update changelog, update example cfg files

config.yaml

@@ -1,7 +1,7 @@
 # full config example. Refer to bbconf/const.py for key names and default values
 
 path:
-  bedstat_output: $HOME/results_pipeline
+  pipelines_output: $HOME/results_pipeline
 
 database:
   host: localhost

config_min.yaml

@@ -1,4 +1,5 @@
 # min config example. Refer to bbconf/const.py for key names and default values
 
 path:
-  bedstat_output: $HOME/results_pipeline
+  bedstat_output: $LABROOT/resources/regions/bedstat_output
+  bedbuncher_output: $LABROOT/resources/regions/bedbuncher_output

docs/bbc_api.md

@@ -88,6 +88,22 @@ Get the total number of the documents in the bedsets index
 
 
 
+```python
+def delete_bedfiles_index(self)
+```
+
+Delete bedfiles index from Elasticsearch
+
+
+
+```python
+def delete_bedsets_index(self)
+```
+
+Delete bedsets index from Elasticsearch
+
+
+
 ```python
 def establish_elasticsearch_connection(self, host=None)
 ```
@@ -112,6 +128,23 @@ Return the path to the config file or None if not set
 
 
 
+```python
+def get_bedfiles_doc(self, doc_id)
+```
+
+Get a document from bedfiles index by its ID
+#### Parameters:
+
+- `doc_id` (`str`):  document ID to return
+
+
+#### Returns:
+
+- `Mapping`:  matched document
+
+
+
+
 ```python
 def get_bedfiles_mapping(self, just_data=True, **kwargs)
 ```
@@ -124,6 +157,23 @@ Get mapping definitions for the bedfiles index
 
 
 
+```python
+def get_bedsets_doc(self, doc_id)
+```
+
+Get a document from bedsets index by its ID
+#### Parameters:
+
+- `doc_id` (`str`):  document ID to return
+
+
+#### Returns:
+
+- `Mapping`:  matched document
+
+
+
+
 ```python
 def get_bedsets_mapping(self, just_data=True, **kwargs)
 ```
@@ -142,9 +192,10 @@ def insert_bedfiles_data(self, data, doc_id=None, **kwargs)
 
 Insert data to the bedfile index a Elasticsearch DB or create it and the insert in case it does not exist.
 
-Document ID argument is optional. If not provided, a random ID will be assigned.
-If provided the document will be inserted only if no documents with this ID are present in the DB.
-However, the document overwriting can be forced if needed.
+Document ID argument is optional. If not provided, a random ID will
+be assigned. If provided the document will be inserted only if no
+documents with this ID are present in the DB. However, the document
+overwriting can be forced if needed.
 #### Parameters:
 
 - `data` (`dict`):  data to insert
@@ -159,8 +210,10 @@ def insert_bedsets_data(self, data, doc_id=None, **kwargs)
 
 Insert data to the bedset index in a Elasticsearch DB or create it and the insert in case it does not exist.
 
-Document ID argument is optional. If not provided, a random ID will be assigned.
-If provided the document will be inserted only if no documents with this ID are present in the DB.
+Document ID argument is optional. If not provided, a random ID will
+be assigned.
+If provided the document will be inserted only if no documents with
+this ID are present in the DB.
 However, the document overwriting can be forced if needed.
 #### Parameters:
 
@@ -241,4 +294,4 @@ or read from a $BEDBASE environment variable
 
 
 
-*Version Information: `bbconf` v0.0.2-dev, generated by `lucidoc` v0.4.2*
+*Version Information: `bbconf` v0.0.2-dev, generated by `lucidoc` v0.4.3*

docs/changelog.md

@@ -2,9 +2,17 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. 
 
-## [0.0.2] - unreleased
+## [0.0.2] - 2020-05-28
+### Added
+- index deleting methods:
+	- `delete_bedsets_index`
+	- `delete_bedfiles_index`
+- multiple new keys constants
+
 ### Changed 
 - make `search_bedfiles` and `search_bedsets` methods return all hits by default instead of just 10. Parametrize it. 
+- added more arguments to `insert_bedfiles_data` and `insert_bedsets_data` method interfaces: `doc_id` and `force_update`
+- Elasticsearch documents are inserted into the indices more securily, `insert_*` methods prevent documents duplication
 
 
 ## [0.0.1] - 2020-02-05