Dear Prof. Peter,
The input for the getpapers was:
getpapers -q "((endophytic bacteria) AND (abiotic stress)) AND (PUB_TYPE:"Review" OR PUB_TYPE:"review-article")" -x -k 200 -o path\to\directory
Which made me download a total of 138 papers in the xml format.
Next, I created a dictionary with around 50 terms, using the command:
ami-dictionary create --terms "many" "terms" "were" "created" --dictionary name of the dictionary --directory path\to\directory -outformats xml,json,html
After running this command, I ran the command to search for the terms in my dictionary in the papers I downloaded to get the data table and the SVG diagrams.
The command I ran was:
ami-search-new -p path\to\files\inXML\format --dictionary path\to\my\dictionary
This normalized the xml to html format. But after doing this, when the count command was running to calculate the frequency of words, an error was thrown.
Please find attached a screenshot for the same.
Also. before this error was thrown, I got the tables for a test run but unfortunately, the SVG files were not formed.
I request you to kindly tell me how can I overcome this error.
The solution that I tried was changing the memory allocation for the JVM. I allocated a 2GB memory to it so that the heap space error can be overcomed, but I couldn't really find an alternative to the predicament.
Hope, the error gets resolved earlier and I can start my work soon.
Best
Rahul
Dear Prof. Peter,
The input for the getpapers was:
getpapers -q "((endophytic bacteria) AND (abiotic stress)) AND (PUB_TYPE:"Review" OR PUB_TYPE:"review-article")" -x -k 200 -o path\to\directoryWhich made me download a total of 138 papers in the xml format.
Next, I created a dictionary with around 50 terms, using the command:
ami-dictionary create --terms "many" "terms" "were" "created" --dictionary name of the dictionary --directory path\to\directory -outformats xml,json,htmlAfter running this command, I ran the command to search for the terms in my dictionary in the papers I downloaded to get the data table and the SVG diagrams.
The command I ran was:
ami-search-new -p path\to\files\inXML\format --dictionary path\to\my\dictionaryThis normalized the xml to html format. But after doing this, when the count command was running to calculate the frequency of words, an error was thrown.
Please find attached a screenshot for the same.
Also. before this error was thrown, I got the tables for a test run but unfortunately, the SVG files were not formed.
I request you to kindly tell me how can I overcome this error.
The solution that I tried was changing the memory allocation for the JVM. I allocated a 2GB memory to it so that the heap space error can be overcomed, but I couldn't really find an alternative to the predicament.
Hope, the error gets resolved earlier and I can start my work soon.
Best
Rahul