V1.2

[aledj2]

This change is 

[andyb3]

+@andyb3

Reviewed 2 of 2 files at r1.
Reviewable status: all files reviewed, 7 unresolved discussions (waiting on @aledj2 and @NMNS93)

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backup_runfolder.py, line 84 at r1 (raw file):

    # Os.path.expanduser allows expands tilde signs (~) to a string containing the user home directory.
    parser.add_argument('-i', '--runfolder', required=True, help='An Illumina runfolder directory', type=os.path.expanduser)
    parser.add_argument('-a', '--auth-token', help='A string or file containing a DNAnexus authorisation key used to access the DNANexus project. Default = ~/.dnanexus_auth_token', default='~/.dnanexus_auth_token', type=os.path.expanduser)

The auth key is now located in /usr/local/src/mokaguys/

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backup_runfolder.py, line 337 at r1 (raw file):

        
        local_file_count = "find " + self.runfolder + " -type f " + grep_ignore + " | wc -l"
        print (local_file_count)

Is this print statement needed?

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backup_runfolder.py, line 343 at r1 (raw file):

        (out, err) = proc.communicate()
        # Write output stream to logfile and terminal
        self.logger.info('%s files to be uploaded (excluding any with ignore terms in filename or path)', out.decode().rstrip())

These should already have been uploaded by this point? Could 'files to be uploaded' be changed to 'files should have been uploaded'

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backup_runfolder.py, line 347 at r1 (raw file):

        # count number of uploaded files
        uploaded_file_count = "dx find data --project %s | wc -l" % (self.project)
        print(uploaded_file_count)

Is this print statement needed?

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backup_runfolder.py, line 353 at r1 (raw file):

        (out, err) = proc.communicate()
        # Write output stream to logfile and terminal
        self.logger.info('%s files present in project', out.decode().rstrip())

Could this be 'present in DNAnexus project'?

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backup_runfolder.py, line 358 at r1 (raw file):

            # test for presense of any ignore strings in project
            uploaded_file_count_ignore = "dx find data --project %s " % (self.project) + grep_ignore.replace("-v","") + " | wc -l" 
            print (uploaded_file_count_ignore)

Is this print statement needed?

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backup_runfolder.py, line 364 at r1 (raw file):

            (out, err) = proc.communicate()
            # Write output stream to logfile and terminal
            self.logger.info('%s files present in project containing one of the ignore terms. NB this may not be accurate if the ignore term is found in the result of dx find data (eg present in project name)', out.decode().rstrip())

Could this be 'present in DNAnexus project'?

[aledj2]

Reviewable status: 1 of 2 files reviewed, 7 unresolved discussions (waiting on @andyb3 and @NMNS93)

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backup_runfolder.py, line 84 at r1 (raw file):

Previously, andyb3 wrote…

The auth key is now located in /usr/local/src/mokaguys/

Done.

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backup_runfolder.py, line 337 at r1 (raw file):

Previously, andyb3 wrote…

Is this print statement needed?

Done.

---

backup_runfolder.py, line 343 at r1 (raw file):

Previously, andyb3 wrote…

These should already have been uploaded by this point? Could 'files to be uploaded' be changed to 'files should have been uploaded'

Done.

---

backup_runfolder.py, line 347 at r1 (raw file):

Previously, andyb3 wrote…

Is this print statement needed?

Done.

---

backup_runfolder.py, line 353 at r1 (raw file):

Previously, andyb3 wrote…

Could this be 'present in DNAnexus project'?

Done.

---

backup_runfolder.py, line 358 at r1 (raw file):

Previously, andyb3 wrote…

Is this print statement needed?

Done.

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backup_runfolder.py, line 364 at r1 (raw file):

Previously, andyb3 wrote…

Could this be 'present in DNAnexus project'?

Done.

[andyb3]

Reviewed 1 of 1 files at r2.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @NMNS93)