Merge branch 'hotfix/v0.15.1' #106

README.md

@@ -110,7 +110,7 @@ You can confirm installation via `conda list`
 (curation) $ conda list ldcoolp
 ```
 
-You should see that the version is `0.14.1`.
+You should see that the version is `0.15.1`.
 
 ### Configuration Settings
 
@@ -199,9 +199,11 @@ We use [SemVer](http://semver.org/) for versioning. For the versions available,
 A list of released features and their issue number(s).
 List is sorted from moderate to minor revisions for reach release.
 
-v0.15.0:
+v0.15.0 - v0.15.1:
  * Implementation of Qualtrics README file #98
  * Folder re-structuring for versioning #100
+ * `perform_move` script to perform move to next curation stage, backwards or
+   to publish #105
 
 v0.14.0 - 0.14.1:
  * Full stdout and file logging #83

ldcoolp/__init__.py

@@ -1,6 +1,6 @@
 from os import path
 
-__version__ = "0.14.1"
+__version__ = "0.15.1"
 
 co_path = path.dirname(__file__)
 

ldcoolp/admin/move.py

@@ -1,4 +1,5 @@
 from os.path import join, dirname, exists
+from os import makedirs, chmod
 import shutil
 from glob import glob
 
@@ -69,7 +70,7 @@ def get_source_stage(self, depositor_name, verbose=True):
             self.log.debug(source_path)
             raise ValueError(err)
         if len(source_path) == 1:
-            source_stage = dirname(source_path[0].replace(join(self.root_directory_main, ''), ''))
+            source_stage = source_path[0].replace(join(self.root_directory_main, ''), '').split('/')[0]
 
             return source_stage
 
@@ -87,12 +88,18 @@ def main(self, depositor_name, source_stage, dest_stage):
 
         # Define paths:
         source_path = join(self.root_directory_main, source_stage, depositor_name)
-        dest_path = join(self.root_directory_main, dest_stage, depositor_name)
+        # Strip out version folder convention for proper move with shutil.move
+        dest_path = dirname(join(self.root_directory_main, dest_stage, depositor_name))
 
         # Move folder
         if exists(source_path):
             self.log.info(f"Moving: {depositor_name} from {source_stage} to ...")
             self.log.info(f" ... {dest_stage} on {self.root_directory_main}")
+            if not exists(dest_path):
+                self.log.info(f"Path does not exist! {dest_path}")
+                self.log.info("Creating...")
+                makedirs(dest_path)
+                chmod(dest_path, 0o777)
             shutil.move(source_path, dest_path)
         else:
             self.log.info(f"WARNING: Unable to find source_path for {depositor_name}")
@@ -110,13 +117,66 @@ def move_to_next(self, depositor_name, verbose=True):
             # Get current path
             source_stage = self.get_source_stage(depositor_name, verbose=verbose)
 
-            # Get destination path
-            dest_stage_i = [i+1 for i in range(len(self.stage_list)) if
-                            self.stage_list[i] == source_stage][0]
-            dest_stage = self.stage_list[dest_stage_i]
+            if source_stage == self.stage_list[-1]:
+                self.log.warn(f"Cannot moved to next stage! Currently in {source_stage}")
+            else:
+                # Get destination path
+                dest_stage_i = [i+1 for i in range(len(self.stage_list)) if
+                                self.stage_list[i] == source_stage][0]
+                dest_stage = self.stage_list[dest_stage_i]
 
-            # Move folder
-            self.main(depositor_name, source_stage, dest_stage)
+                # Move folder
+                self.main(depositor_name, source_stage, dest_stage)
+        except FileNotFoundError:
+            self.log.warn(f"Unable to find source_path for {depositor_name}")
+
+    def move_back(self, depositor_name, verbose=True):
+        """
+        Purpose:
+          Perform move from one curation stage back to previous one
+
+        :param depositor_name: Exact name of the data curation folder with spaces
+        :param verbose: bool that warns source_path does not exist.  Default: True
+        """
+
+        try:
+            # Get current path
+            source_stage = self.get_source_stage(depositor_name, verbose=verbose)
+
+            if source_stage == self.stage_list[0]:
+                self.log.warn(f"Cannot moved to next stage! Currently in {source_stage}")
+            else:
+                # Get destination path
+                dest_stage_i = [i-1 for i in range(len(self.stage_list)) if
+                                self.stage_list[i] == source_stage][0]
+                dest_stage = self.stage_list[dest_stage_i]
+
+                # Move folder
+                self.main(depositor_name, source_stage, dest_stage)
+        except FileNotFoundError:
+            self.log.warn(f"Unable to find source_path for {depositor_name}")
+
+    def move_to_publish(self, depositor_name, verbose=True):
+        """
+        Purpose:
+          Perform move from one curation stage to published stage
+
+        :param depositor_name: Exact name of the data curation folder with spaces
+        :param verbose: bool that warns source_path does not exist.  Default: True
+        """
+
+        try:
+            # Get current path
+            source_stage = self.get_source_stage(depositor_name, verbose=verbose)
+
+            if source_stage == self.published_folder:
+                self.log.warn(f"Already in {source_stage} !!!")
