Does anyone have an implementation of a program that downloads pubmed abstracts with title, author, date, and content to separate plaintext files given a MESH term?
http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_java_help.html has an example. It worked for me like a charm.
I posted the code as a maven project on github
There is a built-in function for downloading different type of files (for example XML, CSV, and plain text files) right on the PubMed homepage. Just make a search and then select "Send to" where you'll be given a plethora of options.
As an alternative to esoap you can also use RESTful API.
Assuming that you want to get all articles with MESH keyword: galactosylceramides then your query would look like:
http://www.ebi.ac.uk/europepmc/webservices/rest/search/resulttype=core&query=KW:galactosylceramides
Of course, you have to parse xml result, but I don't think it's a big problem.
There is an example here, but not in Java. http://www.ncbi.nlm.nih.gov/books/NBK25500/
Related
I would like to know if there are any java libaries which can extract the plain text of a .lyx document, so that I get the unformated content for further analysis. This seems like a relatively easy job, but I so long, I didn't find anything which I could integrate in my project.
Daniel
I'm developing an application where I've requested data from an external institution's website. They have informed me that the data will be provided by OAI-PMH.
Could someone show me some sample code in Java how data is extracted from a OAI-PMH ?
I wonder how different it is from reading and parsing XML data.
Thank you.
Warmest wishes,
Shoubhik
For a Java implementation, for example, you could use some already existent library, like XOAI with an easy to use API. There are some provided samples.
To extract metadata from each Record you could use a XML Parser or a XML bind approach (JAXB). For other languages, like PHP and Perl there are also other alternatives.
How can I merge individual selected PDF files into one PDF upon download?
I want to achieve the following:
http://annualreport2010.landsecurities.com/create-your-own-report.aspx
Do I require an ASP website, or could I do something similar using a static HTML site?
Static HTML won't do it.
You need something on the server side. The other answers have options that would work, I just wanted to also mention pdftk, which you could then call from the server side. Be sure to escape all file names and such, though, because you would have to use system calls.
pdftk is really easy. The very first example from their documentation shows how to merge several PDFs, named 1.pdf, 2.pdf and 3.pdf, into one PDF called 123.pdf:
pdftk 1.pdf 2.pdf 3.pdf cat output 123.pdf
For PHP, there even is pdftk-php, if you want to look into that.
I think that the Apache PDFBox project can be good for you.
In particular, take a look at the PDFMerger class.
You can also use iText but in my opinion it's less easy to use.
See if itext can help in merging. A quick search gives many links - like Java: Merging multiple PDFs into a single PDF using iText.
There is a Java PDF merging software at http://codesforus.blogspot.com/.
p.s. They link to this download page: http://messiahpsychoanalyst.org/Documents/Downloads.html#part1
You can find Source code for PDF split and Merge Source forge PDF SAM
I have a set of complex Excel files (with figures in it) that I want to show in a web browser. So I need to convert them into HTML page first. Since the excel files are very complex, I can not just parse them and generate a HTML table with HTML tags. The current manual solution that works fine is when I use Microsoft Excel software to save the spreadsheet as a HTML page. I want to automate this task in some way since I want to do it progrmatically through Java. Is their any existing solution or a way to do it? Thanks.
EDIT - I was able to create a macro for it but could not figure it out that how can I execute a macro on excel file from a Java program. Does somebody know?
If open office does a good job of the export then you could take a look at the source to see how it does it. OO is a combination of Java and C++ I believe so you might get lucky and find a Java solution.
Otherwise, I would try and use Excel itself to do the export and find some way of calling it programmatically. If you go down this path you'd be better of using a Microsoft stack (C# would be the most similar to Java) as I would expect it to have all the functions you need already defined.
You might look into POI:
http://poi.apache.org/
I think your best bet is to call Excel from Java using JACOB
Creating direct COM calls (which is what you'll be doing from JACOB) is a bit tough, but you'll get the hang of it. I can't imagine that the Excel VBA macro is horribly complicated. Take a look at the sample code (Usage and Documentation) in the JACOB link for what this will look like.
One other thing: Remember to explicitly clear references. JACOB will release COM handles when objects are garbage collected, but if you are doing any sort of high performance work, you will want to close those connections as quickly as possible. We generally write all of our COM code in a series of try/finally statements - the code is messy, but robust.
Try using hypernumbers. (Disclaimer, I'm the CEO)
I ended up using the Scribd API. I uploaded the document to their server through their API in realtime and pasted an iframe with a link in it which is returned by Scribd.
I am helping someone out with a javascript-based web app (even though I know next to nothing about web development) and we are unsure about the best way to implement a feature we'd like to have.
Basically, the user will be using our tool to view all kinds of boring data in tables, columns, etc. via javascript. We want to implement a feature where the user can click a button or link that then allows the user to download the displayed data in a .doc file.
Our basic idea so far is something like:
call a Java function on the server with the desired data passed in as a String when the link is clicked
generate the .doc file on the server
automatically "open" a link to the file in the client's browser to initiate the download
Is this possible? If so, is it feasible? Or, can you recommend a better solution?
edit: the data does not reside on the server; rather, it is queried from a SQL database
Yep, its possible. Your saviour is the Apache POI library. Its HWPF library will help you generate Microsoft word files using java. The rest is just clever use of HTTP.
Your basic idea sounds a bit Rube-Goldbergesque.
Is the data you want in the document present on the server? If so, then all you need to do is display a plain HTML link with GET parameters that describes the data (i.e. data for customer X from date A to date B). The link will be handled on the server by a Servlet that gets the data and produces the .DOC file as its output to be downloaded by the browser - a very simple one-step process that doesn't even involve any JavaScript.
Passing large amount data as GET/POST around might not be the best idea. You could just pass in the same parameters you used to generate the HTML page earlier. You don't even need to use 3rd party library to generate DOC. You could just generate a plain old HTML file with DOC extension and Word will be happy to open it.
Sounds like Docmosis Java library could help - check out theonline demo since shows it something similar to what you're asking - generating a real doc file from a web site based on selections in the web page. Docmosis can query from databases and run pretty much anywhere.