Re: [XMLPipeDB-developer] Eclipse workspace
Brought to you by:
kdahlquist,
zugzugglug
From: Richard B. <rbr...@gm...> - 2011-08-24 02:59:11
|
Thanks for the thoughts on the SQL issue - I should have picked up on the single quotes for the id values =/ I'm back up and running as I mentioned, but i'm having difficulties exporting from a multispecies Postgres db with two species selected. I know I was able to get through the export process before (its how I knew the info table had 3 species names instead of the expected 2) so I dumped the last few changes and reverted back to the latest repository version. I attempted a two species selected export again and it still failed with the error logged below. Now I'm running a single species export from the multispecies db to check and see if I can at least get that without error. Can you shed any light on this for me please? Richard ------------------------------------------------------------------------------------------------------------------------------------------------------------ 0 [main] INFO edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder - ***** GenMAPP Builder started at: 6:25:55 PM PDT 69841 [AWT-EventQueue-0] WARN net.sf.ehcache.config.Configurator - No configuration found. Configuring ehcache from ehcache-failsafe.xml found in the classpath: ja r:file:/C:/Users/rbrous/workspace/xmlpipedb-gmbuilder-brous-laptop/dist/lib/ehcache-1.1.jar!/ehcache-failsafe.xml 70980 [AWT-EventQueue-0] INFO edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder - Getting DB column Pseudomonas aeruginosa 78530 [AWT-EventQueue-0] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ConnectionManager - Using database connection string: jdbc:odbc:Driver={Microsoft Access Driver (*.mdb)};DBQ=C:\Users\rbrous\workspace\xmlpipedb-gmbuilder-brous-laptop\dist\GeneMAPPBuilder.db;DriverID=22;READONLY=false} 137296 [AWT-EventQueue-0] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - System Table: [Pfam] System Code: [Pf] 137296 [AWT-EventQueue-0] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - System Table: [RefSeq] System Code: [Q] 137296 [AWT-EventQueue-0] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - System Table: [GeneId] System Code: [L] 137296 [AWT-EventQueue-0] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - System Table: [InterPro] System Code: [I] 137296 [AWT-EventQueue-0] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - System Table: [PDB] System Code: [Pd] 137296 [AWT-EventQueue-0] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - System Table: [EMBL] System Code: [Em] 137296 [AWT-EventQueue-0] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - System Codes: [[S, T, N, Em, I, L, Pd, Pf, Q]] 137296 [AWT-EventQueue-0] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - Default Display Order: [|S|T|N|Em|I|L|Pd|Pf|Q|] 138450 [Thread-4] WARN edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Export Started at: 6:28:13 PM PDT 138450 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Starting GeneOntology export... 138466 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ConnectionManager - Using database connection string: jdbc:odbc:Driver={Microsoft Access Driver (*.mdb)};DBQ=C:\Users\rbrous\Desktop\Multispecies GDB compare\multispecies testing\3 - both\Pa-Std_20110823.gdb;DriverID=22;READONLY=false} 138513 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - Populating UniProt-GO table... 138513 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - creating: "UniProt-GeneOntology" 152506 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - Populating GeneOntology table... 152506 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - creating: GeneOntology 216591 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - Populating GeneOntologyTree... 216591 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - creating: GeneOntologyTree 366320 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - Populating GeneOntologyCount... 366320 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - creating: GeneOntologyCount 367505 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - Populating UniProt-GO count... 367802 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - creating: "UniProt-GOCount" 2984800 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - done! 2984800 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Finished GeneOntology export... 2984800 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Starting first pass table creation... 2984816 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Getting first-pass table managers 2984816 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing tables - Info table... 