Merge branch 'master' of https://github.com/jhu-archives-and-manuscripts/file-management

Author: Elizabeth England

.gitignore

@@ -45,3 +45,4 @@ $RECYCLE.BIN/
 Network Trash Folder
 Temporary Items
 .apdisk
+*.csv

README.md

@@ -2,13 +2,19 @@
 Scripts for moving files and renaming directories
 
 #### [collapseDirectories.py](/collapseDirectories.py)
-Based on the file path entered, this script moves any file existing below the eighth level folder in a Linux directory structure (i.e. /media/bitCurator/Storage/Collection/IncomingTransfer/BatchNumber/Disc/JobName) up to the eigth level folder. The script writes a log of all files that were moved, including their old location and their new location. The log is written in the command line utility's home directory.
+Based on the file path entered, this script moves any file existing below the eighth level folder in a Linux directory structure (i.e. /media/bitCurator/Storage/Collection/IncomingTransfer/BatchNumber/Disc/JobName) up to the eigth level folder. The script writes a log of all files that were moved, including their old location and their new location.
 
-#### [extractFolderNames.py](/extractFolderNames.py)
+#### [extractFolderNames.py](/extractFilenames.py)
 Based on the file path entered, this script extracts the names of all nested folders and writes them to a CSV file.
 
+#### [extractFilenames.py](/extractFilenames.py)
+Based on the file path entered and file extension specified, this script extracts the names of all relevant files in the directory and writes them to a CSV file. Additionally, you can specify a prefix to be added to the edited file name in the "newFile" column.  Additionally, this script creates a log of all files, whether they have the specified extension or not, in the directory for troubleshooting potential problems.
+
+#### [renameFiles.py](/renameFiles.py)
+Based on the file path entered, this script renames files in the directory according to a specified CSV file with the columns named 'file' and 'newFile,' provided that there is a match between the files and the names in the 'file' column. The script writes a log of all files that were renamed, including their old name and their new name.
+
 #### [renameDirectories.py](/renameDirectories.py)
-Based on the file path entered, this script renames all nested folders according to a CSV file named 'FolderNames.csv' with the columns named 'oldFolder' and 'newFolder,' provided that there is a match between the nested folders and the names in the 'oldFolder' column. The script writes a log of all folders that were renamed, including their old name and their new name. The log is written in the command line utility's home directory.
+Based on the file path entered, this script renames all nested folders according to a CSV file named 'FolderNames.csv' with the columns named 'oldFolder' and 'newFolder,' provided that there is a match between the nested folders and the names in the 'oldFolder' column. The script writes a log of all folders that were renamed, including their old name and their new name.
 
 #### [samplingScript.py](/samplingScript.py)
-Based on the file path entered, the script selects every 10th file of a folder (after skipping the first file) and moves it over identically named folder in a 'sampled' directory while the skipped files are moved into an identically named folder in an 'unsampled' directory. The script also writes 'sampled' and 'unsampled' logs of all files that were moved, including their old location and their new location. The logs are written in the command line utility's home directory.
+Based on the file path entered, the script selects every 10th file of a folder (after skipping the first file) and moves it over identically named folder in a 'sampled' directory while the skipped files are moved into an identically named folder in an 'unsampled' directory. The script also writes 'sampled' and 'unsampled' logs of all files that were moved, including their old location and their new location.

extractFilenames.py

@@ -0,0 +1,25 @@
+import csv
+import os
+import time
+
+filePath = raw_input('Enter file path (C:/Test/): ')
+fileExtension = raw_input('Enter file extension: ')
+prefix = raw_input('Enter prefix to be added: ')
+
+f = csv.writer(open('fileListing.csv', 'wb'))
+f.writerow(['file'] + ['newFile'])
+f2 = csv.writer(open('fullfileListing.csv', 'wb'))
+f2.writerow(['file'] + ['newFile'])
+directories = os.walk(filePath, topdown=True)
+for root, dirs, files in directories:
+    for file in files:
+        f2.writerow([file])
+        if file[-3:] == fileExtension
+            itemID = file[0:5]
+            newFile = prefix + itemID + fileExtension
+            f.writerow([file] + [newFile])
+
+elapsedTime = time.time() - startTime
+m, s = divmod(elapsedTime, 60)
+h, m = divmod(m, 60)
+print 'Total script run time: ', '%d:%02d:%02d' % (h, m, s)

renameFiles.py

@@ -0,0 +1,30 @@
+import os
+import csv
+from datetime import datetime
+import time
+
+filePath = raw_input('Enter file path (C:/Test/): ')
+nameChangeFile = raw_input('Enter name of CSV with name changes: ')
+
+startTime = time.time()
+f=csv.writer(open('renameLog'+datetime.now().strftime('%Y-%m-%d %H.%M.%S')+'.csv','wb'))
+f.writerow(['oldFilename']+['newFilename'])
+for root, dirs, files in os.walk(filePath, topdown=True):
+    for file in files:
+        with open(nameChangeFile) as csvfile:
+            reader = csv.DictReader(csvfile)
+            for row in reader:
+                oldFilename = row['file']
+                newFilename = row['newFile']
+                if file == oldFilename:
+                    print oldFilename
+                    oldPath = os.path.join(root,file)
+                    newPath = os.path.join(root,newFilename)
+                    f.writerow([oldPath]+[newPath])
+                    #Uncomment the following line to acutally rename files rather than just writing a log file of the changes to be made
+                    #os.rename(oldPath,newPath)
+
+elapsedTime = time.time() - startTime
+m, s = divmod(elapsedTime, 60)
+h, m = divmod(m, 60)
+print 'Total script run time: ', '%d:%02d:%02d' % (h, m, s)

samplingScript.py

@@ -11,6 +11,8 @@
 f2=csv.writer(open('unsampledLog'+datetime.now().strftime('%Y-%m-%d %H.%M.%S')+'.csv','wb'))
 f2.writerow(['oldLocation']+['newLocation'])
 
+print filePath
+
 for root, dirs, files in os.walk(filePath, topdown=True):
     print root
     number = 1