Table structure for table `AccessLog`
---
-
-DROP TABLE IF EXISTS `AccessLog`;
-/*!40101 SET @saved_cs_client     = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `AccessLog` (
-  `id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `accesstime` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  `ip_address` char(20) NOT NULL DEFAULT '0.0.0.0',
-  PRIMARY KEY (`id`)
-) ENGINE=MyISAM AUTO_INCREMENT=1366832 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Table structure for table `AvgMethod`
---
-
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-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `AvgMethod` (
-  `Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `AvgMethodId` int(5) DEFAULT NULL,
-  `Name` char(30) NOT NULL DEFAULT '',
-  `Normalization` varchar(30) DEFAULT NULL,
-  PRIMARY KEY (`Id`)
-) ENGINE=MyISAM AUTO_INCREMENT=28 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Table structure for table `BXDSnpPosition`
---
-
-DROP TABLE IF EXISTS `BXDSnpPosition`;
-/*!40101 SET @saved_cs_client     = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `BXDSnpPosition` (
-  `id` int(11) NOT NULL AUTO_INCREMENT,
-  `Chr` char(2) DEFAULT NULL,
-  `StrainId1` int(11) DEFAULT NULL,
-  `StrainId2` int(11) DEFAULT NULL,
-  `Mb` double DEFAULT NULL,
-  `Mb_2016` double DEFAULT NULL,
-  PRIMARY KEY (`id`),
-  FOREIGN KEY (StrainId1) REFERENCES Strain(Id),
-  FOREIGN KEY (StrainId2) REFERENCES Strain(Id),
-  KEY `BXDSnpPosition` (`Chr`,`StrainId1`,`StrainId2`,`Mb`)
-) ENGINE=MyISAM AUTO_INCREMENT=7791982 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Table structure for table `CaseAttribute`
---
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-/*!40101 SET @saved_cs_client     = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `CaseAttribute` (
-  `Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `Name` varchar(30) NOT NULL DEFAULT '',
-  PRIMARY KEY (`Id`)
-) ENGINE=MyISAM AUTO_INCREMENT=34 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Table structure for table `CaseAttributeXRef`
---
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-CREATE TABLE `CaseAttributeXRef` (
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-  `CaseAttributeId` smallint(5) NOT NULL DEFAULT 0,
-  `Value` varchar(100) NOT NULL DEFAULT '',
-  PRIMARY KEY (`ProbeSetFreezeId`,`StrainId`,`CaseAttributeId`),
-  FOREIGN KEY (ProbeSetFreezeId) REFERENCES ProbeSetFreeze(Id),
-  FOREIGN KEY (StrainId) REFERENCES Strain(Id),
-  FOREIGN KEY (CaseAttributeId) REFERENCES CaseAttribute(Id)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Table structure for table `CaseAttributeXRefNew`
---
-
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-/*!40101 SET @saved_cs_client     = @@character_set_client */;
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-CREATE TABLE `CaseAttributeXRefNew` (
-  `InbredSetId` smallint(5) unsigned NOT NULL DEFAULT 0,
-  `StrainId` int(8) unsigned NOT NULL DEFAULT 0,
-  `CaseAttributeId` smallint(5) NOT NULL DEFAULT 0,
-  `Value` varchar(100) NOT NULL DEFAULT '',
-  PRIMARY KEY (`InbredSetId`,`StrainId`,`CaseAttributeId`),
-  FOREIGN KEY (InbredSetId) REFERENCES InbredSet(InbredSetId),
-  FOREIGN KEY (StrainId) REFERENCES Strain(Id),
-  FOREIGN KEY (CaseAttributeId) REFERENCES CaseAttribute(Id)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Table structure for table `CeleraINFO_mm6`
---
-
-DROP TABLE IF EXISTS `CeleraINFO_mm6`;
-/*!40101 SET @saved_cs_client     = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `CeleraINFO_mm6` (
-  `Id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `SNPID` char(14) NOT NULL DEFAULT '',
-  `chromosome` char(3) DEFAULT NULL,
-  `MB_UCSC` double DEFAULT NULL,
-  `MB_celera` double DEFAULT NULL,
-  `allele_B6` char(4) DEFAULT NULL,
-  `allele_D2` char(4) DEFAULT NULL,
-  `allele_AJ` char(4) DEFAULT NULL,
-  `B6_D2` char(1) DEFAULT NULL,
-  `B6_AJ` char(1) DEFAULT NULL,
-  `D2_AJ` char(1) DEFAULT NULL,