2984816 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start getInfoTableManger() 2984816 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Processing 1 rows 2984816 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Insert Count: [1] 2984816 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Update Count: [0] 2984816 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Flushing tables... 2984816 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of records to process: sqlBuffer.size():: 1 2984816 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of records to process: sqlBuffer.toArray().length:: 1 2984816 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of successful passes through for loop: [1] 2984831 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start getRelationsTableManager() 2984831 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing tables - Relations table... 2984847 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Processing 26 rows 2984847 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Insert Count: [26] 2984847 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Update Count: [0] 2984847 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Flushing tables... 2984847 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of records to process: sqlBuffer.size():: 26 2984847 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of records to process: sqlBuffer.toArray().length:: 26 2984862 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of successful passes through for loop: [26] 2984862 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start getOtherTableManager() 2984862 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing tables - Other table... 2984862 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Processing 0 rows 2984862 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Insert Count: [0] 2984862 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Update Count: [0] 2984878 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Flushing tables... 2984878 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start getSystemsTableManager() 2984878 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing tables - Systems table... 2984878 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Processing 10 rows 2984894 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Insert Count: [0] 2984894 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Update Count: [10] 2984894 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Flushing tables... 2984894 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of records to process: sqlBuffer.size():: 10 2984894 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of records to process: sqlBuffer.toArray().length:: 10 2984909 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of successful passes through for loop: [10] 2984909 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start getPrimarySystemTableManager() 2984909 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing tables - Primary System table... 2985034 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - SQL Query: [SELECT entrytype_accession.entrytype_accession_hjid, entrytype_accession.hjvalue FROM entrytype_accession INNER JOIN entrytype ON (entrytype_accession.e ntrytype_accession_hjid = entrytype.hjid) INNER JOIN organismtype ON (entrytype.organism = organismtype.hjid) INNER JOIN dbreferencetype ON (organismtype.hjid = dbr eferencetype.organismtype_dbreference_hjid) WHERE entrytype_accession_hjindex = 0 AND dbreferencetype.type LIKE '%NCBI Taxonomy%' AND dbreferencetype.id = ?] 2990104 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - Total Records: [5558] 2990104 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - Step 1 - Number of rows in TM: [5558] 2990104 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - SQL Query: [SELECT hjvalue FROM entrytype_name WHERE entrytype_name_hjid = ?] 3054220 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - End of Method - Number of rows in TM: [5558] 3054220 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Create Table in GDB. Table Name: [UniProt] 3054220 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Processing 5558 rows 3054251 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Insert Count: [5558] 3054251 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Update Count: [0] 3054251 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Flushing tables... 3054251 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of records to process: sqlBuffer.size():: 5559 3054251 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of records to process: sqlBuffer.toArray().length:: 5559 3057512 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of successful passes through for loop: [5559] 3057512 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start getSystemTableManager() 3057512 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing tables - System tables... 