Hi John, Thanks you this quick reply, I will test it.
Regards, Alexandre [email protected] a écrit : > Send FastBit-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of FastBit-users digest..." > > > Today's Topics: > > 1. Re: selectParser bug (K. John Wu) > 2. Re: query error (K. John Wu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 23 Nov 2009 09:55:04 -0800 > From: "K. John Wu" <[email protected]> > Subject: Re: [FastBit-users] selectParser bug > To: FastBit Users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, Andrew, > > Thanks for reporting the problem. A modification to the associativity > of unary operators +, 1 and ! (not) has been made and it should > address the problem you've noticed. Please give the nightly snapshot > a try when you get the chance. > > John > > PS: The nightly snapshot is available at > <https://codeforge.lbl.gov/snapshots.php?group_id=44> and it is built > in the early morning hours Pacific Time. > > > On 11/19/2009 1:04 PM, Andrew Olson wrote: > >> Hi. >> >> I'm trying to run a query like this but it fails to parse. >> >> select (stop-start+1)/length as proportion where proportion > 0.95 >> >> The complaint is: >> ibis::selectParser encountered syntax error, unexpected numerical value at >> location (stop-start+1)/length as proportion:1.11-12 >> >> It works if I change it to: >> select (1+stop-start)/length as proportion where proportion > 0.95 >> >> Andrew >> _______________________________________________ >> FastBit-users mailing list >> [email protected] >> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >> > > > ------------------------------ > > Message: 2 > Date: Mon, 23 Nov 2009 09:55:20 -0800 > From: "K. John Wu" <[email protected]> > Subject: Re: [FastBit-users] query error > To: FastBit Users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, Alexandre, > > Thanks for reporting the problem and exploring the solutions. It > turned out that we can tweak the lexer a little to recognize all > quoted strings as string literals -- which eliminate the ambiguity in > whether a string a column name or a string literal and correctly > represents the original intend of your query expression. The change > has been checked into the SVN repository. Please give the nightly > snapshot a try when you get the chance. > > John > > PS: The nightly snapshot is available at > <https://codeforge.lbl.gov/snapshots.php?group_id=44> and it is built > in the early morning hours Pacific Time -- which means you will need > to wait till tomorrow morning in order to get your hand on it. If you > want to try it earlier, please let me know, I will send you the source > code separately. > > > On 11/19/2009 3:47 AM, Alexandre Maurel wrote: > >> Hi John, >> >> I came back to the original column name , and I have changed the >> previous query into : >> >> select Inhibitor,Barcode,Row,Col,Sample_name where ( ( ! >> (Inhibitor IN ('DMSO') AND Barcode IN ('105006101') AND Row = 1 AND Col >> = 1 AND Sample_name IN ('PA97'))) AND ( !(Inhibitor IN ('Imatinib') AND >> Barcode IN ('105006101') AND Row = 4 AND Col = 4 AND Sample_name IN >> ('FP83')))) >> >> replacing "=" (in the case of category) by the key word IN . >> >> It's working :). >> >> Is there any other way to solve such problem ? >> >> Regards, >> >> Alexandre >> >> Alexandre Maurel a ?crit : >> >>> Hi John, >>> >>> I found the problem, there is a column named Imatinib which is also a >>> value of the column Inhibitor ! >>> I have rename the column Imatinib into Imatinib2 and the problem is gone. >>> >>> Regards, >>> >>> Alexandre >>> >>> >>> Alexandre Maurel a ?crit : >>> >>>> Hi John, >>>> >>>> As attachment document , you will find the data and the logs from ibis. >>>> In the log file I have highlighted the problem. >>>> >>>> Imatinib, 105006101, 4, 4, FP83, 6 error , this row should not >>>> be there ( ! (Inhibitor = 'Imatinib' AND Barcode = '105006101' AND >>>> Row = 4 AND Col = 4 AND Sample_name = 'FP83')) >>>> >>>> Note , I have run the following queries which are identical, and they >>>> give the same error. >>>> >>>> select Inhibitor,Barcode,Row,Col,Sample_name where ( ( ! (Inhibitor = >>>> 'DMSO' AND Barcode = '105006101' AND Row = 1 AND Col = 1 AND >>>> Sample_name = 'PA97')) AND ( ! (Inhibitor = 'Imatinib' AND Barcode = >>>> '105006101' AND Row = 4 AND Col = 4 AND Sample_name = 'FP83'))) >>>> >>>> select Inhibitor,Barcode,Row,Col,Sample_name where ((Inhibitor != >>>> 'DMSO' OR Barcode != '105006101' OR Row != 1 OR Col != 1 OR >>>> Sample_name != 'PA97') AND (Inhibitor != 'Imatinib' OR Barcode != >>>> '105006101' OR Row != 4 OR Col != 4 OR Sample_name != 'FP83')) >>>> >>>> Regards, >>>> >>>> Alexandre >>>> >>>> [email protected] a ?crit : >>>> >>>>> Send FastBit-users mailing list submissions to >>>>> [email protected] >>>>> >>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >>>>> or, via email, send a message with