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authorPjotr Prins2016-06-26 10:40:01 +0000
committerPjotr Prins2016-06-26 10:40:01 +0000
commita1000128f0c759d13ff79360922cedab387ca3f8 (patch)
treeda57052dceb65b0ea31c5f3436d4472cd9f184bc /doc/database.org
parent7d6a2dcece8df158b52caf04b3f0dbde23181c93 (diff)
downloadgenenetwork2-a1000128f0c759d13ff79360922cedab387ca3f8.tar.gz
doc: ProbeFreeze and ProbeSetFreeze
Diffstat (limited to 'doc/database.org')
-rw-r--r--doc/database.org33
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