3057512 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - systemTable.getKey(): Pfam 3057512 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - getSystemTableManager(): for loop: systemTable.getKey() = Pfa m 3057512 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - getSystemTableManager(): for loop: Pfam is not in the list of DatabaseSpecificSystemTables or SpeciesSpecificSystemTables. 3057512 [Thread-4] INFO edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile - getSystemTableManager(): query used: SELECT distinct id FROM dbreferencetype INNER JOIN (SELECT entrytype.hjid FROM entrytype INNER JOIN organismtype ON (entrytype.organism = organismtype.hjid) INNER JOIN dbreferencetype ON(d breferencetype.organismtype_dbreference_hjid = organismtype.hjid) WHERE dbreferencetype.type = 'NCBI Taxonomy' and (id = ? or id = ?)) as species_entry on dbrefere ncetype.entrytype_dbreference_hjid = species_entry.hjid where type = ? 3057512 [Thread-4] FATAL edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportPanel5Descriptor - Export problem org.postgresql.util.PSQLException: No value specified for parameter 3. at org.postgresql.core.v3.SimpleParameterList.checkAllParametersSet(SimpleParameterList.java:134) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:179) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:437) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:353) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:257) at edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile.getSystemTableManager(UniProtDatabaseProfile.java:587) at edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP.export(ExportToGenMAPP.java:152) at edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportPanel5Descriptor$1.run(ExportPanel5Descriptor.java:90) On Tue, Aug 23, 2011 at 9:36 AM, John David N. Dionisio <do...@lm...>wrote: > Hi Rich, > > Good to hear that Clean worked! Keep that in mind in case Eclipse freaks > again :) > > For SQL, check the table definition --- I believe id is actually a string > (varchar). In that case, you need to enclose the values in quotes (i.e., id > = '287'). (recall that the Java code used setString for these, not setInt > nor setLong). > > > John David N. Dionisio, PhD > Associate Professor, Computer Science > Loyola Marymount University > > > On Aug 23, 2011, at 6:10 AM, Richard Brous <rbr...@gm...> wrote: > > Project > Clean worked like magic thank goodness!!!! > > I retraced my steps and was adding logging to DatabaseProfile.java when all > went haywire. > > But I'm back on track and adding the logging back in again to try and catch > that extra loop in Info table. > > > ------------------------------------------------------------------------------------------------------ > > Also I still need help with the sql: > > > SELECT distinct id FROM dbreferencetype > INNER JOIN (SELECT entrytype.hjid FROM entrytype > INNER JOIN organismtype ON (entrytype.organism = organismtype.hjid) > INNER JOIN dbreferencetype > ON(dbreferencetype.organismtype_dbreference_hjid = organismtype.hjid) > WHERE dbreferencetype.type = 'NCBI Taxonomy' and (id = 287 or id = > 282458)) > as species_entry on dbreferencetype.entrytype_dbreference_hjid = > species_entry.hjid where type = 'OrderedLocusNames'; > > > When I attempt to run this PGAdmin I get the following error: > > ERROR: operator does not exist: character varying = integer > LINE 5: ...RE dbreferencetype.type = 'NCBI Taxonomy' and (id = 287 or i... > > I'm not quite sure what this is telling me. > > Thanks! > > Richard > > > On Mon, Aug 22, 2011 at 10:07 PM, John David N. Dionisio <do...@lm...>wrote: > > >> Hi Rich, >> >> I'm all updated and compiling OK on my end. So my guess is that the >> directory where Eclipse stores your build products (typically ./bin/) is >> messed up somehow. Try cleaning your project to get it back in gear: choose >> Project > Clean... then select the malfunctioning project(s). Wait a bit, >> then see if things get better. >> >> Sorry couldn't get on early enough to help you address this sooner. Hope >> this suggestion helps. >> >> John David N. Dionisio, PhD >> Associate Professor, Computer Science >> Loyola Marymount University >> >> >> >> On Aug 22, 2011, at 8:14 PM, Richard Brous wrote: >> >> > In case your workspace is perfectly fine, here are some of the errors >> i'm seeing: >> > >> > DatabaseProfile.java >> > >> > public >> > >> > abstract class DatabaseProfile extends Profile { Error here says: >> Profile