I recently upgraded sqldeveloper to 22.x, I can't remember the previous version it was on. Now commands such as mkdir and spool are failing on scripts I used to run daily.
For example
host mkdir "C:\Users\Isaac\Requests\"
This script was completely unchanged and now it fails with
The filename, directory name, or volume label syntax is incorrect
Spool also fails with
SP2-0556: Invalid file name.
Again, this was a script I would run every single day, for the past year. I can't find what is causing this. Any ideas would be really helpful.
Remove the "quotes"
clear screen
host mkdir c:\Users\JDSMITH\Requests\
cd c:\Users\JDSMITH\Requests\
spool regions.csv
select /*csv*/ * from regions;
spool off
!type regions.csv
!dir
There's a chance this is a side effect of going to Java 11 from Java 8.
If you need a directory name with spaces, you can also use SQLcl.
See the 'sql.exe' in your bin directory, or download latest from oracle.com/sqlcl
Disclaimer: I'm an Oracle employee and a product manager for SQL Developer.
Related
I was trying to export files along with their revision history inside my depot folder from 2015.2 to 2019 perforce server.Also , I would want perforce to create new user on my new server corresponding to the commiter/submitter on my original 2015 repo.
Perforce replicate looked like overkill for my current task and then I came across this read on perforce's website that mentioned P4 zip.
This looked like it will solve my problem, but the article has a few issues I could not understand.
Let's say I am moving data from server1_ip:port --> server2_ip:port
I am currently following these steps
Making zip of folder to be copied using
p4 remote my_remote_spec , setting
Address: server1_ip:port
DepotMap://depot/... //depot2/...
p4 -p server1_ip:port zip -o test.zip -r my_remote_spec -A //depot/.... But on this step I get permission denied error. This is weird to me because the user although not super/admin has access to files i ask to get zipped.
Also, when i did try with a super user, i could not find test.zip even though i was not prompted any errors.
Isn't the above command supposed to generate a zip file inside the directory which i run it from?
Is the unzip command supposed to be run after a p4 login from user of second server?
Lastly, from the document why is a third port , 1667 mentioned in the transfer of files from server running on 1666 and 1777.
on this step I get permission denied error. This is weird to me because the user although not super/admin has access to files i ask to get zipped.
This is expected:
C:\Perforce\test>p4 help zip
zip -- Package a set of files and their history for use by p4 unzip
...
The zip command requires super permission granted by p4 protect.
Isn't the above command supposed to generate a zip file inside the directory which i run it from?
Similar to p4 admin checkpoint, the zip file is written to the server machine (relative to the server root, if you don't specify an absolute path), rather than being transferred to the local client directory. This is not explicitly stated in the documentation (which seems like an oversight), but if you look in the root directory of the server where you ran the zip, you should find your test.zip there.
Is the unzip command supposed to be run after a p4 login from user of second server?
Yes, any time you run a command against a particular server, you will need to be logged in to that server. In the case of p4 unzip you will need at least admin permission on the second server.
Lastly, from the document why is a third port , 1667 mentioned in the transfer of files from server running on 1666 and 1777.
I'm pretty sure that's a typo; whoever wrote the article started off using ports 1666 and 1777, changed their mind halfway through, and didn't proofread. :)
I'm using my Windows PC, and I'm trying to import a "dump.sql" into the database "TEST" created with Postgres, using command prompt. I do it in two steps:
Step 1:
cd C:\Program Files\PostgreSQL\12\bin
Step 2:
psql -U username -d TEST < C:\Users\Username\Desktop\University\Politechnic\III year\INFORMATIC TECHNOLOGIES FOR THE WEB\PDF SL\SL\Materials\TIW_IOL_ServletJSP\db\dump.sql`
Long path, I know. But the result is: "Impossible to find specified file".
What can I do?
Not sure how security is where you are at, but can you attempt to write to a file with a simpler destination? Such that you take out any possibility of spaces and/or length being the issue? Then you will at least be able to remove those variables or narrow down to them depending on the outcome. Note that the max path length is 260 characters
(From comment on question)
I run this command:
COPY XXX FROM 'D:/XXX.csv' WITH (FORMAT CSV, HEADER TRUE, NULL 'NULL')
In Windows 7, it successfully imports CSV files of less than 1GB.
If the file is more then 1GB big, I get an “unknown error”.
[Code: 0, SQL State: XX000] ERROR: could not stat file "'D:/XXX.csv' Unknown error
How can I fix this issue?
You can work around this by piping the file through a program. For example I just used this to copy from a 24GB file on Windows 10 and PostgreSQL 11.
copy t(c,d) from program 'cmd /c "type x:\path\to\file.txt"' with (format text);
This copies the text file file.txt into the table t, columns c and d.
The trick here is to run cmd in a single command mode, with /c and telling it to type out the file in question.
https://github.com/MIT-LCP/mimic-code/issues/493
alistairewj commented Nov 3, 2018 • ►
edited
Okay, the could not stat file "CHARTEVENTS.csv": Unknown error is actually a bug in PostgreSQL 11. Under the hood it makes a call to fstat() to make sure the file is not a directory, and unfortunately fstat() is a 32-bit program which can't handle large files like chartevents. I tested the build on Windows with PostgreSQL 10.5 and I didn't get this error so I think it's fairly new.
