Hello, I'm importing a schema into v0.8rc6 that contains a number of m*n relationships. Typically, I would have 3 tables, say one for Proteins, one for EC_Numbers, and one that maps the previous 2 using the protein_id and the ec_number. For some reason, the 3 tables are imported as 3 different data sources (FKs are properly defined in the source schema), but this is more a cosmetic issue. The problem is than I can't seem to be able to integrate the 3 sources together when creating a report. Following the tutorial, I managed to link the tables Protein and Map. And Map and EC_Number. But not all 3 together as it generates an error on the web interface. From the log (see below), it seems that the SQL query that is generated is incomplete. So given a protein, I can get the corresponding EC number, but not the related data from the EC table. Similarly, given an EC, I can get the associated protein IDs, but the protein details. So I was wondering if this was a configuration issue, a bug or simply not supported yet. Thanks a lot! Thomas
-- Thomas Triplet, Ph.D. http://www.thomastriplet.net Centre for Structural and Functional Genomics Concordia University 7141 West Sherbrooke St Montreal QC H4B 1R6 2011-10-25 12:27:23,047 INFO [901833818@qtp-2099901365-8:Log.java:164]: Incoming XML query: <!DOCTYPE Query><Query client="biomartclient" processor="TSVX" limit="1000" header="1"><Dataset name="proteomics" config="Proteins"><Filter name="Protein__name_101" value="gw1.3.876.1"/><Attribute name="Protein__proteinWID_101"/><Attribute name="Protein__name_101"/><Attribute name="Protein__sequence_101"/><Attribute name="Protein2EcNode__ecNodeWID_103"/><Attribute name="EcNode__EcTransfert__ecNumber_101"/></Dataset></Query> Source: SELECT "biomart"."proteomics"."Protein"."proteinWID", "biomart"."proteomics"."Protein2EcNode"."ecNodeWID", "biomart"."proteomics"."Protein"."proteinWID", "biomart"."proteomics"."Protein"."name", "biomart"."proteomics"."Protein"."sequence" FROM "biomart"."proteomics"."Protein" WHERE "biomart"."proteomics"."Protein"."name"='gw1.3.876.1' org.postgresql.util.PSQLException: ERROR: missing FROM-clause entry for table "Protein2EcNode" Position: 55 at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2102) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1835) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:500) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:388) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:273) at org.biomart.queryEngine.SubQuery.executeDatabaseQuery(SubQuery.java:746) at org.biomart.queryEngine.SubQuery.executeQuery(SubQuery.java:717) at org.biomart.queryEngine.QueryRunnerThread.recurseSubQueries(QueryRunnerThread.java:171) at org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:73) at org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:37) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:679) 2011-10-25 12:27:23,106 INFO [901833818@qtp-2099901365-8:Log.java:164]: Total query time is 51 ms
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