I have to traduce a code to another one in which you can upload the fasta file chosen by you and download the alignment in pdf format. I have tried during a long time and I cannot achieve it.
The code (you have to upload a specific file) is:
library(shiny)
library(msa)
runApp(list(
mySequences <- readDNAStringSet("/Users/-----/dna3.fas", format = "fasta"),
myFirstAlignment <- msa(mySequences),
ui = fluidPage(downloadButton('downloadPDF')),
server = function(input, output) {
output$downloadPDF = downloadHandler(
filename = 'myreport.pdf',
content = function(file) {
msaPrettyPrint(
myFirstAlignment
, file = 'myreport.pdf'
, output="pdf"
, showNames="none"
, showLogo="top"
, consensusColor="BlueRed"
, logoColors="accessible area"
, askForOverwrite=FALSE)
file.rename("myreport.pdf", file)
},
contentType = 'application/pdf'
)
}
))
II would appreciate any help. Thank you
Related
My flume config:
agent.sinks = s3hdfs
agent.sources = MySpooler
agent.channels = channel
agent.sinks.s3hdfs.type = hdfs
agent.sinks.s3hdfs.hdfs.path = s3a://mybucket/test
agent.sinks.s3hdfs.hdfs.filePrefix = FilePrefix
agent.sinks.s3hdfs.channel = channel
agent.sinks.s3hdfs.hdfs.useLocalTimeStamp = true
agent.sources.MySpooler.channels = channel
agent.sources.MySpooler.type = spooldir
agent.sources.MySpooler.spoolDir = /flume_to_aws
agent.sources.MySpooler.fileHeader = true
agent.channels.channel.type = memory
agent.channels.channel.capacity = 100
Now I will add a file in /flume_to_aws folder with the following content (text):
Oracle and SQL Server
After it is uploaded in S3, I downloaded the file and opened it, and it show the following text:
SEQ!org.apache.hadoop.io.LongWritable"org.apache.hadoop.io.BytesWritable
Œúg ÊC•ý¤ïM·T.C ! †"ûþ Oracle and SQL ServerÿÿÿÿŒúg ÊC•ý¤ïM·T.C
Why the file is not uploaded only with the text "Oracle and SQL Server"??
Problem solved. I have found this question in stackoverflow here
Flume is generating files in binary format instead of text format.
So, I have added the following lines:
agent.sinks.s3hdfs.hdfs.writeFormat = Text
agent.sinks.s3hdfs.hdfs.fileType = DataStream
I am currently uploading files to an Amazon S3 using MediaConvert via Lambda functions. However part of my processing is to create thumbnail images from uploaded videos. To do this I am using the AmazonMediaConvetClient and creating a job request.
However the files that are generated have a suffix applied to them of 0000000 which from what I can gather is in reference to the frame captured.
However I do not want this suffix on the filename. Is there anyway to ensure that the filename created from a video thumbnail is what I specify with no suffix?
var jpgOutput = new Output
{
NameModifier = $"-Medium",
ContainerSettings = new ContainerSettings { Container = ContainerType.RAW },
Extension = "jpg",
VideoDescription = new VideoDescription
{
CodecSettings = new VideoCodecSettings()
{
Codec = VideoCodec.FRAME_CAPTURE,
FrameCaptureSettings = new FrameCaptureSettings()
{
MaxCaptures = 1, Quality = 100
}
},
Height = thumbnail.Height,
Width = thumbnail.Width
}
};
In the code snippet above the file is created as 1-Medium.000000.jpg but I want 1-Medium.jpg
I have a latex file with bib text file. I have the problem that I would like to add on my literatur add my local pdf path so that when i have my pdf file I can open it direktly from my local hard drive.