The best workaround is to keep the files compressed (i.e. keep them as .csv.gz files) and use 7zip to load in the data directly from compressed files. In testing this seemed to still work. There is a pretty detailed tutorial on how to do this here: https://mimic.physionet.org/tutorials/install-mimic-locally-windows/
The brief version of above is that you keep the .csv.gz files, you add the 7zip binary to your windows environment path, and then you call the postgres_load_data_7zip.sql file to load in the data. You can use the postgres_checks.sql file after everything to make sure you loaded in all the data correctly.
edit: For your later error, where you are using this 7zip approach, I'm not sure why it's not loading. Try redownloading just the ADMISSIONS.csv.gz file and seeing if it still throws you that same error. Maybe there is a new version of 7zip which requires me to update the script or something!
For anyone else who googled this Postgres error message after attempting to work with a >1gb file in Postgres 11, I can confirm that #亚军吴's answer above is spot-on. It is indeed a size issue.
I tried a different approach, though, than #亚军吴's and #Loren's: I simply uninstalled Postgres 11 and installed the stable version of Postgres 10.7. (I'm on Windows 10, by the way, in case that matters.)
I re-ran the original code that had prompted the error and voila, a few minutes later I'd filled in a new table with data from a medium-ish-size csv file (~3gb). I initially tried to use CSVSplitter, per #Loren, which was working fine until I got close to running out of storage space on my machine. (Thanks, Battlefield 5.)
In my case, there isn't anything in PGSQL 11 that I was relying on that wasn't in version 10.7, so I think this could be a good solution for anyone else who runs into this problem. Thanks everyone above for contributing, especially to the OP for posting this in the first place. I cured a huge, huge headache!
This has been fixed in commit bed90759f in PostgreSQL v14.
The file limit for the error is actually 4 GB.
The fix was too invasive to be backported, so you can only upgrade to avoid the problem. Once the fix has had some field testing, you could lobby the pgsql-hackers mailing list to get it backported.
With pgAdmin and AWS, I used CSVSplitter to split into files less than 1GB. Lame, but worked. pgAdmin import appends to the existing table. (Changed escape character from ' to " in order to avoid error due to unquoted text in the source file. Typically I apply quotes in LibreOffice, but these files were too big to open.)
It seems this is not a database problem, but a problem of psql / pgadmin. The workaround is using an admin software from the previous psql versions:
Use the existing PostgreSQL 11 database
Install psql or pgadmin from the PostgreSQL 10 installation and use it to upload the file (with the command shown in the question)
Hope this helps anyone coming across the same problem.
Add two lines to your CSV file: One at the begining and one at the end:
COPY XXX FROM STDIN WITH (FORMAT CSV, HEADER TRUE, NULL 'NULL');
<here are the lines your file already contains>
\.
Don't forget another newline after the \. line. Then call
psql -h hostname -d dbname -U username -f 'D:/XXX.csv'
This is what worked for me:
\COPY member_data.lab_result FROM PROGRAM 'gzip -dcf lab_result.dat.gz' WITH (FORMAT 'csv', DELIMITER '|', QUOTE '`')
I am configuring Blast+ on my mac (os sierra) and am having trouble configuring my nr and nt databases that I also downloaded locally. I am trying to follow NCBI's instructions here, and am getting hung up on the Configuration and Example Execution steps.
They say to change my .bash_profile so that it says:
export PATH=$PATH:$HOME/Documents/Luke/Research/Pedulla\ 17-18/blast/ncbi-blast-2.6.0+/bin
That works fine, and they say configure a path for BLASTDB "similarly" but to the file where my DB will be, so I have done this:
export BLASTDB=$BLASTDB:$HOME/Documents/Luke/Research/Pedulla\ 17-18/blast/blastdb/nt.00
which specifies the exact folder that I got when I unzipped the nt tar file from their FTP. With this path, if I run the command...
blastn -query test_query.fa -db nt.00 -task blastn -outfmt "7 qseqid sseqid evalue bitscore" -max_target_seqs 5
then it runs successfully and I get results, but I am worried that these are only being checked against the nt.00 section of the entire nt.00 database file, especially because if I run my test_query.fa sequence on the Web Blast, I get different results.
