Hi John,
The problem is still there.
As attached document you will find ibis log file , generated by the
following command,
%IBIS% -l log.txt -d .\dimensions\ColPart -q "select Inhibitor where
Inhibitor = 'Imatinib'"
%IBIS% -l log.txt -d .\dimensions\ColPart -q "select Inhibitor where
Inhibitor IN ('Imatinib')"
Regards,
Alexandre
[email protected] a écrit :
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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.
ibis::util::setLogFileName opened log.txt on Thu Dec 03 10:28:57 2009 for
FastBit ibis
C:\Soft\fastbit\fastbit-scm-latest\fastbit-scm-2009-11-26\trunk\win\Debug\ibis.exe:
batch mode, log level 5
ibis::resource::read -- can not find any of the following configuration files:
ibis.rc
.ibisrc
tablesFromDir -- examining .\dimensions\ColPart
fileManager::ctor found the physical memory size to be 2145587200 bytes
fileManager initialization complete
-- maxBytes=1072791552, maxOpenFiles=60
part::readMetaData -- opened .\dimensions\ColPart\-part.txt for reading
Completed construction of an ibis::part named
Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat -- Data initialy wrote with
ibis::tablex interface on Fri Nov 13 11:21:40 2009 with 19 columns and 1152 rows
activeDir = ".\dimensions\ColPart"
ibis::part: Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat (Data initialy
wrote with ibis::tablex interface on Fri Nov 13 11:21:40 2009 with 19 columns
and 1152 rows) with 1152 rows, 19 columns
Column list:
Antibody: (KEY) []
Array: (KEY) []
ATP_conc_: (FLOAT) [1.79769e+308, -1.79769e+308]
Barcode: (KEY) []
Col: (FLOAT) [1.79769e+308, -1.79769e+308]
Cycle: (FLOAT) [1.79769e+308, -1.79769e+308]
Exposure_time: (FLOAT) [1.79769e+308, -1.79769e+308]
Filter: (FLOAT) [1.79769e+308, -1.79769e+308]
Image: (KEY) []
Imatinib: (KEY) []
Imatinib_Resistant: (FLOAT) [1.79769e+308, -1.79769e+308]
Inhibitor: (KEY) []
Inhibitor_conc_: (FLOAT) [1.79769e+308, -1.79769e+308]
Row: (FLOAT) [1.79769e+308, -1.79769e+308]
Sample_name: (KEY) []
Sample_volume: (FLOAT) [1.79769e+308, -1.79769e+308]
Strip: (FLOAT) [1.79769e+308, -1.79769e+308]
Temperature: (FLOAT) [1.79769e+308, -1.79769e+308]
Visual_QC: (KEY) []
Partition[1]:
Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat
Query[1]:
select Inhibitor where Inhibitor = 'Imatinib'
doQuery -- processing "SELECT Inhibitor FROM
Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat WHERE Inhibitor = 'Imatinib'"
newToken -- generated new token "PKY4o3gMWCZ----0" for user Alexandre
query[PKY4o3gMWCZ----0]::setWhereClause -- add a new where clause "Inhibitor =
'Imatinib'".
query[PKY4o3gMWCZ----0]::setWhereClause -- WHERE "Inhibitor = 'Imatinib'"
Translated the WHERE clause into: Inhibitor == Imatinib
ibis::selected::select -- SELECT Inhibitor
query[PKY4o3gMWCZ----0]::setSelectClause -- SELECT Inhibitor
query[PKY4o3gMWCZ----0]::estimate -- starting to estimate query
column[Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat.Inhibitor](CATEGORY)::getNullMask
-- get null mask (1152, 1152) [st.st_size=7560, sz=1152, ierr=-101]
ibis::query[PKY4o3gMWCZ----0]::doEstimate(0x0190eec0: Inhibitor == Imatinib)
--> [0, 1152]
query[PKY4o3gMWCZ----0]::getBounds -- number of hits in [0, 1152]
query[PKY4o3gMWCZ----0]::estimate -- time to compute the bounds: 0 sec(CPU),
0.00054084 sec(elapsed).