-  `MB_UCSC_OLD` double DEFAULT NULL,
-  `allele_S1` char(4) DEFAULT NULL,
-  `allele_X1` char(4) DEFAULT NULL,
-  `flanking5` char(100) DEFAULT NULL,
-  `flanking3` char(100) DEFAULT NULL,
-  PRIMARY KEY (`Id`),
-  KEY `celeraIndex` (`chromosome`,`MB_celera`),
-  KEY `celeraIndex2` (`chromosome`,`MB_UCSC`),
-  KEY `chromosome_2` (`chromosome`,`MB_UCSC`),
-  KEY `MB_UCSC_2` (`MB_UCSC`,`chromosome`),
-  KEY `SNPID` (`SNPID`)
-) ENGINE=MyISAM AUTO_INCREMENT=3028848 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Table structure for table `Chr_Length`
---
-
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-/*!40101 SET @saved_cs_client     = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `Chr_Length` (
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-  `SpeciesId` smallint(5) unsigned NOT NULL DEFAULT 0,
-  `OrderId` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `Length` int(10) unsigned NOT NULL DEFAULT 0,
-  `Length_2016` int(10) unsigned NOT NULL DEFAULT 0,
-  `Length_mm8` int(10) unsigned DEFAULT NULL,
-  UNIQUE KEY `nameIdx` (`SpeciesId`,`Name`),
-  UNIQUE KEY `SpeciesIdx` (`SpeciesId`,`OrderId`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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---
--- Table structure for table `DBList`
---
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-  `Name` char(50) NOT NULL DEFAULT '',
-  `Code` char(50) DEFAULT NULL,
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-  KEY `DBIndex` (`DBTypeId`,`FreezeId`)
-) ENGINE=MyISAM AUTO_INCREMENT=907 DEFAULT CHARSET=latin1;
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---
--- Table structure for table `DatasetMapInvestigator`
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---
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-  `species` varchar(255) DEFAULT NULL,
-  `cross` varchar(255) DEFAULT NULL,
-  `tissue` varchar(255) DEFAULT NULL,
-  `database` varchar(255) DEFAULT NULL,
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-  `GeoSeries` varchar(30) DEFAULT NULL,
-  `PublicationTitle` longtext DEFAULT NULL,
-  `Summary` longtext DEFAULT NULL,
-  `ExperimentDesign` longtext DEFAULT NULL,
-  `AboutCases` longtext DEFAULT NULL,
-  `AboutTissue` longtext DEFAULT NULL,
-  `AboutPlatform` longtext DEFAULT NULL,
-  `AboutDataProcessing` longtext DEFAULT NULL,
-  `Contributors` longtext DEFAULT NULL,
-  `Citation` longtext DEFAULT NULL,
-  `Acknowledgment` longtext DEFAULT NULL,
-  `Notes` longtext DEFAULT NULL,
-  `InvestigatorId` int(5) NOT NULL,
-  `DatasetStatusId` int(5) NOT NULL,
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-  `Start_2016` int(11) DEFAULT NULL,
-  `End` int(11) NOT NULL,
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-  `Strand` int(11) NOT NULL,
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---
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-  `genes` text DEFAULT NULL,
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-) ENGINE=MyISAM AUTO_INCREMENT=17510 DEFAULT CHARSET=latin1;
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---
--- Table structure for table `Genbank`
---
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-  `Sequence` text DEFAULT NULL,
-  `SpeciesId` smallint(5) unsigned NOT NULL DEFAULT 0,
-  PRIMARY KEY (`Id`),
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-  KEY `Id` (`Id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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---
--- Table structure for table `GeneCategory`
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---
--- Table structure for table `GeneChip`
---
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-CREATE TABLE `GeneChip` (
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-  `GeneChipId` int(5) DEFAULT NULL,
-  `GeneChipName` varchar(200) DEFAULT NULL,
-  `Name` char(30) NOT NULL DEFAULT '',
-  `GeoPlatform` char(15) DEFAULT NULL,
-  `Title` varchar(100) DEFAULT NULL,
-  `SpeciesId` int(5) DEFAULT 1,