subject or body 'help' to >>>>> [email protected] >>>>> >>>>> You can reach the person managing the list at >>>>> [email protected] >>>>> >>>>> When replying, please edit your Subject line so it is more specific >>>>> than "Re: Contents of FastBit-users digest..." >>>>> >>>>> >>>>> Today's Topics: >>>>> >>>>> 1. Re: bundle segment method reorder the raw data (Alexandre Maurel) >>>>> >>>>> >>>>> ---------------------------------------------------------------------- >>>>> >>>>> Message: 1 >>>>> Date: Wed, 18 Nov 2009 09:54:37 +0100 >>>>> From: Alexandre Maurel <[email protected]> >>>>> Subject: Re: [FastBit-users] bundle segment method reorder the raw >>>>> data >>>>> To: [email protected] >>>>> Message-ID: <[email protected]> >>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>>> >>>>> Hi John, >>>>> >>>>> Problem is solved , >>>>> >>>>> Thanks, >>>>> >>>>> Alexandre >>>>> >>>>> [email protected] a ?crit : >>>>> >>>>> >>>>>> Send FastBit-users mailing list submissions to >>>>>> [email protected] >>>>>> >>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >>>>>> or, via email, send a message with subject or body 'help' to >>>>>> [email protected] >>>>>> >>>>>> You can reach the person managing the list at >>>>>> [email protected] >>>>>> >>>>>> When replying, please edit your Subject line so it is more specific >>>>>> than "Re: Contents of FastBit-users digest..." >>>>>> >>>>>> >>>>>> Today's Topics: >>>>>> >>>>>> 1. Re: bundle segment method reorder the raw data (K. John Wu) >>>>>> >>>>>> >>>>>> ---------------------------------------------------------------------- >>>>>> >>>>>> Message: 1 >>>>>> Date: Mon, 16 Nov 2009 17:25:27 -0800 >>>>>> From: "K. John Wu" <[email protected]> >>>>>> Subject: Re: [FastBit-users] bundle segment method reorder the raw >>>>>> data >>>>>> To: FastBit Users <[email protected]> >>>>>> Message-ID: <[email protected]> >>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>>>> >>>>>> Hi, Alexandre, >>>>>> >>>>>> I have implemented some changes that I think will address the >>>>>> problem you've encountered. The code has been checked in to SVN. >>>>>> If you get the chance, please give the nightly snapshot a try and >>>>>> let us know if it does address the problem. >>>>>> >>>>>> The nightly snapshot is available at >>>>>> <https://codeforge.lbl.gov/snapshots.php?group_id=44>. You might >>>>>> have to wait till the new snapshot is built during the middle of >>>>>> the night pacific time. >>>>>> >>>>>> John >>>>>> >>>>>> >>>>>> On 11/16/2009 1:24 AM, Alexandre Maurel wrote: >>>>>> >>>>>> >>>>>>> Hi John, >>>>>>> >>>>>>> I think I found a problem in function ibis::column::selectValuesT. >>>>>>> When a query does not specify a where clause or when mask.cnt() == >>>>>>> mask.size(), the method ibis::column::selectValuesT return a >>>>>>> pointer on raw data ... >>>>>>> Which cause the bundle segment method to reorder the raw data ! >>>>>>> >>>>>>> template <typename T> >>>>>>> long ibis::column::selectValuesT(const bitvector& mask, >>>>>>> ibis::array_t<T>& vals) const { >>>>>>> ... >>>>>>> ... >>>>>>> if (mask.cnt() == mask.size()) >>>>>>> return getValuesArray(&vals); >>>>>>> ... >>>>>>> ... >>>>>>> if (tot == mask.size()) { // read all values >>>>>>> ierr = ibis::fileManager::instance().getFile(dfn, vals); >>>>>>> return ierr; >>>>>>> } >>>>>>> >>>>>>> } >>>>>>> >>>>>>> Regards, >>>>>>> >>>>>>> Alexandre >>>>>>> _______________________________________________ >>>>>>> FastBit-users mailing list >>>>>>> [email protected] >>>>>>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >>>>>>> >>>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> _______________________________________________ >>>>>> FastBit-users mailing list >>>>>> [email protected] >>>>>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >>>>>> >>>>>> >>>>>> End of FastBit-users Digest, Vol 27, Issue 15 >>>>>> ********************************************* >>>>>> >>>>>> >>>>>> >>>>> ------------------------------ >>>>> >>>>> _______________________________________________ >>>>> FastBit-users mailing list >>>>> [email protected] >>>>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >>>>> >>>>> >>>>> End of FastBit-users Digest, Vol 27, Issue 16 >>>>> ********************************************* >>>>> >>>>> >>>>> >> _______________________________________________ >> FastBit-users mailing list >> [email protected] >> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >> > > > ------------------------------ > > _______________________________________________ > FastBit-users mailing list > [email protected] > https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > > > End of FastBit-users Digest, Vol 27, Issue 20 > ********************************************* > > _______________________________________________ FastBit-users mailing list [email protected] https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users