Also, their instructions say that the path only needs to point to the folder that contains the whole database folder nt.00, from the tar I unzipped--and not the specific nt.00 itself--, which in my case would just be "blastdb/" (As opposed to "blastdb/nt.00/" which then contains nt.00.nhd, nt.00.nal, etc.). That makes sense because when I am working I want to be able to blastn on the nt database but also blastp on the nr one, etc. by changing the -db flag on my command, and there shouldn't be a problem with having them all in this folder, right? But if I must specify the path for BLASTDB with the nt.00 DB added to the end, how could I ever use nr.00 in the same folder (blastdb/)? Essentially, I want to do as the instructions say, and just have this:
export BLASTDB=$BLASTDB:$HOME/Documents/Luke/Research/Pedulla\ 17-18/blast/blastdb/
And then depending on what database I want to use I could just say so after the -db flag on my command. But when I make the path like that above, it gives me this error:
BLAST Database error: No alias or index file found for nucleotide database [nt] in search path [/Users/LJStout::/Users/LJStout/Documents/Luke/Research/Pedulla 17-18/blast/blastdb:]
I have tried running that same blastn command from above and swapping out "nt" for "nt.00", and have tried these commands with the path for BLASTDB ending in both "blastdb/" and "blastdb/nt" and of course "blastdb/nt.00" which is the only one that runs without errors.
Here's an example of another thread I read where the OP is worried about his executions not checking the entire nt.00 folder, this was different than my problem however.
Thanks for you help!
This whole problem came down to having the nt.00 & nr.00 files, the original folders that result from unzipping their respective .tar.gz's, in the same parent folder when it should be that their contents are in the same parent folder. I simply deleted the folders they came in and copied the contents over to my new, singular parent. I was kind of mislead by the instructions, it was a simple mistake. Now, I have one folder, blastdb/ that contains all of the contents of every database I plan on using, including nt,nr, and refseq.
I am using Pentaho CE 5 on windows. I would like to use CTools but I can't make them show up in the File -> New menu to use them.
Being behind a proxy, I can not use the Marketplace plugin, so I have tried a manual installation.
First, I tried to use the ctools-installer.sh. I have run the following command line in cygwin (wget and unzip are installed):
./ctools-installer.sh -s /cygdrive/d/Users/[user]/Mes\ Programmes/pentaho/biserver-ce/pentaho-solutions/ -w /cygdrive/d/Users/[user]/Mes\ programmes/pentaho/biserver-ce/tomcat/webapps/pentaho/
The script starts, asks me what module I want to install, and begins the downloads.
For each module, I get an output like (set -x added to the script) :
echo -n 'Downloading CDF...' Downloading CDF...+ wget -q --no-check-certificate 'http://ci.analytical-labs.com/job/Webdetails-CDF-5-Release/lastSuccessfulBuild/artifact/bi-platform-v2-plugin/dist/zip/dist.zip'
-O .tmp/cdf/dist.zip SYSTEM_WGETRC = c:/progra~1/wget/etc/wgetrc syswgetrc = C:\Program Files (x86)\GnuWin32/etc/wgetrc
'[' '!' -z '' ']'
rm -f .tmp/dist/marketplace.xml
unzip -o .tmp/cdf/dist.zip -d .tmp End-of-central-directory signature not found. Either this file is not a zipfile, or it
constitutes one disk of a multi-part archive. In the latter case
the central directory and zipfile comment will be found on the last
disk(s) of this archive. unzip: cannot find zipfile directory in
.tmp/cdf/dist.zip,
and cannot find .tmp/cdf/dist.zip.zip, period.
chmod -R u+rwx .tmp
echo Done Done
Then the script ends. I have seen on this page (pentaho-bi-suite) that it is the normal output. Nevertheless, it seems a bit strange to me and when I start my pentaho server (login: admin/password), I cannot see any new tools in the menus.
After a look to a few other tutorials and the script itself, I have downloaded the .zip snapshots for every tool and unzipped them in the system directory of my pentaho server. Same result.
I would like to make the .sh works, what can I try or adjust ?
Thanks
EDIT 05/06/2014
I checked the dist.zip files dowloaded by the script and they are all empty. It seems that wget cannot fetch the zip files, and therefore the installation fails.
When I try to get any webpage through wget, it fails. I think it is because of the proxy.
Here is my .wgetrc file, located in my user's cygwin home folder:
use_proxy=on
http_proxy=http://[url]:[port]
https_proxy=http://[url]:[port]
proxy_user=[user]
proxy_password=[password]
How could I make this work?
EDIT 10/06/2014
In the end, I have changed my network connection settings to bypass the proxy. It seems that there is an offline mode for the installer, so one can download all needed files on a proxy-free environment and then run the script offline.
I guess this is related with the -r option.
I consider this post solved, since it not a CTools issue anymore.
Difficult to identify the issue in the above procedure..
but you can refer this blog he is key member of pentaho itself..
In the end, I have changed my network connection settings to bypass the proxy. It seems that there is an offline mode for the installer, so one can download all needed files on a proxy-free environment and then run the script offline. I guess this is related with the -r option.
I consider this post solved, since it is not a CTools issue anymore.
You can manually install the components from http://www.webdetails.pt/ctools/ or if you have pentaho 5.1 or above, you add the following parameters to CATALINA_OPTS option (in start-pentaho.bat or start-pentaho.sh):
-Dhttp.proxyHost= -Dhttp.proxyPort= -Dhttp.nonProxyHosts="localhost|127.0.0.1|10...*"
http://docs.treasuredata.com/articles/pentaho-dataintegration#tips-how-can-i-use-pentaho-through-a-proxy