-  `GO_tree_value` varchar(50) DEFAULT NULL,
-  PRIMARY KEY (`Id`),
-  FOREIGN KEY (SpeciesId) REFERENCES Species(SpeciesId)
-) ENGINE=MyISAM AUTO_INCREMENT=67 DEFAULT CHARSET=latin1;
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---
--- Table structure for table `GeneChipEnsemblXRef`
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-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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---
--- Table structure for table `GeneIDXRef`
---
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-CREATE TABLE `GeneIDXRef` (
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-  `rat` int(11) NOT NULL DEFAULT 0,
-  `human` int(11) NOT NULL DEFAULT 0,
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-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
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---
--- Table structure for table `GeneList`
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-  `Id` int(10) unsigned NOT NULL AUTO_INCREMENT,
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-  `GeneDescription` text DEFAULT NULL,
-  `Chromosome` varchar(10) DEFAULT NULL,
-  `TxStart` double DEFAULT NULL,
-  `TxStart_2016` double DEFAULT NULL,
-  `TxEnd` double DEFAULT NULL,
-  `TxEnd_2016` double DEFAULT NULL,
-  `Strand` char(1) DEFAULT NULL,
-  `GeneID` varchar(10) DEFAULT NULL,
-  `NM_ID` varchar(15) DEFAULT NULL,
-  `kgID` varchar(10) DEFAULT NULL,
-  `GenBankID` varchar(15) DEFAULT NULL,
-  `UnigenID` varchar(15) DEFAULT NULL,
-  `ProteinID` varchar(15) DEFAULT NULL,
-  `AlignID` varchar(10) DEFAULT NULL,
-  `exonCount` int(7) NOT NULL DEFAULT 0,
-  `exonStarts` text DEFAULT NULL,
-  `exonEnds` text DEFAULT NULL,
-  `cdsStart` double DEFAULT NULL,
-  `cdsStart_2016` double DEFAULT NULL,
-  `cdsEnd` double DEFAULT NULL,
-  `cdsEnd_2016` double DEFAULT NULL,
-  `TxStart_mm8` double DEFAULT NULL,
-  `TxEnd_mm8` double DEFAULT NULL,
-  `Strand_mm8` char(1) DEFAULT NULL,
-  `exonCount_mm8` int(7) DEFAULT NULL,
-  `exonStarts_mm8` text DEFAULT NULL,
-  `exonEnds_mm8` text DEFAULT NULL,
-  `cdsStart_mm8` double DEFAULT NULL,
-  `cdsEnd_mm8` double DEFAULT NULL,
-  `Chromosome_mm8` varchar(10) DEFAULT NULL,
-  `Info_mm9` text DEFAULT NULL,
-  `RGD_ID` int(10) DEFAULT NULL,
-  UNIQUE KEY `geneId` (`SpeciesId`,`Id`),
-  FOREIGN KEY (SpeciesId) REFERENCES Species(SpeciesId),
-  FOREIGN KEY (GenBankID) REFERENCES Genbank(Id),
-  KEY `geneSymbol` (`GeneSymbol`),
-  KEY `geneSymbol2` (`SpeciesId`,`GeneSymbol`),
-  KEY `Loc1` (`SpeciesId`,`Chromosome`,`TxStart`),
-  KEY `Loc2` (`SpeciesId`,`Chromosome`,`TxEnd`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Table structure for table `GeneList_rn3`
---
-
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-  `ProbeSet` varchar(16) DEFAULT NULL,
-  `geneSymbol` varchar(15) DEFAULT NULL,
-  `geneID` varchar(10) DEFAULT NULL,
-  `kgID` varchar(10) DEFAULT NULL,
-  `geneDescription` text DEFAULT NULL,
-  `genBankID` varchar(15) DEFAULT NULL,
-  `unigenID` varchar(15) DEFAULT NULL,
-  `score` int(4) DEFAULT NULL,
-  `qStart` int(3) DEFAULT NULL,
-  `qEnd` int(3) DEFAULT NULL,
-  `qSize` int(3) DEFAULT NULL,
-  `identity` varchar(7) DEFAULT NULL,
-  `chromosome` varchar(8) DEFAULT NULL,
-  `strand` char(1) DEFAULT NULL,
-  `txStart` double DEFAULT NULL,
-  `txEnd` double DEFAULT NULL,
-  `txSize` double DEFAULT NULL,
-  `span` int(7) DEFAULT NULL,
-  `specificity` double DEFAULT NULL,
-  `sequence` text DEFAULT NULL,
-  `flag` int(1) DEFAULT NULL,
-  PRIMARY KEY (`id`),
-  KEY `geneSymbol` (`geneSymbol`),
-  KEY `Loc1` (`chromosome`,`txStart`),
-  KEY `Loc2` (`chromosome`,`txEnd`)
-) ENGINE=MyISAM AUTO_INCREMENT=14917 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Table structure for table `GeneList_rn33`
---
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-DROP TABLE IF EXISTS `GeneList_rn33`;
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--- Dump completed on 2021-07-14  5:26:53