query[PKY4o3gMWCZ----0]::estimate -- # of hits for query "Inhibitor =
'Imatinib'" is in [0, 1152]
doQuery -- the number of hits is between 0 and 1152
query[PKY4o3gMWCZ----0]::evaluate -- starting to evaluate the query for user
"Alexandre"
ibis::part[Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat]::doScan - starting
scaning data for "Inhibitor == Imatinib" with mask (1152 out of 1152)
ibis::part[Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat]::doScan --
evaluating Inhibitor == Imatinib on 1152 records (total: 1152) took 0.0028886
sec elapsed time and produced 0 hits
ibis::query[PKY4o3gMWCZ----0]::doEvaluate(0x0190eec0: Inhibitor == Imatinib,
mask.cnt()=1152) --> 0, ierr = 0
ibis::query::computeHits() hit vector
This bitvector stores 1147 bits of a 1152-bit (0 set) sequence in a 1-word
array and 5 bits in the active word
0 1 1 2 2 3
0123456789012345678901234567890
-------------------------------
0 80000025 1147*0
00000000 00000
query[PKY4o3gMWCZ----0]::evaluate -- time to compute the 0 hit: 0 sec(CPU),
0.00336484 sec(elapsed).
query[PKY4o3gMWCZ----0]::evaluate -- user Alexandre SELECT Inhibitor FROM
Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat WHERE Inhibitor = 'Imatinib'
==> 0 hit.
query[PKY4o3gMWCZ----0]::evaluate -- read(unistd.h) accessed 5 pages during the
execution of this function
doQuery:: evaluate(SELECT Inhibitor FROM
Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat WHERE Inhibitor = 'Imatinib')
produced 0 hit, took 0 CPU seconds, 0.00497692 elapsed seconds
query[PKY4o3gMWCZ----0]::clear -- clearing all stored information about the
query
clearing data partition Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat
Cleaning up the file manager
Total pages accessed through read(unistd.h) is estimated to be 8
--- Thu Dec 03 10:28:57 2009
The number of memory mapped files is 0. (max = 60)
Size of all mapped files is 0
The number of files read into memory is 0.
The total size of all files read into memory is 0
Size of all named storages is 0
Size of all unnamed storages is 0
The total size of all named and unnamed storages is 0
The prescribed maximum size is 1072791552
Number of pages accessed (recorded so far) is 8 (page size = 4096)
C:\Soft\fastbit\fastbit-scm-latest\fastbit-scm-2009-11-26\trunk\win\Debug\ibis.exe
-- total CPU time 0.046 s, total elapsed time 0.0404395 s
ibis::util::setLogFileName opened log.txt on Thu Dec 03 10:28:57 2009 for
FastBit ibis
C:\Soft\fastbit\fastbit-scm-latest\fastbit-scm-2009-11-26\trunk\win\Debug\ibis.exe:
batch mode, log level 5
ibis::resource::read -- can not find any of the following configuration files:
ibis.rc
.ibisrc
tablesFromDir -- examining .\dimensions\ColPart
fileManager::ctor found the physical memory size to be 2145587200 bytes
fileManager initialization complete
-- maxBytes=1072791552, maxOpenFiles=60
part::readMetaData -- opened .\dimensions\ColPart\-part.txt for reading
Completed construction of an ibis::part named
Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat -- Data initialy wrote with
ibis::tablex interface on Fri Nov 13 11:21:40 2009 with 19 columns and 1152 rows
activeDir = ".\dimensions\ColPart"
ibis::part: Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat (Data initialy
wrote with ibis::tablex interface on Fri Nov 13 11:21:40 2009 with 19 columns
and 1152 rows) with 1152 rows, 19 columns
Column list:
Antibody: (KEY) []
Array: (KEY) []
ATP_conc_: (FLOAT) [1.79769e+308, -1.79769e+308]
Barcode: (KEY) []
Col: (FLOAT) [1.79769e+308, -1.79769e+308]
Cycle: (FLOAT) [1.79769e+308, -1.79769e+308]
Exposure_time: (FLOAT) [1.79769e+308, -1.79769e+308]
Filter: (FLOAT) [1.79769e+308, -1.79769e+308]
Image: (KEY) []
Imatinib: (KEY) []
Imatinib_Resistant: (FLOAT) [1.79769e+308, -1.79769e+308]
Inhibitor: (KEY) []
Inhibitor_conc_: (FLOAT) [1.79769e+308, -1.79769e+308]
Row: (FLOAT) [1.79769e+308, -1.79769e+308]
Sample_name: (KEY) []
Sample_volume: (FLOAT) [1.79769e+308, -1.79769e+308]
Strip: (FLOAT) [1.79769e+308, -1.79769e+308]
Temperature: (FLOAT) [1.79769e+308, -1.79769e+308]
Visual_QC: (KEY) []
Partition[1]:
Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat
Query[1]:
select Inhibitor where Inhibitor IN ('Imatinib')
doQuery -- processing "SELECT Inhibitor FROM
Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat WHERE Inhibitor IN
('Imatinib')"
newToken -- generated new token "PKY4o3gMWCZ----0" for user Alexandre
query[PKY4o3gMWCZ----0]::setWhereClause -- add a new where clause "Inhibitor IN
('Imatinib')".
