I'm trying to import some nodes+relationships using neo4j-import but seem to have encountered some problems. I went into the bin directory, where the import tool is hosted, and typed in the following:
./neo4j-import --into graph.db --nodes CLass.csv --nodes Company.csv --nodes Person.csv --nodes ResearchField.csv --nodes ResearchGroup.csv --nodes project.csv --relationships rels.csv
Below are the a snapshot of my files when I type in "emacs":
Class.csv:
ClassId:ID,name,:LABEL
3,Discrete Mathematics,Class
4,Introduction to Digital Design,Class
5,Solar System Physics,Class
Company.csv
CompanyId:ID,name,:LABEL
395,AirForce,Company
396,MITRE Corporation,Company
397,Lockheed Martin,Company
The other nodes are structured in a similar way. As for emacs rels.csv, this is what I have:
:START_ID,:END_ID,:TYPE
422,446,Directs
422,447,researches
422,430,researches
However, when I tried to execute, this error message is returned: ]
Input error: Expected '--nodes' to have at least 1 item, but had 0 ([])
...and if I remove the "./" in the beginning, this is returned:
bash: neo4j-import: command not found
Can you guys let me know what did I do wrong?
It might be the capital L in your filename (CLass.csv) which might cause it to find nothing.
Otherwise I would try it with only one --nodes argument at a time to figure out which file is the problem and go from there.
The ./ is definitely needed as that is how you execute binaries on *NIX-style systems
Related
I'm getting this error on Arduino(1.8.9).
usage: esptool write_flash [-h] [--erase-all]
[--flash_freq {keep,40m,26m,20m,80m}]
[--flash_mode {keep,qio,qout,dio,dout}]
[--flash_size FLASH_SIZE]
[--spi-connection SPI_CONNECTION] [--no-progress]
[--verify] [--compress | --no-compress]
<address> <filename> [<address> <filename> ...]
esptool write_flash: error: argument <address>
<filename>: [Errno 2] No such file or directory:'/home/USER/.arduino15/packages/esp32/hardware/esp32/1.0.2/tools/partitions/boot_app0.bin'
esptool write_flash: error: argument <address> <filename>: [Errno 2] No such file or directory: '/home/USER/.arduino15/packages/esp32/hardware/esp32/1.0.2/tools/partitions/boot_app0.bin'
Although boot_app0.bin file is present:
image link
To fix this problem you can try to edit the platform.txt file which you can find in your esp package directory.
So, you need to replace inner section with code written below:
## Combine gc-sections, archives, and objects
recipe.c.combine.pattern={recipe.hooks.linking.prelink.1.pattern} & "{compiler.path}{compiler.c.elf.cmd}" {build.exception_flags} -Wl,-Map "-Wl,{build.path}/{build.project_name}.map" {compiler.c.elf.flags} {compiler.c.elf.extra_flags} -o "{build.path}/{build.project_name}.elf" -Wl,--start-group {object_files} "{archive_file_path}" {compiler.c.elf.libs} -Wl,--end-group "-L{build.path}" & {recipe.objcopy.hex.1.pattern}
The key thing here is "{recipe.hooks.linking.prelink.1.pattern} &" at start and "& {recipe.objcopy.hex.1.pattern}" at the end. The text between is the part of the platform.txt file, that you dont need to change.
The above is true for OS Windows. In OS Linux set {recipe.hooks.linking.prelink.1.pattern} ;" and "; {recipe.objcopy.hex.1.pattern}".
Its solve my problem for ESP8266, I hope its will be helpful for you too.
Reference link https://www.eclipse.org/forums/index.php/t/1095090/
if you are using esptool. Make sure you actually download the files from github using the download button instead of using the save as option when u right click on the file name.
I've read plenty of articles about this issue on here, but I still can't seem to get around this issue. I've been trying to use Neo4j-import on some large genome data CSVs I have, but it doesn't seem to recognise the files. My command line input is as follows:
user#LenovoPC ~/.config/Neo4j Desktop/Application/neo4jDatabases/database-2f182948-e170-45b1-b9f4-19d236ff5d43/installation-3.5.1 $ \
bin/neo4j-import --into data/databases/graph.db --id-type string \
--nodes:Allele variants.csv --nodes:Chromosome chromosome.csv --nodes:Phenotype phenotypes.csv \
--nodes:Sample samples.csv --relationships:BELONGS_TO variant_chromosomes.csv \
--relationships: sample_phenotypes.csv --relationships:ALTERNATIVE_TO variant_variants.csv \
--relationships:HAS sample_variants50-99.csv.gz
But I'm getting the following error:
WARNING: neo4j-import is deprecated and support for it will be removed in a future version of Neo4j; please use neo4j-admin import instead.