Latex:
\bibliographystyle{natdin}
\bibliography{Literatur}
example in my file "Literatur.bib":
#article{myarticle,
author = {my autor},
year = {2016},
title = {my title},
url = {http://myarticle.org/myarticle.pdf},
urldate = {08.12.2016},
file = {...\\myfolder\\12341234.pdf:pdf}
}
What I get:
my autor, 2016, my title, http://myarticle.org/myarticle.pdf
What I want:
my autor, 2016, my title, http://myarticle.org/myarticle.pdf, 12341234.pdf
You can use the note field to hold an external href link, like so:
#article{myarticle,
author = {my autor},
year = {2016},
title = {my title},
url = {http://myarticle.org/myarticle.pdf},
urldate = {08.12.2016},
note = {\href{run:../myfolder/12341234.pdf}{12341234.pdf}},
}
Note the corrected path format. The result will be like this:
I'm new to CodeIgniter and having the following issue. When I upload a file, its successfully uploaded on my local folder and the file name saved to the db. The problem is, file name has been changed after uploading.
eg:
file name "screenshot image 123.png" -> "screenshot_image_123.png"
It just convert the space into underscore;this issue occurred only when the file name having space.Other than this issue all the other files uploading successfully. Given below is my code which I used on my controller page:
public function upload_pic()
{
$image_path = realpath(APPPATH . '../uploads');
$config['upload_path'] = $image_path;
$config['allowed_types'] = "gif|jpg|jpeg|png";
$config['file_name'] = $_FILES['file']['name'];
$config['encrypt_name'] = TRUE;
$config['overwrite'] = TRUE;
$this->load->library('upload',$config);
$this->upload->initialize($config);
if(!$this->upload->do_upload('file'))
{
echo $this->upload->display_errors();
}
else
{
$finfo=$this->upload->data();
$data['uploadInfo'] = $finfo;
}
}
Can anyone help me????
Try before saving file name generate some unique
$filename = $_FILES['file']['name'];
$ext = pathinfo($filename, PATHINFO_EXTENSION);
$filename = sha1_file($filename). md5(date('Y-m-d H:i:s:u')) . '.'. $ext; //not only this you can generate any format
$config['file_name'] = $filename; //Use this file name is db too
i was searching for a way to upload a file to server and found the following code ..
File file ;
int maxFileSize = 5000 * 1024;
int maxMemSize = 5000 * 1024;
ServletContext context = pageContext.getServletContext();
String filePath = context.getInitParameter("file-upload");
// Verify the content type
String contentType = request.getContentType();
if ((contentType.indexOf("multipart/form-data") >= 0)) {
DiskFileItemFactory factory = new DiskFileItemFactory();
// maximum size that will be stored in memory
factory.setSizeThreshold(maxMemSize);
// Location to save data that is larger than maxMemSize.
factory.setRepository(new File("/user2/tst/test"));
// Create a new file upload handler
ServletFileUpload upload = new ServletFileUpload(factory);
// maximum file size to be uploaded.
upload.setSizeMax( maxFileSize );
try{
// Parse the request to get file items.
List fileItems = upload.parseRequest(request);
// Process the uploaded file items
Iterator i = fileItems.iterator();
out.println("<html>");
out.println("<head>");
out.println("<title>JSP File upload</title>");
out.println("</head>");
out.println("<body>");
while ( i.hasNext () )
{
FileItem fi = (FileItem)i.next();
if ( !fi.isFormField () )
{
// Get the uploaded file parameters
String fieldName = fi.getFieldName();
String fileName = fi.getName();
boolean isInMemory = fi.isInMemory();
long sizeInBytes = fi.getSize();
// Write the file
if( fileName.lastIndexOf("\\") >= 0 ){
file = new File( filePath +
fileName.substring( fileName.lastIndexOf("\\"))) ;
}else{
file = new File( filePath +
fileName.substring(fileName.lastIndexOf("\\")+1)) ;
}
fi.write( file ) ;
out.println("Uploaded Filename: " + filePath +
fileName + "<br>");
}
}
out.println("</body>");
out.println("</html>");
}catch(Exception ex) {
System.out.println(ex);
}
}else{
out.println("<html>");
out.println("<head>");
out.println("<title>Servlet upload</title>");
out.println("</head>");
out.println("<body>");
out.println("<p>No file uploaded</p>");
out.println("</body>");
out.println("</html>");
}
this code is working perfectly fine .. the only problem i am facing is , the file that is updated is getting stored in apache/bin folder ..
for this it was specified to add the following code to web.xml that is available in ROOT/WEB-INF
<context-param>
<description>Location to store uploaded file</description>
<param-name>file-upload</param-name>
<param-value>
/user2/tst
</param-value>
</context-param>
even after this the file is getting stored in bin folder ..
i needed some help in this regard .. thanks in advance ..