diff options
Diffstat (limited to 'doc/database.org')
| -rw-r--r-- | doc/database.org | 33 |
1 files changed, 31 insertions, 2 deletions
diff --git a/doc/database.org b/doc/database.org index c20e4564..d4c04848 100644 --- a/doc/database.org +++ b/doc/database.org @@ -490,7 +490,6 @@ select count(*) from ProbeSet limit 5; 2 rows in set (0.00 sec) - ** ProbeSetData Probedata - main molecular data. Probesets, metabolome, @@ -661,7 +660,36 @@ move into NoSQL. There is plenty redundancy in that table now. I know it is going to be a pain to reorganize the database, but if we want to use it in the long run we are going to have to simplify it. +** ProbeSetFreeze and ProbeFreeze (/dataset/name.json) + +GN_SERVER: /dataset/HC_M2_0606_P.json + +ProbesetFreeze contains DataSet information, such as name, fullname of +datasets, as well as whether they are public and how the data is +scaled: + +select * from ProbeSetFreeze; +| Id | ProbeFreezeId | AvgID | Name | Name2 | FullName | ShortName | CreateTime | OrderList | public | confidentiality | AuthorisedUsers | DataScale | +| 112 | 30 | 2 | HC_M2_0606_P | Hippocampus_M430_V2_BXD_PDNN_Jun06 | Hippocampus Consortium M430v2 (Jun06) PDNN | Hippocampus M430v2 BXD 06/06 PDNN | 2006-06-23 | NULL | 2 | 0 | NULL | log2 | + +Another table contains a tissue reference and a back reference to the cross +type: + +select * from ProbeFreeze; +| Id | ProbeFreezeId | ChipId | TissueId | Name | FullName | ShortName | CreateTime | InbredSetId | +| 30 | 30 | 4 | 9 | Hippocampus Consortium M430v2 Probe (Jun06) | | | 2006-07-07 | 1 | + +NOTE: these tables can probably be merged into one. +show indexes from ProbeSetFreeze; ++----------------+------------+-----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+ +| Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | Index_comment | ++----------------+------------+-----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+ +| ProbeSetFreeze | 0 | PRIMARY | 1 | Id | A | 2 | NULL | NULL | | BTREE | | | +| ProbeSetFreeze | 0 | FullName | 1 | FullName | A | 2 | NULL | NULL | | BTREE | | | +| ProbeSetFreeze | 0 | Name | 1 | Name | A | 2 | NULL | NULL | YES | BTREE | | | +| ProbeSetFreeze | 1 | NameIndex | 1 | Name2 | A | 2 | NULL | NULL | | BTREE | | | ++----------------+------------+-----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+ ** Publication and publishdata (all pheno) @@ -735,7 +763,8 @@ What happens at the main search menu can be emulated with curl. : curl "http://localhost:5003/search?species=mouse&group=BXD&ppocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=&search_terms_and=MEAN%3D%2815+16%29+LRS%3D%2823+46%29+&FormID=searchResult" -the first SQL query checks whether a dataset is confidential or not: +the first SQL query checks whether a dataset is confidential or not ayd +fetches full name info INFO:base.data_set:.sql: geno_mrna_confidentiality: u'SELECT Id, Name, FullName, confidentiality,AuthorisedUsers FROM ProbeSetFreeze WHERE |