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Code Block
~>hostname
fremont
~>/usr/bin/mysql -u platform -h repo.c5sxx7pot9i8.us-east-1.rds.amazonaws.com -p
Enter password:
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 6212
Server version: 5.5.8-log Source distribution

Copyright (c) 2000, 2010, Oracle and/or its affiliates. All rights reserved.
This software comes with ABSOLUTELY NO WARRANTY. This is free software,
and you are welcome to modify and redistribute it under the GPL v2 license

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| innodb             |
| mysql              |
| performance_schema |
| repositorydb       |
+--------------------+
5 rows in set (0.07 sec)

mysql> use repositorydb;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

showDatabase changed
mysql> show tables;
+------------------------+
| Tables_in_repositorydb |
+------------------------+
| GAEJDOANALYSISRESULTJDOANALYSISRESULT   |
| GAEJDOANNOTATIONSJDOANNOTATIONS      |
| GAEJDODATASETJDODATASET          |
| GAEJDODATASETANALYSISJDODATASETANALYSIS  |
| GAEJDODATEANNOTATIONJDODATEANNOTATION   |
| GAEJDODOUBLEANNOTATIONJDODOUBLEANNOTATION |
| GAEJDOINPUTDATALAYERJDOINPUTDATALAYER   |
| GAEJDOLAYERLOCATIONJDOLAYERLOCATION    |
| GAEJDOLAYERLOCATIONSJDOLAYERLOCATIONS   |
| GAEJDOLONGANNOTATIONJDOLONGANNOTATION   |
| GAEJDOPROJECTJDOPROJECT          |
| GAEJDORESOURCEACCESSJDORESOURCEACCESS   |
| GAEJDOREVISIONJDOREVISION         |
| GAEJDOSCRIPTJDOSCRIPT           |
| GAEJDOSTRINGANNOTATIONJDOSTRINGANNOTATION |
| GAEJDOUSERJDOUSER             |
| GAEJDOUSERGROUPJDOUSERGROUP        |
| NUCLEUS_TABLES         |
+------------------------+
18 rows in set (0.08 sec)

mysql> desc GAEJDODATASETJDODATASET;
+---------------------+--------------+------+-----+---------+----------------+
| Field               | Type         | Null | Key | Default | Extra          |
+---------------------+--------------+------+-----+---------+----------------+
| ID                  | bigint(20)   | NO   | PRI | NULL    | auto_increment |
| ANNOTATIONS_ID_OID  | bigint(20)   | YES  | MUL | NULL    |                |
| CREATION_DATE       | datetime     | YES  |     | NULL    |                |
| CREATOR             | varchar(256) | YES  |     | NULL    |                |
| DESCRIPTION         | varchar(256) | YES  |     | NULL    |                |
| NAME                | varchar(256) | YES  |     | NULL    |                |
| NEXT_VERSION_ID_OID | bigint(20)   | YES  | MUL | NULL    |                |
| RELEASE_DATE        | datetime     | YES  |     | NULL    |                |
| REVISION_ID_OID     | bigint(20)   | YES  | MUL | NULL    |                |
| STATUS              | varchar(256) | YES  |     | NULL    |                |
+---------------------+--------------+------+-----+---------+----------------+
10 rows in set (0.07 sec)

mysql> select count(*) from GAEJDODATASETJDODATASET ;
+----------+
| count(*) |
+----------+
|      114 |
+----------+
1 row in set (0.08 sec)

mysql> quit

...

How to load data into an empty repository service

This is a bit of a mess right now, but it does do the trick. Expect this to get better over time. You can use this to load data into a repository service whether it is running on beanstalk or locally on your laptop. You can run datasetCsvLoader.py -h and datasetNuker.py -h to see more documentation.

Code Block
>ssh fremont
>cd /work/platform/DatasetMetadataLoader
/work/platform/DatasetMetadataLoader> curl http://dhcp149222.fhcrc.org:8080/repo/v1/dataset
{"results":[],"totalNumberOfResults":0,"paging":{}}
/work/platform/DatasetMetadataLoader> ./datasetCsv2LoaderdatasetCsvLoader.py --debug -d TheDatasets2.csv -l AllDatasetLayerLocations.csv -e dhcp149222.fhcrc.org:8080
lot of output here . . .
/work/platform/DatasetMetadataLoader> curl http://dhcp149222.fhcrc.org:8080/repo/v1/dataset?limit=1
{
   "results":[
      {
         "name":"Gastric Cancer ACRG",
         "annotations":"/repo/v1/dataset/0/annotations",
         "id":"0",
         "version":"0.0.1",
         "creator":"Asian Cancer Research Group, Inc., (ACRG)",
         "description":null,
         "creationDate":1299375144172,
         "status":"Future",
         "uri":"/repo/v1/dataset/0",
         "etag":"384011750",
         "releaseDate":null,
         "layer":"/repo/v1/dataset/0/layer",
         "hasExpressionData":false,
         "hasGeneticData":false,
         "hasClinicalData":false
      }
   ],
   "totalNumberOfResults":114,
   "paging":{
      "next":"/repo/v1/dataset?offset=2&limit=1"
   }
}

...