Develop Reference

stanford nlp coreference resolution error: Exception in thread "main" java.lang.IllegalArgumentException: File doesn't exist: example_file.txt

I downloaded stanfordCoreNLP module version stanford-corenlp-full-2018-02-27 from the download page and unzipped the file. created a example_file.txt file in the directory where it was extracted. I added the text My name is Sam. I want to be an astronaut. I had snacks a while ago.. I navigated to the folder it was extracted to and tried to run the example code given for co-reference resolution in the command line
stanfordNLP page
java -Xmx5g -cp stanford-corenlp-3.9.1.jar:stanford-corenlp-3.9.1-sources.jar:* edu.stanford.nlp.pipeline.StanfordCoreNLP -annotators tokenize,ssplit,pos,lemma,ner,parse,mention,coref -coref.algorithm neural -file example_file.txt
I am getting below error message
Exception in thread "main" java.lang.IllegalArgumentException: File doesn't exist: example_file.txt
at edu.stanford.nlp.io.FileSequentialCollection$FileSequentialCollectionIterator.primeNextFile(FileSequentialCollection.java:364)
at edu.stanford.nlp.io.FileSequentialCollection$FileSequentialCollectionIterator.<init>(FileSequentialCollection.java:269)
at edu.stanford.nlp.io.FileSequentialCollection.iterator(FileSequentialCollection.java:238)
at edu.stanford.nlp.pipeline.StanfordCoreNLP.processFiles(StanfordCoreNLP.java:1166)
at edu.stanford.nlp.pipeline.StanfordCoreNLP.processFiles(StanfordCoreNLP.java:1010)
at edu.stanford.nlp.pipeline.StanfordCoreNLP.run(StanfordCoreNLP.java:1365)
at edu.stanford.nlp.pipeline.StanfordCoreNLP.main(StanfordCoreNLP.java:1427)
Any help on this?

Java lookup resources within the classpath that you defined with -cp option. The directory that contains example_file.txt should probably be included in it
-cp ".:stanford-corenlp-3.9.1.jar:stanford-corenlp-3.9.1-sources.jar:*"
The dot added to the class path means this directory which apparently contains your file. Also, double quotes prevent the shell to expand the wildcard at the end that it should not be there in my opinion unless it contains jars relevant to the app. At most, it could be *.jar.

Java error while running maxent in biomod2

I am running maxent from R, in the package biomod2 and the following error appeared. I do not come from a technical background and wasn't sure why is this error happening. Is it a memory problem or someone said the java path is not set. But I followed the instructions to set maxent to run in R and also downloaded Java Platform, Standard Edition Development Kit and set a path for it as explained in this pdf: http://modata.ceoe.udel.edu/dev/dhaulsee/class_rcode/r_pkgmanuals/MAXENT4R_directions.pdf
I would be really grateful if you could help me understand this problem and any solution to it.
Thanks a lot
Error in file(file, "rt") : cannot open the connection
In addition: Warning messages:
1: running command 'java' had status 1
2: running command 'java -mx512m -jar E:\bioclim_2.5min\model/maxent.jar environmentallayers
="rainfed/models/1432733200/m_47203134/Back_swd.csv"
samplesfile="rainfed/models/1432733200/m_47203134/Sp_swd.csv"
projectionlayers="rainfed/models/1432733200/m_47203134/Predictions/Pred_swd.csv"
outputdirectory="rainfed/models/1432733200/rainfed_PA1_Full_MAXENT_outputs"
outputformat=logistic redoifexists visible=FALSE linear=TRUE quadratic=TRUE
product=TRUE threshold=TRUE hinge=TRUE lq2lqptthreshold=80 l2lqthreshold=10
hingethreshold=15 beta_threshold=-1 beta_categorical=-1 beta_lqp=-1
beta_hinge=-1 defaultprevalence=0.5 autorun nowarnings notooltips
noaddsamplestobackground' had status 1
3: In file(file, "rt") :
cannot open file 'rainfed/models/1432733200/rainfed_PA1_Full_MAXENT_outputs/rainfed_PA1_
Full_Pred_swd.csv': No such file or directory

I've just manage to solve this problem - it is a problem with the file path specified. For me, I had a space in one of the folder names which was not accepted in the path to the maxent.jar file. From looking at your error, it looks like it might be the two backslashes.
E:\bioclim_2.5min\model/maxent.jar
should probably read
E:/bioclim_2.5min/model/maxent.jar

R xlsx package error

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, :
java.util.zip.ZipException: invalid code -- missing end-of-block
Does anyone have this error when you try to use
dat <- read.xlsx("data.xlsx", sheetIndex=1, colIndex=colIndex, rowIndex=rowIndex)?

I had this problem with a file downloaded from the internet using R command line, for an online course. Found that apparently the download mode needs to be set properly as write-binary (wb) since xlsx is basically a binary file (zip). Who knew?
If that's what you did too, re-download the file with the mode set properly; like:
download.file(fileUrl, destfile='./data/sample.xlsx', mode='wb')

The version of java you have installed is likely incompatible with the xslx package. Try replacing your default java with the 64 bit version: https://www.java.com/en/download/faq/java_win64bit.xml.

cannot find org.neo4j.batchimport

I am continuing to have trouble with the import.bat file for the Neo4j batch importer. I started a new thread as the original problem was resolved.
from the command prompt I run
import.bat test.db sample\nodes.csv sample\rels.csv
With some variations on the path listing for the files, including absolute paths. I continue to get the following error message
The system cannot find the path specified.
Error: Could not find or load main class org.neo4j.batchimport.Importer
I also tried running import.sh from Cygwin and in my Debian VM but keep getting the error
Error: Could not find or load main class org.neo4j.batchimport.Importer
What am I doing wrong?

Please download the zip-file, not the github clone.
This is a pre-build binary as outlined in the readme, that doesn't require that you have to have maven installed to build it.

Error in installing DBpedia Spotlight while running the server class in jar

I get the following error:
org.dbpedia.spotlight.exceptions.ConfigurationException: Cannot find spotter file ../dist/src/deb/control/data/usr/share/dbpedia-spotlight/spotter.dict
at org.dbpedia.spotlight.model.SpotterConfiguration.<init>(SpotterConfiguration.java:54)
at org.dbpedia.spotlight.model.SpotlightConfiguration.<init>(SpotlightConfiguration.java:143)
at org.dbpedia.spotlight.web.rest.Server.main(Server.java:70)
Usage:
java -jar dbpedia-spotlight.jar org.dbpedia.spotlight.web.rest.Server [config file]
or:
mvn scala:run "-DaddArgs=[config file]"

Quick solution:
wget http://spotlight.dbpedia.org/download/release-0.5/dbpedia-spotlight-quickstart.zip
unzip dbpedia-spotlight-quickstart.zip
cd dbpedia-spotlight-quickstart/
./run.sh
Explanation:
DBpedia Spotlight looks for ~3.5M things of ~320 types in text and tries to disambiguate them to their global unique identifiers in DBpedia. Therefore it needs data files to accompany its jar. A minuscule example is distributed along with the source, but for real use cases you may need the larger files. After you've downloaded the files, you need to modify the configuration in server.properties with the correct path to the files. The error message you got tells you that one of the necessary files (spotter.dict) could not be found in the path you indicated in your server.properties.
More information available here:
https://github.com/dbpedia-spotlight/dbpedia-spotlight/wiki/Run-from-a-JAR