+            else:
+                # Get destination path
+                dest_stage = self.published_folder
+
+                # Move folder
+                self.main(depositor_name, source_stage, dest_stage)
         except FileNotFoundError:
             self.log.warn(f"Unable to find source_path for {depositor_name}")
 

ldcoolp/scripts/perform_move

@@ -0,0 +1,110 @@
+#!/usr/bin/env python
+
+from os.path import dirname, exists, join
+from os import mkdir, stat
+
+import argparse
+
+from datetime import date
+
+from ldcoolp.admin.move import MoveClass
+from ldcoolp.curation.depositor_name import DepositorName
+from ldcoolp.curation.api.figshare import FigshareInstituteAdmin
+from ldcoolp.logger import LogClass, get_user_hostname
+from ldcoolp.admin import permissions
+
+# Version and branch info
+from ldcoolp import __version__
+from ldcoolp.git_info import get_active_branch_name, get_latest_commit
+from ldcoolp import __file__ as library_path
+
+# Config loader
+from ldcoolp.config import dict_load
+
+today = date.today()
+
+library_root_path = dirname(dirname(library_path))  # Retrieve parent directory to ldcoolp
+
+
+if __name__ == '__main__':
+    # Parse command-line arguments
+    parser = argparse.ArgumentParser(description='Command-line driver for data curation moves.')
+    parser.add_argument('--config', required=True, help='path to configuration file')
+    parser.add_argument('--article_id', required=True, help='Figshare article ID')
+    parser.add_argument('--direction', required=True, help='Direction to move. Either "next", "back" or "publish"')
+    args = parser.parse_args()
+
+    if not exists(args.config):
+        raise FileNotFoundError(f"WARNING!!! Config file not found: {args.config}")
+
+    if args.direction not in ['next', 'back', 'publish']:
+        raise ValueError(f"WARNING!!! --direction flag not properly set. Either next, back, or publish")
+
+    branch_name = get_active_branch_name(library_root_path)
+    git_commit, git_short_commit = get_latest_commit(library_root_path)
+
+    # Load configuration
+    config_dict = dict_load(args.config)
+
+    curation_dict = config_dict['curation']
+
+    # Define logfile
+    root_directory_main = curation_dict[curation_dict['log_parent_dir']]
+
+    log_dir = join(root_directory_main, curation_dict['log_dir'])
+    if not exists(log_dir):
+        mkdir(log_dir)
+    logfile_prefix = 'perform_move'
+    logfile = f"{logfile_prefix}.{today.strftime('%Y-%m-%d')}.log"
+
+    log = LogClass(log_dir, logfile).get_logger()
+
+    log.info("****************************")
+
+    log.debug(f"LD-Cool-P branch: {branch_name}")
+    log.debug(f"LD-Cool-P version: {__version__} ({git_short_commit})")
+    log.debug(f"LD-Cool-P commit hash: {git_commit}")
+
+    # Retrieve username, hostname, IP
+    sys_info = get_user_hostname()
+    log.debug(f"username : {sys_info['user']}")
+    log.debug(f"hostname : {sys_info['hostname']}")
+    log.debug(f"IP Addr  : {sys_info['ip']}")
+    log.debug(f"Op. Sys. : {sys_info['os']}")
+
+    # Separate comma-separated list of articles
+    articles = args.article_id.split(',')
+    num_articles = len(articles)
+
+    log.info(f"Number of Deposits: {num_articles}")
+
+    fs_admin = FigshareInstituteAdmin(figshare_dict=config_dict['figshare'], log=log)
+    mc = MoveClass(curation_dict=curation_dict, log=log)
+
+    # Loop over each article
+    count = 0
+    for ii in range(len(articles)):
+        dn = DepositorName(articles[ii], fs_admin, log=log)
+        log.info(f"Performing move with --direction {args.direction}")
+        if args.direction == 'next':
+            mc.move_to_next(dn.folderName)
+        if args.direction == 'back':
+            mc.move_back(dn.folderName)
+        if args.direction == 'publish':
+            mc.move_to_publish(dn.folderName)
+
+        count += 1
+
+        log.info(f"Completed: {articles[ii]} ...")
+        log.info(f"Completed: {count} / {num_articles}")
+
+    # Change permission to mode=666 (rw for all)
+    status = stat(join(log_dir, logfile))
+    if oct(status.st_mode)[-3:] == '666':
+        log.debug("Permissions set for logfile")
+    else:
+        log.debug("Changing permissions on logfile...")
+        permissions.curation(join(log_dir, logfile), mode=0o666)
+
+    log.info("****************************")
+    log.info("Exit 0")

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name='ldcoolp',
-    version='v0.14.1',
+    version='v0.15.1',
     packages=['ldcoolp'],
     url='https://github.com/ualibraries/LD_Cool_P',
     license='MIT License',