20710d4500737f2022bed8e3935ee8428fd88702 kent Wed Sep 4 08:05:28 2019 -0700 Adding test files and script. Test script isn't perfect yet, it's a little tricky working with stuff that modifies a database like this. diff --git src/hg/sqlUpdateRelated/tests/inDb.sql src/hg/sqlUpdateRelated/tests/inDb.sql new file mode 100644 index 0000000..76cfb3e --- /dev/null +++ src/hg/sqlUpdateRelated/tests/inDb.sql @@ -0,0 +1,1914 @@ +-- MySQL dump 10.15 Distrib 10.0.36-MariaDB, for Linux (x86_64) +-- +-- Host: localhost Database: hcat +-- ------------------------------------------------------ +-- Server version 10.0.36-MariaDB + +/*!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 utf8 */; +/*!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 `hcat_assaytech` +-- + +DROP TABLE IF EXISTS `hcat_assaytech`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `hcat_assaytech` ( + `id` int(11) NOT NULL AUTO_INCREMENT, + `short_name` varchar(50) NOT NULL, + `description` varchar(250) NOT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `hcat_assaytech_short_name_fc7a5a4b_uniq` (`short_name`) +) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `hcat_assaytech` +-- + +LOCK TABLES `hcat_assaytech` WRITE; +/*!40000 ALTER TABLE `hcat_assaytech` DISABLE KEYS */; +INSERT INTO `hcat_assaytech` VALUES (1,'10x Chromium V2','10x single-cell sequencing Chromium V2 chemistry'),(2,'smart-seq2 PE','smart-seq2 library prep paired end sequencing of single cells'),(3,'smart-seq2 SE','smart-seq2 library prep single ended sequencing of single cells'),(4,'bulk RNA','bulk RNA sequencing of some sort, not single cell'),(5,'scATAC-seq','Single cell ATAC-seq'),(6,'bulk DNA','sequencing of bulk, non-single-cell, DNA'); 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Further research advised.'),(5,'unconsented','Don\'t work on unconsented stuff, it\'ll break your heart'),(6,'human no sequence','Concented to share expression matrix and higher level stuff but not reads.'); +/*!40000 ALTER TABLE `hcat_consent` ENABLE KEYS */; +UNLOCK TABLES; + +-- +-- Table structure for table `hcat_consent_comments` +-- + +DROP TABLE IF EXISTS `hcat_consent_comments`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `hcat_consent_comments` ( + `id` int(11) NOT NULL AUTO_INCREMENT, + `consent_id` int(11) NOT NULL, + `comment_id` int(11) NOT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `hcat_consent_commen_consent_id_com_76d4e001_uniq` (`consent_id`,`comment_id`), + KEY `hcat_consent_comments_consent_id_e5172468` (`consent_id`), + KEY `hcat_consent_comments_comment_id_44f3bb6f` (`comment_id`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `hcat_consent_comments` +-- + +LOCK TABLES `hcat_consent_comments` WRITE; 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+/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `hcat_project` +-- + +LOCK TABLES `hcat_project` WRITE; +/*!40000 ALTER TABLE `hcat_project` DISABLE KEYS */; +INSERT INTO `hcat_project` VALUES (1,'HumanInnateLymphoidCells','Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs)','Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs) from three independent tonsil donors.',5,7,5,1,50000,1,NULL,'','','uploads/project/GSE70580.xlsx','','','','GSE70580',NULL,NULL,NULL,NULL,NULL,NULL,'2019-08-31',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,6,6),(2,'TabulaMuris','A single cell atlas of the mouse','This is a large study combining several single cell sequencing techniques run out of the biohub.',7,NULL,4,2,1000000,2,NULL,'','','','','','','Tabula Muris',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,7),(3,'RevisedAirwayEpithelialHierarchy','A revised airway epithelial hierarchy includes CFTR-expressing ionocytes','Airways conduct gases to the lung and are disease sites of asthma and cystic fibrosis. Here we study the cellular composition and hierarchy of the mouse tracheal epithelium by single-cell RNA-sequencing (scRNA-seq) and in vivo lineage tracing. We identify a rare cell type, the Foxi1+ pulmonary ionocyte; functional variations in club cells by proximodistal location; a distinct cell type in high turnover squamous epithelial structures that we term \'hillocks\'; and disease-relevant subsets of tuft and goblet cells. We developed \'pulse-seq\' , combining scRNA-seq and lineage tracing, to show that tuft, neuroendocrine and ionocyte cells are continually and directly replenished by basal progenitor cells. Ionocytes are the major source of transcripts of the cystic fibrosis transmembrane conductance regulator in both mouse (Cftr) and human (CFTR). Knockout of Foxi1 in mouse ionocytes causes loss of Cftr expression and disrupts airway fluid and mucus physiology, phenotypes that characterize cystic fibrosis. By associating cell-type-specific expression programs with key disease genes, we establish a new cellular narrative for airways disease.',5,7,4,2,0,1,NULL,'','','uploads/project/GSE103354_s8tqNaC.xlsx','','','','GSE103354',NULL,NULL,NULL,NULL,NULL,NULL,'2019-08-31',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,4,4),(5,'humphreysKidneyOrganoids1','Ben Humphreys Kidney Organoid snRNA-seq','Single nuclei rna-seq was performed on kidney organoids...',5,NULL,3,NULL,0,2,NULL,'','','','','','','',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,4,4); +/*!40000 ALTER TABLE `hcat_project` ENABLE KEYS */; +UNLOCK TABLES; + +-- +-- Table structure for table `hcat_project_assay_tech` +-- + +DROP TABLE IF EXISTS `hcat_project_assay_tech`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `hcat_project_assay_tech` ( + `id` int(11) NOT NULL AUTO_INCREMENT, + `project_id` int(11) NOT NULL, + `assaytech_id` int(11) NOT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `hcat_project_assay_tech_project_id_assaytech_id_099970cc_uniq` (`project_id`,`assaytech_id`), + KEY `hcat_project_assay_tech_project_id_0d1877f7` (`project_id`), + KEY `hcat_project_assay_tech_assaytech_id_1a961e03` (`assaytech_id`) +) ENGINE=MyISAM AUTO_INCREMENT=6 DEFAULT CHARSET=latin1; 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Aligning reads, registering images, etc.'),(10,'cell matrix','a matrix that relates cell to cell measurements, typically RNA levels'),(11,'cell clusters','Have a mechanically generated typology of cells inferred from the data'),(12,'cell types','Have a manually curated set of cell types relevant to this data set'),(13,'integrated analysis','work has been done integrating this with other HCA data sets'); +/*!40000 ALTER TABLE `hcat_projectstate` ENABLE KEYS */; +UNLOCK TABLES; + +-- +-- Table structure for table `hcat_projectstate_comments` +-- + +DROP TABLE IF EXISTS `hcat_projectstate_comments`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `hcat_projectstate_comments` ( + `id` int(11) NOT NULL AUTO_INCREMENT, + `projectstate_id` int(11) NOT NULL, + `comment_id` int(11) NOT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `hcat_projectstate_c_projectstate_id_voc_93194194_uniq` (`projectstate_id`,`comment_id`), + KEY `hcat_projectstate_comments_projectstate_id_c5520db9` (`projectstate_id`), + KEY `hcat_projectstate_comments_comment_id_6343cefb` (`comment_id`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; 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