Input error: Expected '--nodes' to have at least 1 valid item, but had 0 []
Caused by:Expected '--nodes' to have at least 1 valid item, but had 0 []
java.lang.IllegalArgumentException: Expected '--nodes' to have at least 1 valid item, but had 0 []
at org.neo4j.kernel.impl.util.Validators.lambda$atLeast$6(Validators.java:144)
at org.neo4j.helpers.Args.validated(Args.java:670)
at org.neo4j.helpers.Args.interpretOptionsWithMetadata(Args.java:637)
at org.neo4j.tooling.ImportTool.extractInputFiles(ImportTool.java:623)
at org.neo4j.tooling.ImportTool.main(ImportTool.java:445)
at org.neo4j.tooling.ImportTool.main(ImportTool.java:380)
I included the file path, as I'm using Neo4j Desktop and am not sure if this has a different file structure? My csv files are stored in the import folder (but I also have copies in the current folder and the graph.db folder just in case).
The import directory is as follows:
user#LenovoPC ~/.config/Neo4j Desktop/Application/neo4jDatabases/database-2f182948-e170-45b1-b9f4-19d236ff5d43/installation-3.5.1/import $ dir
chromosomes.csv samples.csv variants.csv
phenotypes.csv sample_variants50-99.csv.gz variants.csv.gz
sample_phenotypes.csv variant_chromosomes.csv
variant_variants.csv
I can only assume that it's my filepath, but I've tried quite a few alternatives and had no luck at all. If anyone could shed some light on what the issue is, I would really appreciate it!
Best is to cd into the desktop directory, place the csv files into the import folder.
then you can do:
cd ~/.config/Neo4j Desktop/Application/neo4jDatabases/database-2f182948-e170-45b1-b9f4-19d236ff5d43/installation-3.5.1
bin/neo4j-import --into data/databases/graph.db --id-type string \
--nodes:Allele import/variants.csv \
--nodes:Chromosome import/chromosome.csv \
--nodes:Phenotype import/phenotypes.csv \
--nodes:Sample import/samples.csv \
--relationships:BELONGS_TO import/variant_chromosomes.csv \
--relationships import/sample_phenotypes.csv \
--relationships:ALTERNATIVE_TO import/variant_variants.csv \
--relationships:HAS import/sample_variants50-99.csv.gz
Some more notes:
HAS is a pretty generic relationship type
I left off the colon here: --relationships import/sample_phenotypes.csv not sure if you have the rel-type in the file
is this a single file? --relationships:HAS import/sample_variants50-99.csv.gz
I have 25GB TSV file and trying to import it with command:
D:\sphinx\bin>indexer.exe -c D:\sphinx\sphinx.conf products --rotate
It works some time, but then shows error
ERROR: index 'products': source 'products_tsv': read error 'No error' (line=4595827, pos=908, docid=4595827).
But record at line 4595827 have no problems.
I have two questions:
What's usually causes this problem?
Does indexer have any flags for ignoring errors?
Lost a lot of time on checking datafile and found a lot of hidden symbols such as SYM (\U001A), NULL (\0000) and a more of them, which turns Sphinx crazy.
Simply(if «simply» can be said about 25GB file) replaced all SYM to ' and removed others.
We moved forward and faced another issue, but this is another question.
Try to add extra line break after the last line in your .tsv data source, so the last line is empty. In my case it helped. Thanks to #stefobark and his repository stefobark/index_tsv
I have a problem with path in a tcl file. I tried to use
source " /tmp/mob.tcl "
and this path in bash file :
/opt/ns-allinone-2.35/ns-2.35/indep-utils/cmu-scen-gen/setdest/setdest -v 1 -n $n -p 10 -M 64 -t 100 -x 250 -y 250 >> /tmp/mob.tcl
The terminal give me this output:
..."
(procedure "source" line 8)
invoked from within
"source "/tmp/mob.tcl" "
(file "mobilita_source.tcl" line 125)
How I can do this?
Firstly, this:
source " /tmp/mob.tcl "
is very unlikely to be correct. The spaces around the filename inside the quotes will confuse the source command. (It could be correct, but only if you have a directory in your current directory whose name is a single space. That's really unlikely, unless you're a great deal more evil than I am.)
It really helps a lot if you stop making this error.
Secondly, the error message is both
Incomplete, with just an ellipsis instead of a full error on the first line
Really worrying, with source claimed to be a procedure (second line of that short trace).