cannot be resolved to a type. >> > ------------------------------------------------------------------- >> > >> > public >> > >> > String getProfileName() { >> > >> > return getName(); Error here says: Method is undefined >> > } >> > >> > >> > >> > /** >> > * Returns the profile description. >> > >> > * >> > >> > * >> > >> > @return >> > */ >> > >> > >> > public String getProfileDescription() { >> > >> > return getDescription(); Error here says: Method is undefined >> > } >> > >> > I then check Profile.java and the class constructor and methods are in >> fact defined.... >> > >> > more unusual stuff... >> > >> > springutilities can't be resolved on exportpanel1 >> > ExportToGenMAPP can't resolve TableCoordinator >> > >> > >> > I really don't get this. What could I have possibly done to my config? >> > >> > Richard >> > >> > >> > On Mon, Aug 22, 2011 at 7:40 PM, Richard Brous <rbr...@gm...> >> wrote: >> > OK, I'll add some logging to that loop and change that last ? to >> OrderedLocusNames ( I think thats what it should be ) >> > >> > I do have another odd problem tho... >> > >> > I'm not sure what I did but I now have errors throughout some of the >> class files: >> > ExportPanel1.java >> > DatabaseProfile.java >> > SpeciesProfile.java >> > and many more... >> > >> > I'm not sure what I did but doing a resync to the repository did not >> bring me back to a non-error state. >> > >> > I don't know what to do to fix it. When you sync to sourceforge do you >> get source files without error? >> > >> > Help please =/ >> > >> > Richard >> > >> > >> > On Mon, Aug 22, 2011 at 4:30 PM, John David N. Dionisio <do...@lm...> >> wrote: >> > Greetings, >> > >> > The plan sounds good, all around. >> > >> > Regarding the "type = ?" clause in our SQL, recall that the "?"s in the >> query are placeholders for actual parameter values. If you follow where >> that last setString call (which thus sets the right side of the "type = ?" >> clause) gets its value, you'll see where that comes from (and what it leads >> to in the GDB). Hint: "GeneId" is one of the values that this clause takes. >> :) >> > >> > The doubling up of Sa is interesting. Either there is a bug in your >> Species column string building code, or there are multiple taxon IDs that >> actually have the same species name. I think some judicious debug logging >> will resolve that. >> > >> > Once these GDBs have been duly vetted, I think we can move on to the >> relationship tables. >> > >> > John David N. Dionisio, PhD >> > Associate Professor, Computer Science >> > Loyola Marymount University >> > >> > >> > >> > On Aug 22, 2011, at 10:03 AM, Richard Brous wrote: >> > >> > > OK, I have exported single species Sa and Pa GDBs from the current >> working build and from the pre-multispecies build (all from my existing Pa >> and Sa postgres databases. >> > > >> > > Then exported a multipspecies Sa and Pa gdb from the current working >> build from my existing Sa/Pa multispecies postrgres database. >> > > >> > > I will post all GDB exports to the db wiki shortly... >> > > >> > > >> ----------------------------------------------------------------------------------------------------------------------------------------------- >> > > getSystemTableManager() >> > > >> > > >> > > So in effort to check the correctness of the multispecies changes to >> the System table I was going to run the SQL commands from within PGAdmin >> then compare the results to those within the multispecies GDB. >> > > >> > > Is my method correct? >> > > >> > > >> ----------------------------------------------------------------------------------------------------------------------------------------------- >> > > would use sql command (with errors =/): >> > > >> > > SELECT distinct id FROM dbreferencetype >> > > INNER JOIN (SELECT entrytype.hjid FROM entrytype >> > > INNER JOIN organismtype ON (entrytype.organism = >> organismtype.hjid) >> > > INNER JOIN dbreferencetype >> ON(dbreferencetype.organismtype_dbreference_hjid = organismtype.hjid) >> > > WHERE dbreferencetype.type = 'NCBI Taxonomy' and (id = 287 or id >> = 282458)) >> > > as species_entry on dbreferencetype.entrytype_dbreference_hjid = >> species_entry.hjid where type = ?; >> > > >> > > >> > > But I get an error for the = signs on line 5 and I'm not sure what the >> ? is at the end of the last line... I thought it was taxonID but then >> thought maybe it was something else. >> > > >> > > >> --------------------------------------------------------------------------------------------------------------------------------------------- >> > > >> > > getInfoTableManager() >> > > >> > > To check the Info Table I opened the multispecies GDB in Access and >> did a visual check. >> > > >> > > All colums looked ok (when compared to single species exports) except >> for the Species column which had one too many entries. Will have to >> determine why Sa is listed twice but a quick review of the loop didn't >> reveal any issues. >> > > Info >> > > Species >> > > Pseudomonas aeruginosa|Staphylococcus aureus (strain >> MRSA252)|Staphylococcus aureus (strain MRSA252) >> > > >> > > >> > > >> > > Richard >> > > >> > > >> > > On Sat, Aug 20, 2011 at 9:37 AM, John David N. Dionisio < >> do...