removing all files other than ace to datomic specific files

README.md

@@ -1,48 +1,58 @@
-#db
+# AceDB to Datomic 
 
-*The database migration project at WormBase.*
+- Reading and writing ACeDB model files.
+- Generating Datomic schemas based on ACeDB models.
+- Model-driven import of ACeDB data into multiple databases (currently Datomic and MongoDB).
+- Emulating an ACeDB server (currently incomplete).
 
-**THIS IS A PRIVATE REPOSITORY**
+Installation
 
-## FULL-SCALE DATOMIC PROTOTYPE
+sudo yum -y install perl-autodie perl-IPC-System-Simple
 
-This can be found in the `pseudoace` directory.  See the [wiki](https://github.com/wormbase/db/wiki)
-for more information.
 
-## LAYOUT
+##Ace to Datomic
 
-   README.md
-   data/       -- sample data files, organized by date
-   ec2/        -- scripts and credentials for developing
-                  and benchmarking on the AWS cloud
-   platforms/  -- one directory for each system under evaluation
+This tool is used to import databases from ACeDB to Datomic
 
-##DEVELOPMENT PROCEDURE
 
-Follow the GitFlow mechanism for branching and commiting changes as detailed [here](https://datasift.github.io/gitflow/IntroducingGitFlow.html)
-
-## DATA
+   - To get help run the following command
 
-smallace datasets, versioned by date, prepared by @khowe. Please
-reference which dataset you use in your documentation.
+lein run ace-to-datomic --help
 
-## CONVENTIONS
+###Help Output
 
-I suggest we use some standard bioinformatics conventions. For each platform:
+Ace to dataomic is tool for importing data from ACeDB into to Datomic database
 
-* scripts in bin/ (or scripts/)
-* lib/ if required, etc.
-* If your code requires third party modules, please document them and (if possible) include them as submodules.
-* There is a stub README in each directory. This would be a good place to collect documentation for now.
+Usage: ace-to-datomic [options] action
 
-## DOCUMENTATION STANDARDS
+Options:
+      --model PATH                             Specify the model file that you would like to use that is found in the models folder e.g. models.wrm.WS250.annot
+      --url URL                                Specify the url of the Dataomic transactor you would like to connect. Example: datomic:free://localhost:4334/WS250
+      --schema-filename PATH                   Specify the name of the file for the schema view to be written to when selecting Action: generate-schema-view exampls schema250.edn
+      --log-dir PATH                           Specifies the path to and empty directory to store the Datomic logs in. Example: /datastore/datomic/tmp/datomic/import-logs-WS250/
+      --acedump-dir PATH                       Specifies the path to the directory of the desired acedump. Example /datastore/datomic/tmp/acedata/WS250/
+      --backup-file PATH                       Secify the path to the file in which you would like to have the database dumped into
+      --datomic-database-report-filename PATH  Specify the relative or full path to the file that you would like the report to be written to
+  -v, --verbose
+  -f, --force
+  -h, --help
 
-Minimally, documentation should include the shell commands necessary to load your resource, expected
-input files and any output created.
+Actions: (required options for each action are provided in square brackets)
+  create-database                      Select this option if you would like to create a Datomic database from a schema. Required options [model, url]
+  generate-datomic-schema-view         Select if you would like the schema to the database to be exported to a file. Required options [schema-filename, url]
+  acedump-to-datomic-log               Select if you are importing data from ACeDB to Datomic and would like to create the Datomic log files [url, log-dir, acedump-dir]
+  sort-datomic-log                     Select if you would like to sort the log files generated from your ACeDB dump [log-dir]
+  import-logs-into-datomic             Select if you would like to import the sorted logs back into datomic [log-dir, url]
+  excise-tmp-data                      Select in order to remove all the tmp data that was created in the database to import the data [url]
+  test-datomic-data                    Select if you would like to perform tests on the generated database [url acedump-dir]
+  all-import-actions                   Select if you would like to perform all actions from acedb to datomic [model url schema-filename log-dir acedump-dir]
+  generate-datomic-database-report     Select if you want to generate a summary report of the contents of a particular Datomic database [url datomic-database-report-filename]
+  list-databases                       Select if you would like to get a list of the database names [url]
+  delete-database                      Select this option if you would like to delete a database in datomic [url]. If the force option you will not be asked if you are certain about your decision
+  backup-database                      Select if you would like to backup a datomic database into a file
 
-Better yet, assume a naive user and vanilla system. Include all commands necessary to get that
-system up and running with your platform and loaded with the test data.  This will enable any of us
-to test, verify or extend any of the platforms with minimal work by launching a new instance on AWS. 
-We can (and should) automate the installation, configuration and loading of each platform so that we
-can easily evaluate more complicated scenarios.
+
+Example command
+
+lein run ace-to-datomic generate-datomic-database-report --url datomic:free://localhost:4334/WS250 --datomic-database-report-filename /home/ec2-user/git/db/pseudoace/hello.t -v