Merge pull request #2 from ctjacobs/review

Addressing JOSS reviewer comments

Author: ctjacobs

README.md

@@ -17,10 +17,16 @@ Both of these dependencies can be installed via `pip` using
 sudo pip install -r requirements.txt
 ```
 
+Alternatively, users can install Git-RDM and its dependencies with [Conda](http://conda.pydata.org/); see the details in the next section.
+
 Note that once PyRDM is installed, you will need to setup Figshare/Zenodo authentication tokens and copy them into the PyRDM configuration file in order to publish your data. See the [PyRDM documentation](https://pyrdm.readthedocs.io/en/latest/getting_started.html) for instructions on how to do this.
 
 ## Installing
 
+Git-RDM can either be installed from source, or via Conda packages; see the appropriate sub-section for more details. Once Git-RDM is installed, Git should automatically detect the plugin and recognise the `rdm` command; for example, run `git rdm -h` to list the RDM-related subcommands described in the Usage section below.
+
+### From source
+
 After downloading or cloning this software using
 
 ```
@@ -39,7 +45,25 @@ and running
 sudo python setup.py install
 ```
 
-Once Git-RDM is installed, Git should automatically detect the plugin and recognise the `rdm` command; for example, run `git rdm -h` to list the RDM-related subcommands described in the Usage section below.
+Alternatively, a local user installation can be achieved using
+
+```
+python setup.py install --prefix=/path/to/custom/install/directory
+```
+
+and adding `/path/to/custom/install/directory/bin` to the `PATH` environment variable:
+
+```
+export PATH=$PATH:/path/to/custom/install/directory/bin
+```
+
+### Conda package
+
+Conda users can install the Git-RDM package and its dependencies using
+
+```
+conda install -c ctjacobs -c pypi -c auto -c ioos -c conda-forge git-rdm
+```
 
 ## Usage
 
@@ -139,6 +163,17 @@ git-rdm INFO: 		/home/christian/test/test3.png (2016-06-13 @ 00:29:03, revision
 git-rdm INFO: 		/home/christian/test/test2.txt (2016-06-13 @ 00:29:03, revision '1eeccabba810b8c91eef82e692713fdb05ca4a32')
 ```
 
+To check the raw, unformatted contents of the entire publications database, use the `--raw` flag:
+
+```
+~/test $ git rdm ls --raw
+git-rdm INFO: Database dump:
+git-rdm INFO: id, path, date, time, sha, pid, doi
+git-rdm INFO: 13, /home/christian/test/test1.txt, 2016-06-13, 00:29:03.016951, 1eeccabba810b8c91eef82e692713fdb05ca4a32, 3428222, 10.6084/m9.figshare.3428222
+git-rdm INFO: 14, /home/christian/test/test3.png, 2016-06-13, 00:29:03.016951, 1eeccabba810b8c91eef82e692713fdb05ca4a32, 3428222, 10.6084/m9.figshare.3428222
+git-rdm INFO: 15, /home/christian/test/test2.txt, 2016-06-13, 00:29:03.016951, 1eeccabba810b8c91eef82e692713fdb05ca4a32, 3428222, 10.6084/m9.figshare.3428222
+```
+
 ### git rdm show
 
 The full publication record maintained by the data repository service can be shown using `git rdm show`. It expects two arguments: the name of the hosting service (`figshare` or `zenodo`) and the publication ID. For example, for the publication whose Figshare publication ID is 3428222 (and DOI is `10.6084/m9.figshare.3428222`), the (truncated) output is:
@@ -177,6 +212,12 @@ git-rdm INFO: {
 ## License
 This software is released under the MIT license. See the file called `LICENSE` for more information.
 
+## Citing
+
+If you use Git-RDM during the course of your research, please consider citing the following paper:
+
+* C. T. Jacobs, A. Avdis (Under Review). Git-RDM: A research data management plugin for the Git version control system. *Journal of Open Source Software*.
+
 ## Contact
 Please send any questions or comments about Git-RDM via email to [Christian Jacobs](http://christianjacobs.uk) at <[email protected]>.
 

codemeta.json

@@ -13,5 +13,5 @@
   "keywords": "research data management, git, version control, digital curation, data, publishing, figshare, zenodo",
   "license": "MIT",
   "title": "Git-RDM",
-  "version": "v1.0.0"
-}
+  "version": "v1.0.1"
+}

git-rdm

@@ -172,15 +172,38 @@ class GitRDM:
 
         return
 
-    def ls(self, path=None, by_doi=True):
+    def ls(self, path=None, by_doi=True, raw=False):
         """ List all published files, and files to be published. If a file has multiple DOIs associated with it then they are all listed together.
         
         :arg path: The relative/absolute path to the file to be listed.
         :arg bool by_doi: List the files by DOI first (i.e. each DOI will be listed at the top level, with names of the files associated with that DOI underneath).
+        :arg bool raw: Print out the entire SQL database table without any formatting.
         """
-        
-        self.db_connect()  
-        
+
+        self.db_connect()
+
+        # Raw database dump of all the rows
+        if raw:
+            _LOG.info("Database dump:")
+
+            query = "SELECT * FROM %s" % PUBLICATIONS_TABLE
+
+            with self.connection:
+                c = self.connection.cursor()
+                c.execute(query)
+                result = c.fetchall()
+                if len(result) > 0:
+                    # Column names
+                    names = list(map(lambda x: x[0], c.description))
+                    _LOG.info(", ".join(names))
+
+                    # Rows
+                    for r in result:
+                        values = [str(r[name]) for name in names]
+                        _LOG.info(", ".join(values))
+
+            return
+
         # If a path is provided, then specify all the publications/DOIs associated with that path.
         if path:
             path = os.path.abspath(path)  # Get the absolute path
@@ -194,7 +217,7 @@ class GitRDM:
                     for r in result:
                         _LOG.info("\t" + str(r["doi"]) + " (" + str(r["date"]) + " @ " + str(r["time"]).split(".")[0] + ", revision '%s')" % r["sha"])
             return
-                
+
         # List all published files.
         if by_doi:
             query = "SELECT * FROM %s WHERE doi IS NOT NULL ORDER BY doi" % PUBLICATIONS_TABLE
@@ -483,6 +506,7 @@ if(__name__ == "__main__"):
     ls_parser = subparsers.add_parser("ls", help="List the published files, and files staged for publishing.")
     ls_parser.add_argument("--path", required=False, help="The path to the file to list.", action="store", type=str, default=None)
     ls_parser.add_argument("--by-doi", help="Group files by DOI.", action="store_true", default=False, dest="by_doi")
+    ls_parser.add_argument("--raw", help="Print out the entire SQL database table without any formatting.", action="store_true", default=False, dest="raw")
 
     # 'git rdm publish'
     publish_parser = subparsers.add_parser("publish", help="Publish the files in the publishing staging area.")
@@ -511,7 +535,7 @@ if(__name__ == "__main__"):
     elif args.subcommand == "rm":
         rdm.rm(args.path)
     elif args.subcommand == "ls":
-        rdm.ls(path=args.path, by_doi=args.by_doi)
+        rdm.ls(path=args.path, by_doi=args.by_doi, raw=args.raw)
     elif args.subcommand == "publish":
         rdm.publish(service=args.service, pid=args.pid)
     elif args.subcommand == "show":

setup.py

@@ -28,7 +28,7 @@
 from distutils.core import setup
 
 setup(name='git-rdm',
-      version='1.0',
+      version='1.0.1',
       description='Git-RDM is a research data management plugin for the Git version control system.',
       author='Christian T. Jacobs, Alexandros Avdis',
       author_email='[email protected]',