@lm...> wrote: >> > > Hi Rich, >> > > >> > > The JDBC mention was meant mainly to help with your use of >> PreparedStatement. If you've gotten that working, it's fine to move along. >> I think it would be good now to see how the system and info table code does >> with multiple species (if you haven't already done so). I prefer this way >> before going into the relationship tables, just so we know that the work >> done so far is OK for the full case, and because the relationship code will >> be tougher to navigate. >> > > >> > > The main thing about the old-school loop when dealing solely with the >> count was just that I prefer not to declare variables that I don't use (in >> this case, the iterated object). Plus, with the use of an index, you also >> obviate the need for that boolean first variable. Admittedly not an issue >> of correctness here (as you said, your original code ran fine), but more of >> a refinement/"best fit" choice. >> > > >> > > >> > > John David N. Dionisio, PhD >> > > Associate Professor, Computer Science >> > > Loyola Marymount University >> > > >> > > >> > > On Aug 20, 2011, at 9:17 AM, Richard Brous <rbr...@gm...> >> wrote: >> > > >> > >> also, I have compiled and run a new export. >> > >> >> > >> the GDB looks good for single species so which method should I go to >> next OR do you want me to read JDBC before proceeding? >> > >> >> > >> richard >> > >> >> > >> On Sat, Aug 20, 2011 at 9:07 AM, Richard Brous <rbr...@gm...> >> wrote: >> > >> Interesting about the looping through species profiles vs old-school >> int loop: >> > >> >> > >> My choice of looping through the species still provided the correct >> count, but what I think you are saying is that it is more appropriate to use >> int looping because i'm not actually using the species profile objects for >> anything? >> > >> >> > >> >> > >> I'll check out the JDBC portion shortly... I'm still working on the >> details surrounding question #1 on the syllabus. I have been reading the >> text in time slots avail when awaiting your feedback but honestly attempting >> to prioritize GM builder coding. I have finished digesting E/R and am >> working through UML... >> > >> >> > >> Richard >> > >> On Sat, Aug 20, 2011 at 12:02 AM, John David N. Dionisio < >> do...@lm...> wrote: >> > >> Hi Rich, >> > >> >> > >> Having now taken a closer look at the code, I definitely recommended >> that you do what was suggested in the previous reply, which is to form and >> issue the SQL query directly before coding it up. More details have been >> committed in comments, so go ahead and take a look. >> > >> >> > >> You are also now getting further exposure to the JDBC (Java Database >> Connectivity) API. There is a section in the textbook that provides a brief >> introduction to JDBC, and there are extensive tutorials and references >> available on the web. If you haven't already done so, it might be >> worthwhile to glance at these. Looking at the PreparedStatement class in >> particular may help solidify your understanding of the code in question. >> > >> >> > >> Happy querying :) >> > >> >> > >> John David N. Dionisio, PhD >> > >> Associate Professor, Computer Science >> > >> Loyola Marymount University >> > >> >> > >> >> > >> >> > >> On Aug 19, 2011, at 8:47 PM, Richard Brous wrote: >> > >> >> > >> > Fatal error during export which was related to "as" which I suspect >> I left out a right parens when building the ps string. >> > >> > >> > >> > Rerunning export now but must head to bed. >> > >> > >> > >> > Will commit the changes I have and look for email comments in the >> morn. >> > >> > >> > >> > Richard >> > >> > >> > >> > On Fri, Aug 19, 2011 at 8:04 PM, Richard Brous <rbr...@gm...> >> wrote: >> > >> > OK, made changes to getSystemTableManager() based on your comments >> below. >> > >> > >> > >> > The ps string is programmatically created by adding "id = ?" for >> each species profile within selectedSpeciesProfiles >> > >> > >> > >> > also added for loops below to cycle through the ps.set... >> > >> > >> > >> > and a for loop to grab each species customization. >> > >> > >> > >> > Running an export now which will be done in an hour or so to review >> prior to submitting changes to sourceforge. >> > >> > >> > >> > Richard >> > >> > >> > >> > On Thu, Aug 18, 2011 at 11:19 PM, John David N. Dionisio < >> do...