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~>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 | +------------------------+ | GAEJDOANALYSISRESULT | | GAEJDOANNOTATIONS | | GAEJDODATASET | | GAEJDODATASETANALYSIS | | GAEJDODATEANNOTATION | | GAEJDODOUBLEANNOTATION | | GAEJDOINPUTDATALAYER | | GAEJDOLAYERLOCATION | | GAEJDOLAYERLOCATIONS | | GAEJDOLONGANNOTATION | | GAEJDOPROJECT | | GAEJDORESOURCEACCESS | | GAEJDOREVISION | | GAEJDOSCRIPT | | GAEJDOSTRINGANNOTATION | | GAEJDOUSER | | GAEJDOUSERGROUP | | NUCLEUS_TABLES | +------------------------+ 18 rows in set (0.08 sec) mysql> desc GAEJDODATASET; +---------------------+--------------+------+-----+---------+----------------+ | 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 GAEJDODATASET ; +----------+ | 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.
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>ssh fremont
>cd /work/platform/DatasetMetadataLoader
/work/platform/DatasetMetadataLoader> curl http://charon-vpn-010162.fhcrc.org:8080/repo/v1/dataset
{"results":[],"totalNumberOfResults":0,"paging":{}}
/work/platform/DatasetMetadataLoader> ./datasetCsv2Loader.py TheDatasets2.csv charon-vpn-010162.fhcrc.org:8080 AllDatasetLayerLocations.csv
lot of output here . . .
/work/platform/DatasetMetadataLoader> curl http://charon-vpn-010162.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"
}
}
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Notes for the sake of posterity
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