It's legal to make a procedure called source, and sometimes the right thing to do, but if you're doing it then you have to be ever so careful to duplicate the semantics of the standard Tcl command or odd things will happen.
Thirdly, you've got a file of what is apparently generated code, and you're hitting a problem in it, and you're not telling us what is on/around line 125 of the file (the error trace is pretty clear on that front) or in the contents of the source procedure (which is non-standard; the standard source is implemented in C) and you're expecting us to guess what's going wrong for you??? Seriously?
Tcl error traces are usually quite clear enough for you to figure out what went wrong and where. If there's an unclear error, and it didn't come from user code (by calling error or return -code error) then let us know; we'll help (or possibly even change Tcl to make things clearer in the future). But right now, there's a complete shortage of information.
Here's an example of what a normal source error looks like:
% source /tmp/foo/bar/boo
couldn't read file "/tmp/foo/bar/boo": no such file or directory
% puts $errorInfo
couldn't read file "/tmp/foo/bar/boo": no such file or directory
while executing
"source /tmp/foo/bar/boo"
If a script generates an error directly, it's encouraged to be as clear as that, but we cannot enforce it. Sometimes you have to be a bit of a detective yourself…
I'm compiling a deb package and when I run dpkg-buildpackage I get:
dpkg-shlibdeps: error: no dependency information found for /usr/local/lib/libopencv_highgui.so.2.3
...
make: *** [binary-arch] Error 2
This happens because I installed the dependency manually. I know that the problem will be fixed if I install the dependency (or use checkinstall), and I want to generate the package anyway because I'm not interested on dependency checking. I know that I can give to dpkg-shlibdeps the option --ignore-missing-info which prevents a fail if dependency information can't be found. But I don't know how to pass this option to dpkg-shlibdeps since I'm using dpkg-buildpackage and dpkg-buildpackage calls dpkg-shlibdeps...
I have already tried:
sudo dpkg-buildpackage -rfakeroot -d -B
And with:
export DEB_DH_MAKESHLIBS_ARG=--ignore-missing-info
as root.
Any ideas?
use:
override_dh_shlibdeps:
dh_shlibdeps --dpkg-shlibdeps-params=--ignore-missing-info
if your rule file hasn't the dh_shlibdeps call in it. That's usually the case if you've
%:
dh $#
as only rule in it ... in above you must use a tab and not spaces in front of the dh_shlibdeps
If you want it to just ignore that flag, change the debian/rules line from:
dh_shlibdeps
to:
dh_shlibdeps --dpkg-shlibdeps-params=--ignore-missing-info
Yet another way, without modifying build scripts, just creating one file.
You can specify local shlib overrides by creating debian/shlibs.local with the following format: library-name soname-version dependencies
For example, given the following (trimmed) ldd /path/to/binary output
libevent-2.0.so.5 => /usr/lib/libevent-2.0.so.5 (0x00007fc9e47aa000)
libgcrypt.so.20 => /usr/lib/libgcrypt.so.20 (0x00007fc9e4161000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fc9e3b1a000)
The contents of debian/shlibs.local would be:
libevent-2.0 5 libevent-2.0
libgcrypt 20 libgcrypt
libpthread 0 libpthread
The "dependencies" list (third column) doesn't need to be 100% accurate - I just use the library name itself again.
Of course this isn't needed in a sane debian system which has this stuff defined in /var/lib/dpkg/info (which can be used as inspiration for these overrides). Mine isn't a sane debian system.
Instead of merely ignoring the error, you might also want to fix the source of the error, which is usually either a missing or an incorrect package.shlibs or package.symbols file in package which contains the shared library triggering the error.
[1] documents how dpkg-shlibdeps uses the package.shlibs resp. package.symbols, files, [2] documents the format of the package.shlibs and package.symbols files.
[1] https://manpages.debian.org/jessie/dpkg-dev/dpkg-shlibdeps.1.en.html
[2] https://www.debian.org/doc/debian-policy/ch-sharedlibs.html
You've just misspelled your export. It should be like this:
export DEB_DH_SHLIBDEPS_ARGS_ALL=--dpkg-shlibdeps-params=--ignore-missing-info
dpkg-buildpackage uses make to process debian/rules. in this process, dpkg-buildpackage it might call dpkg-shlibdeps.
thus, the proper way to pass modify a part of the package building process is to edit debian/rules.
it's hard to give you any more hints, without seeing the actual debian/rules.
Finally I did it in the brute way:
I edited the script /usr/bin/dpkg-shlibdeps, changing this :
my $ignore_missing_info = 0;
to
my $ignore_missing_info = 1;
You can use this:
dh_makeshlibs -a -n
exactly after dh_install