@lm...> wrote: >> > >> > Greetings, >> > >> > >> > >> > OK, the transitional prep code (i.e., using the get(0) trick) looks >> good. Looks like we can safely hunker down now, starting with >> getSystemTableManager. >> > >> > >> > >> > I agree that the clause: >> > >> > >> > >> > WHERE dbreferencetype.type = 'NCBI Taxonomy' and id = ? >> > >> > >> > >> > ...where "?" becomes the single taxon ID to be exported should now >> become: >> > >> > >> > >> > WHERE dbreferencetype.type = 'NCBI Taxonomy' and (id = ? or >> id = ? or id = ? ......) >> > >> > >> > >> > ...where the "?"s each get a taxon ID. This requires that this >> single large string must be built programmatically before being passed into >> prepareStatement. Plus, the ps.set.... calls now change from a single >> statement into a loop. >> > >> > >> > >> > On a side note, you can change ps.setString to ps.setLong, thus >> avoiding the concatenation with the empty string. >> > >> > >> > >> > I traced where that speciesCustomizeTextField value leads and found >> that it ultimately goes into the getSpeciesName property of the species >> profile, which is in turn what is used in the Species column of the ID >> tables. It appears that the purpose of speciesCustomizeTextField was to >> allow the user to modify the species name; seeing as we hardly (if ever) >> made use of this customization, I propose that we just auto-set this >> property in the species profiles to the actual species name stored in the >> UniProt records. >> > >> > >> > >> > John David N. Dionisio, PhD >> > >> > Associate Professor, Computer Science >> > >> > Loyola Marymount University >> > >> > >> > >> > >> > >> > >> > >> > On Aug 18, 2011, at 8:17 PM, Richard Brous wrote: >> > >> > >> > >> > > Posted new working copy to the db wiki >> > >> > > Committed changes to SourceForge >> > >> > > >> > >> > > On Thu, Aug 18, 2011 at 7:41 PM, Richard Brous < >> rbr...@gm...> wrote: >> > >> > > getRelationsTableManager() >> > >> > > Interim changes complete using selectedSpeciesProfiles.get(0) >> > >> > > we skipped this one as its pretty complex. Need to discuss how I >> need to tackle this. >> > >> > > >> > >> > > getSystemTableManager() >> > >> > > Interim changes complete using selectedSpeciesProfiles.get(0) >> > >> > > After reviewing the code I think the way to update this method is >> to loop through each selected species profile prior to if conditional at >> line 525? >> > >> > > Seem sound? >> > >> > > >> > >> > > getRelationshipTableManager() >> > >> > > Interim changes complete using selectedSpeciesProfiles.get(0) >> > >> > > Not quite sure how to make method aware of multispecies. Use >> looping or a single command vs actually changing the sql table commands? >> > >> > > >> > >> > > getSecondPassTableManager() >> > >> > > Interim change complete using selectedSpeciesProfiles.get(0) >> > >> > > I think we need to loop through each species profile here, to add >> the customizations for each species >> > >> > > >> > >> > > >> ------------------------------------------------------------------------------------------------------------------------------------- >> > >> > > >> > >> > > Attempted another Ms export and this time figured out what was >> going on. >> > >> > > >> > >> > > As Dr. D noted, no IDs existed in the previous GDB attempt and >> this is related to the speciesCustomizeTextField which we had commented out >> a few weeks ago. I changed it to >> speciesCustomizeTextField.setText(selectedSpecies.get(0).getName()); to >> ensure the field was populated with something and that did the trick. Now >> exports are nearly identical for Ms for pre-multispecies build and the >> current working build. >> > >> > > >> > >> > > I'm going to place my current working multispecies build (which >> only exports a single species still) up on the db class wiki for your >> review. >> > >> > > >> > >> > > Look for SourceForge changes soonish... >> > >> > > >> > >> > > Richard >> > >> > > >> > >> > > >> > >> > > >> > >> > > On Thu, Aug 18, 2011 at 11:40 AM, Kam Dahlquist < >> kda...@lm...