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I discovered a configuration issue in our current live Biomart at http://www.phytozome.net/biomart/martview Select the Phytozome 7.0 Families dataset, enter a valid transcript ID (18801347 is my test case that should return 7 gene clusters) in Filters -> Clusters -> Limit to Clusters With -> PAC Transcript ID. Click on Results and get an exception error that boils down to: Table 'phytozome_mart_v7_1.members__dm' doesn't exist I can query directly in MySQL and get a result: mysql> select * from phytozome_clusters__members__dm where member_transcript_id = 18801347; +----------------+-----------------+----------------------+------------+ | cluster_id_key | member_proteome | member_transcript_id | is_founder | +----------------+-----------------+----------------------+------------+ | 28656658 | Egrandis | 18801347 | 1 | | 28733888 | Egrandis | 18801347 | 1 | | 28779242 | Egrandis | 18801347 | 1 | | 28937929 | Egrandis | 18801347 | 1 | | 29033551 | Egrandis | 18801347 | 1 | | 29126997 | Egrandis | 18801347 | 1 | | 28307459 | Egrandis | 18801347 | 1 | +----------------+-----------------+----------------------+------------+ 7 rows in set (0.09 sec) In MartEditor, this filter is set with tableConstraint "members__dm", complete with the correct number of underscores. After turning on Log4Perl debugging, I see that the SQL statement for this join is generated as: SELECT phytozome_clusters__members__dm.member_transcript_id, main.cluster_id_key, main.cluster_name, main.cluster_node FROM phytozome_mart_v7_1_1.members__dm, phytozome_mart_v7_1_1.phytozome_clusters__members__dm, phytozome_mart_v7_1_1.phytozome_clusters__clusters__main main WHERE (members__dm.member_transcript_id = '18801347') AND main.cluster_id_key=members__dm.cluster_id_key AND main.cluster_id_key=phytozome_clusters__members__dm.cluster_id_key LIMIT 200 Another example join filter that is working is the Annotation filter for KOG Letter using Filters -> Annotation Filters -> Limit to Clusters with KOG Letters and an example KOG letter of Y generates this correct SQL and displays results: SELECT phytozome_clusters__members__dm.member_transcript_id, main.cluster_id_key, main.cluster_name, main.cluster_node FROM phytozome_mart_v7_1_1.phytozome_clusters__kog_letter__dm, phytozome_mart_v7_1_1.phytozome_clusters__members__dm, phytozome_mart_v7_1_1.phytozome_clusters__clusters__main main WHERE (phytozome_clusters__kog_letter__dm.kog_letter = 'Y') AND main.cluster_id_key=phytozome_clusters__kog_letter__dm.cluster_id_key AND main.cluster_id_key=phytozome_clusters__members__dm.cluster_id_key LIMIT 200 tableConstraint in MartEditor for the Filter is "kog_letter__dm" When I update the top broken example on a development copy of this dataset instance to change the tableConstraint from "members__dm" to the full table name "phytozome_clusters__members__dm" I get successful results from the same example PAC Transcript ID 18801347, with SQL generated as: SELECT phytozome_clusters__members__dm.member_transcript_id, main.cluster_id_key, main.cluster_name, main.cluster_node FROM phytozome_mart_v7_1_1.phytozome_clusters__members__dm, phytozome_mart_v7_1_1.phytozome_clusters__clusters__main main WHERE (phytozome_clusters__members__dm.member_transcript_id = '18801347') AND main.cluster_id_key=phytozome_clusters__members__dm.cluster_id_key LIMIT 200 Could there be conflict with some other section of the MartEditor config? We are still running v0.6, but I can reproduce the same error in a dev installation of v0.7 as well. Thanks, -- Richard D. Hayes, Ph.D. Joint Genome Institute / Lawrence Berkeley National Lab http://www.phytozome.net
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