Re: DBD::CSV::st execute failed:

[Tux]

If you use f_ext => ".csv/r", you explicitly tell the driver that the extension is required. If you add the /r, you should not add .csv to the table name. The driver will still be able to open your file, but it is not quaranteed anymore which file it opens: newCsv, newCsv.csv, or newCsv.csv.csv.

Another issue is case sensitivity. On Windows newCsv will match against any casing. On Linux you might need to check if your file name matches.

$ cat newCsv.csv
foo,bar,baz
1,2,3
$ perl -MDP -MDBI -e'my$s=DBI->connect("dbi:CSV:",undef,undef,{f_ext=>
+".csv/r"})->prepare("select * from newCsv");$s->execute;DDumper$s->fe
+tchrow_hashref'
{   bar              => 2,
    baz              => 3,
    foo              => 1
    }
$ perl -MDP -MDBI -e'my$s=DBI->connect("dbi:CSV:",undef,undef,{f_ext=>
+".csv/r"})->prepare("select * from newCsv.csv");$s->execute;DDumper$s
+->fetchrow_hashref'
{   bar              => 2,
    baz              => 3,
    foo              => 1
    }
$ perl -MDP -MDBI -e'my$s=DBI->connect("dbi:CSV:",undef,undef,{f_ext=>
+".csv/r"})->prepare("select * from newcsv");$s->execute;DDumper$s->fe
+tchrow_hashref'
DBD::CSV::st execute failed:
Execution ERROR: Cannot open /tmp/ne.csv: No such file or directory (2
+) at /pro/lib/perl5/site_perl/5.24.0/x86_64-linux-thread-multi-ld/DBI
+/DBD/SqlEngine.pm line 1624.
.

 [for Statement "select * from newcsv"] at -e line 1.
DBD::CSV::st fetchrow_hashref failed: Attempt to fetch row without a p
+receding execute () call or from a non-SELECT statement [for Statemen
+t "select * from newcsv"] at -e line 1.
undef

I see that the error message could use some improvement :)

[Tux]

The wrong error message actually proved to be a bug in DBI, which I now fixed and pushed.

[Sandy_Bio_Perl]

Thank you, Tux. I have removed the file extension .csv, and I note your comments on case sensitivity - all table headings etc are lower case and the csv file is correctly cased - if that is the right expression - as newCsv.csv.

Sadly, I still get the same error messages. Still seeking divine guidance from the Monastery!!

[erix]

It might be handy to post a part of the file, perhaps a head -n 20 (that is to say, the first 20 lines) so that experimentation is easier.

(and the actual filename)

[Sandy_Bio_Perl]

Hello again erix, here are the first 4 colums (sid, genotype, gender and tgroup, together with the first 19 rows of data. Thanks for helping me.

sid    genotype    gender    tgroup
1    c    female    3
2    b    male    3
3    c    male    3
4    b    male    1
5    c    female    3
6    b    male    1
7    a    female    2
8    a    male    3
9    d    male    1
10    a    female    2
11    d    male    2
12    d    female    2
13    d    male    2
14    d    female    1
15    d    female    4
16    d    female    2
17    d    male    3
18    c    male    1
19    a    male    1

[Sandy_Bio_Perl]

Thank you erix. The headings of my spreadsheet, which is called newCsv.csv (that is the correct case sensitivity) are

Headings of spreadsheet are: sid name genotype gender tgroup dnabl dnatw2 dnatw4 dnatw8 dnatw12 dnatw16 dnatw24 dnatw48 dnatw8-bl eagabscr eagabbl eagabtw12 eagabtw24 eagabtw48 altscr altbl alttw2 alttw4 alttw8 alttw12 alttw16 alttw24 alttw48 coretcellbl coretcelltw4 coretcelltw8 coretcelltw12 coretcelltw16 coretcelltw24 coretcelltw48 surfacetcellbl surfacetcelltw4 surfacetcelltw8 surfacetcelltw12 surfacetcelltw16 surfacetcelltw24 surfacetcelltw48 hla_a_1 hla_a_2 hla_b_1 hla_b_2 drb1*_1 drb1*_2 drb3*_1 drb3*_2 drb4*_1 drb4*_2 drb5*_1 drb5*_2 x_1 x_2

Is that what you wanted?