Hello,
What is the template for where the raw files are stored once they are imported? Currently, I am importing files into an Assay run without filling out any of the run properties and just clicking "save and import next file", mostly because the files are named in a specific format and I don't want to have to re-input the name of each file for each assay id. In the R view I am creating, when I print out labkey.data, it has columns for links, name, run_groups, batch, batch_name, folder, rowid, batch_folder, batch_rowid, among some other ones. Is there a way for me to take the information in labkey.data to access those raw files?
Right now, I am guessing where the files are stored. The error is that the path to the files that I am guessing does not exist in current working directory ('/usr/bin/apache-tomcat-7.0.57/temp/reports_temp/Report_db_58/40'), which is why I am curious if there is a way to build a valid path to the files using the information from labkey.data |
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| Jon (LabKey DevOps) responded: |
2015-07-23 16:55 |
Hello,
When you import an Assay Run, the file should end up in the @files/assaydata directory for the Assay's folder/project under LABKEY_HOME/files/ and then the project name (and folder path), the @files directory, then the assaydata subdirectory.
You should be able to do something like read.csv(file="FULL_FILE_PATH", header=TRUE, sep=",") and dictate the physical path of the file that contains the assay run data.
Regards,
Jon |
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