Re: [XMLPipeDB-developer] Eclipse workspace
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Re: [XMLPipeDB-developer] Eclipse workspace
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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
>> > >> > >
>> > >> > >
>> > >> > >
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