Feature/remove neo4j

.gitignore

@@ -157,7 +157,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
 
 # Ignore the default SQLite database.
 *.sqlite3
@@ -196,3 +196,6 @@ default_root_uid.txt
 make_build/
 venv.tar.gz
 *.tar.gz
+
+# id_map folder
+id_name_map/

README.md

@@ -1,43 +1,21 @@
 # Supergraph plugin
 
-[Complex rest](https://github.com/ISGNeuroTeam/complex_rest/tree/develop) plugin for graph management.
-
-For an introduction check out the [User guide](docs/user-guide.md).
-
-## Installation
-
-These instructions will get you a copy of the plugin up and running on your local machine for development and testing purposes. See [deployment](#deployment) for notes on how to deploy the plugin on a live system.
+[Complex rest](https://github.com/ISGNeuroTeam/complex_rest/tree/develop) plugin for graph management.  For an introduction check out the [User guide](docs/user-guide.md).
 
 ### Prerequisites
 
 1. Deploy [complex rest](https://github.com/ISGNeuroTeam/complex_rest).
-2. Install [Neo4j](https://neo4j.com/docs/operations-manual/current/installation/) graph database.
-    1. Follow installation instructions for your OS [ [Linux](https://neo4j.com/docs/operations-manual/current/installation/linux/) | [Windows](https://neo4j.com/docs/operations-manual/current/installation/windows/) | [Mac](https://neo4j.com/docs/operations-manual/current/installation/osx/) ]. Pay attention to the [required Java version](https://neo4j.com/docs/operations-manual/current/installation/requirements/#deployment-requirements-java); you may need to change system defaults.
-    2. [Set initial password](https://neo4j.com/docs/operations-manual/current/configuration/set-initial-password/) to `password` with the following command:
-        ```sh
-        neo4j-admin set-initial-password password
-        ```
-        > This must be performed before starting up the database for the first time.
-    3. Run the service, make sure it is available on port `7687`:
-        ```sh
-        systemctl start neo4j
-        ```
-    4. (optional) If you installed *Cypher shell*, you can try to connect to Neo4j to make sure everything is ok:
-        ```sh
-        cypher-shell -a neo4j://localhost:7687 -u neo4j -p password
-        ```
 
 ### Deploy from GitHub or Nexus
 
 You can get the latest build from either [GitHub releases](https://github.com/ISGNeuroTeam/complex_rest_dtcd_supergraph/releases) page or Nexus - the archives are identical.
 
 1. Download an archive with the latest build.
 2. Unpack the archive into `complex_rest/plugins` directory.
-3. Run the [initialization script](#initialization-script) to prepare the database.
 
 ### Deploy via Make
 
-If you want to have an access to feature branch version, you can build this plugin locally.
+If you want to have access to feature branch version, you can build this plugin locally.
 
 1. Clone the Git repository:
     ```sh
@@ -49,7 +27,6 @@ If you want to have an access to feature branch version, you can build this plug
     make pack
     ```
 3. Unpack the archive into `complex_rest/plugins` directory.
-4. Run the [initialization script](#initialization-script) to prepare the database.
 
 ### Deploy manually
 
@@ -78,66 +55,18 @@ If you are a developer, then follow this section.
     cd complex_rest/plugins
     ln -s pathtofolder/repo/complex_rest_dtcd_supergraph
     ```
-6. [Re-install constraints and indexes](#re-installing-constraints-and-indexes), [initialize the default `Root` node](#initializing-the-default-root).
 
 ## Deployment
 
-For deployment we need to get a build archive - see the previous section on how to do that. Then:
+For deployment, we need to get a build archive - see the previous section on how to do that. Then:
 
 1. Stop `complex_rest`.
 2. Unpack the archive into `complex_rest/plugins` directory.
-3. Run the [initialization script](#initialization-script) to prepare the database.
-4. **TODO** Backup / reset / migrate the database.
-5. Start `complex_rest`.
-
-## Notes
-
-### Re-installing constraints and indexes
-
-Neo4j provides support for applying [indexes](https://neo4j.com/docs/getting-started/current/graphdb-concepts/#graphdb-indexes) and [constraints](https://neo4j.com/docs/getting-started/current/graphdb-concepts/#graphdb-constraints).
-
-To do this, activate plugin's virtual environment and run:
-
-```sh
-address="bolt://neo4j:password@localhost:7687"
-neomodel_remove_labels --db $address
-neomodel_install_labels models --db $address
-```
-
-For password and port use values from `supergraph.conf`.
-
-### Initializing the default Root
-
-We need to create the default root node in order to keep backwards compatibility with the API v0.2.0. There is a script just for that!
-
-Activate plugin's virtual environment, navigate to script's parent directory and run:
-
-```sh
-python create_default_root.py
-```
-
-It will create a single `Root` node and save its `uid` attribute in the file `default_root_uid.txt` inside source code directory.
-
-### Initialization script
-
-There is a helper script `database_init.sh` that prepares the plugin for work when deploying *from build archive*. It combines activation of correct virtual environment, [re-installation of constraints and indexes](#re-installing-constraints-and-indexes) with [default Root creation](#initializing-the-default-root) in one place.
-
-You can run it from anywhere you like:
-
-```sh
-./database_init.sh
-```
+3. Start `complex_rest`.
 
 ## TODO
 
 - Update [User guide](docs/user-guide.md).
-- Resolve `RelationshipClassRedefined` error when trying to test `neomodel` models directly (see `test_managers.py`).
-- User-defined properties that were saved before *stay on the node after merge* even if they are missing in new structure and should be deleted (see how `create_or_update` works). We handle it in converter, but this is not nice.
-- Some database queries are inefficient (`n+1` problems).
-
-## Built With
-
-- [Neo4j](https://neo4j.com/) - Graph data platform.
 
 ## Versioning
 
@@ -146,6 +75,7 @@ We use [SemVer](http://semver.org/) for versioning. For the versions available,
 ## Authors
 
 - Aleksei Tsysin (atsysin@isgneuro.com)
+- Nikita Serditov (nserditov@isgneuro.com)
 
 ## License