query[PKY4o3gMWCZ----0]::setWhereClause -- WHERE "Inhibitor IN ('Imatinib')"
Translated the WHERE clause into: Inhibitor == "Imatinib"
ibis::selected::select -- SELECT Inhibitor
query[PKY4o3gMWCZ----0]::setSelectClause -- SELECT Inhibitor
query[PKY4o3gMWCZ----0]::estimate -- starting to estimate query
column[Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat.Inhibitor](CATEGORY)::getNullMask
-- get null mask (1152, 1152) [st.st_size=7560, sz=1152, ierr=-101]
relic[Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat.Inhibitor]::read
finished reading the header from .\dimensions\ColPart\Inhibitor.idx
relic[Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat.Inhibitor]::ctor --
construct an equality index with 3 bitmaps for 1152 rows
ibis::query[PKY4o3gMWCZ----0]::doEstimate(0x0039eec0: Inhibitor == "Imatinib")
--> [450, 450]
query[PKY4o3gMWCZ----0]::estimate -- time to compute the bounds: 0 sec(CPU),
0.00371124 sec(elapsed).
query[PKY4o3gMWCZ----0]::estimate -- # of hits for query "Inhibitor IN
('Imatinib')" is 450
query[PKY4o3gMWCZ----0]::estimate -- read(unistd.h) accessed 4 pages during the
execution of this function
doQuery -- the number of hits is 450
query[PKY4o3gMWCZ----0]::evaluate -- starting to evaluate the query for user
"Alexandre"
query[PKY4o3gMWCZ----0]::evaluate -- the hit vector contains 1152 bits with 450
bits set(=1) taking 176 bytes; the estimated clustering factor is 1; had the
bits been randomly spread out, the expected size would be 160 bytes; estimated
number of bytes to be read in order to access 4-byte values is 4096
query[PKY4o3gMWCZ----0]::evaluate -- time to compute the 450 hits: 0 sec(CPU),
0.00011616 sec(elapsed).
query[PKY4o3gMWCZ----0]::evaluate -- user Alexandre SELECT Inhibitor FROM
Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat WHERE Inhibitor IN
('Imatinib') ==> 450 hits.
query[PKY4o3gMWCZ----0]::createBundle -- time to generate the bundle: 0
sec(CPU), 0.00239132 sec(elapsed)
Bundle1 PKY4o3gMWCZ----0 has 1 distinct value
Inhibitor (with counts)
Imatinib, 450
doQuery:: evaluate(SELECT Inhibitor FROM
Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat WHERE Inhibitor IN
('Imatinib')) produced 450 hits, took 0 CPU seconds, 0.0073934 elapsed seconds
query[PKY4o3gMWCZ----0]::clear -- clearing all stored information about the
query
clearing data partition Array_{FA56FEBD-064F-413D-9564-181D69F5DB20}.dat
Cleaning up the file manager
Total pages accessed through read(unistd.h) is estimated to be 8
--- Thu Dec 03 10:28:57 2009
The number of memory mapped files is 0. (max = 60)
Size of all mapped files is 0
The number of files read into memory is 0.
The total size of all files read into memory is 0
Size of all named storages is 0
Size of all unnamed storages is 0
The total size of all named and unnamed storages is 0
The prescribed maximum size is 1072791552
Number of pages accessed (recorded so far) is 8 (page size = 4096)
C:\Soft\fastbit\fastbit-scm-latest\fastbit-scm-2009-11-26\trunk\win\Debug\ibis.exe
-- total CPU time 0.046 s, total elapsed time 0.0416787 s
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