> wrote: >> > >> > > Hi, >> > >> > > >> > >> > > That's good news. Let me know when there's a build that I can >> run. >> > >> > > >> > >> > > Also, would you guys mind changing the subject line to more >> closely >> > >> > > reflect the task being described in the message? >> > >> > > >> > >> > > Thanks, >> > >> > > Kam >> > >> > > >> > >> > > At 10:29 AM 8/18/2011, you wrote: >> > >> > > >Greetings, >> > >> > > > >> > >> > > >FYI I've committed some changes to the GO import handling. The >> most >> > >> > > >recent "breakage" in GO importing was caused by GO's addition of >> an >> > >> > > ><ontology> element to the <header>. Interestingly, the text in >> this >> > >> > > >element was simply "go" --- an interesting change, implying that >> > >> > > >other ontologies may be accommodated. >> > >> > > > >> > >> > > >In any case, I've updated the GO database libraries and source >> code, >> > >> > > >and I did a successful test import on a daily OBO file >> downloaded >> > >> > > >yesterday. So, it looks like we can use the latest OBO files >> again, >> > >> > > >at least until another element gets added to the schema. >> > >> > > > >> > >> > > >John David N. Dionisio, PhD >> > >> > > >Associate Professor, Computer Science >> > >> > > >Loyola Marymount University >> > >> > > >> > >> > > >> > >> > > >> ------------------------------------------------------------------------------ >> > >> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> > >> > > user administration capabilities and model configuration. Take >> > >> > > the hassle out of deploying and managing Subversion and the >> > >> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> > >> > > _______________________________________________ >> > >> > > xmlpipedb-developer mailing list >> > >> > > xml...@li... >> > >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > >> > > >> > >> > > >> > >> > > <ATT00001..txt><ATT00002..txt> >> > >> > >> > >> > >> > >> > >> ------------------------------------------------------------------------------ >> > >> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> > >> > user administration capabilities and model configuration. Take >> > >> > the hassle out of deploying and managing Subversion and the >> > >> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> > >> > _______________________________________________ >> > >> > xmlpipedb-developer mailing list >> > >> > xml...@li... >> > >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > >> > >> > >> > >> > >> > <ATT00001..txt><ATT00002..txt> >> > >> >> > >> >> > >> >> ------------------------------------------------------------------------------ >> > >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> > >> user administration capabilities and model configuration. Take >> > >> the hassle out of deploying and managing Subversion and the >> > >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> > >> _______________________________________________ >> > >> xmlpipedb-developer mailing list >> > >> xml...@li... >> > >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > >> >> > >> >> > >> >> ------------------------------------------------------------------------------ >> > >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> > >> user administration capabilities and model configuration. Take >> > >> the hassle out of deploying and managing Subversion and the >> > >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> > >> _______________________________________________ >> > >> xmlpipedb-developer mailing list >> > >> xml...@li... >> > >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > > >> > > >> ------------------------------------------------------------------------------ >> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> > > user administration capabilities and model configuration. Take >> > > the hassle out of deploying and managing Subversion and the >> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> > > _______________________________________________ >> > > xmlpipedb-developer mailing list >> > > xml...@li... >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > > >> > > >> > > <ATT00001..txt><ATT00002..txt> >> > >> > >> > >> ------------------------------------------------------------------------------ >> > uberSVN's rich system and user administration capabilities and model >> > configuration take the hassle out of deploying and managing Subversion >> and >> > the tools developers use with it. Learn more about uberSVN and get a >> free >> > download at: http://p.sf.net/sfu/wandisco-dev2dev >> > _______________________________________________ >> > xmlpipedb-developer mailing list >> > xml...@li... >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > >> > >> > <ATT00001..txt><ATT00002..txt> >> >> >> >> ------------------------------------------------------------------------------ >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> user administration capabilities and model configuration. Take >> the hassle out of deploying and managing Subversion and the >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> _______________________________________________ >> xmlpipedb-developer mailing list >> xml...@li... >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> >> > > > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > |