ricgraph 2.12__tar.gz → 2.13__tar.gz

{ricgraph-2.12/ricgraph.egg-info → ricgraph-2.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ricgraph
-Version: 2.12
+Version: 2.13
 Summary: Ricgraph - Research in context graph
 Author: Rik D.T. Janssen
 License-Expression: MIT

{ricgraph-2.12 → ricgraph-2.13}/README.md

@@ -390,4 +390,4 @@ please let me know by creating a GitHub *Issue* at the top left of that page.
 <!-- Do not change the lines below. The version number will be
      modified by script maintenance/update_version.bash -->
 This README.md file is part of the 
-documentation for version 2.12 of Ricgraph - Research in context graph.
+documentation for version 2.13 of Ricgraph - Research in context graph.

{ricgraph-2.12 → ricgraph-2.13}/pyproject.toml

@@ -7,7 +7,7 @@ packages = ["ricgraph"]
 
 [project]
 name = "ricgraph"
-version = "2.12"
+version = "2.13"
 authors = [
   { name="Rik D.T. Janssen" },
 ]

{ricgraph-2.12 → ricgraph-2.13}/ricgraph/__init__.py

@@ -43,6 +43,7 @@ from .ricgraph_constants import *
 from .ricgraph_cache import *
 from .ricgraph_utils import *
 from .ricgraph_file import *
+from .ricgraph_cypher import *
 from .ricgraph_graphdb import *
 from .ricgraph_researchinfo import *
 from .ricgraph_harvest import *

{ricgraph-2.12 → ricgraph-2.13}/ricgraph/ricgraph.py

@@ -98,8 +98,8 @@ In the default configuration of Ricgraph, the following properties are included:
 """
 
 
-import numpy
-import pandas
+from numpy import nan
+from pandas import DataFrame, concat, set_option
 from typing import Union
 from .ricgraph_graphdb import (timestamp,
                                create_update_node, create_two_nodes_and_edge,
@@ -116,7 +116,7 @@ __package__ = 'Ricgraph'
 # __version__ should be placed here instead of in __init__.py.
 # If not here, it cannot be found when executing something like
 # PYTHONPATH=../ricgraph ../bin/python ricgraph_explorer.py
-__version__ = '2.12'
+__version__ = '2.13'
 
 
 # ##############################################################################
@@ -131,7 +131,7 @@ def get_ricgraph_version() -> str:
 
 
 # Note the similarity with create_nodepairs_and_edges_df().
-def update_nodes_df(nodes: pandas.DataFrame) -> None:
+def update_nodes_df(nodes: DataFrame) -> None:
     """Update the values in a node, but only if values have been changed.
     This is done for all the nodes passed in the DataFrame.
 
@@ -143,7 +143,7 @@ def update_nodes_df(nodes: pandas.DataFrame) -> None:
     """
     nodes_clean = nodes.copy(deep=True)
     # Ensure that all '' values are NaN, so that those rows can be easily removed with dropna()
-    nodes_clean.replace('', numpy.nan, inplace=True)
+    nodes_clean.replace('', nan, inplace=True)
     nodes_clean.dropna(axis=0, how='any', inplace=True)
     nodes_clean.drop_duplicates(keep='first', inplace=True, ignore_index=True)
 
@@ -171,7 +171,7 @@ def update_nodes_df(nodes: pandas.DataFrame) -> None:
     return
 
 
-def create_nodepairs_and_edges_df(left_and_right_nodepairs: pandas.DataFrame) -> None:
+def create_nodepairs_and_edges_df(left_and_right_nodepairs: DataFrame) -> None:
     """Create two nodes (called 'node pairs') and two directed edges between those nodes.
     This is done for all the nodes passed. The nodes are specified in a DataFrame.
     One row in the DataFrame contains two nodes which are to be connected.
@@ -235,10 +235,10 @@ def create_nodepairs_and_edges_params(name1: Union[dict, str], category1: Union[
     :return: None.
     """
     if isinstance(value1, str):
-        left_and_right_nodepairs = pandas.DataFrame(data={'value1': value1},
+        left_and_right_nodepairs = DataFrame(data={'value1': value1},
                                                     index=[0])
     else:
-        left_and_right_nodepairs = pandas.DataFrame(data=value1).copy(deep=True)
+        left_and_right_nodepairs = DataFrame(data=value1).copy(deep=True)
         left_and_right_nodepairs.rename(columns={value1.name: 'value1'}, inplace=True)
 
     # This makes programming more efficient
@@ -258,14 +258,14 @@ def create_nodepairs_and_edges_params(name1: Union[dict, str], category1: Union[
                 if isinstance(other_value, str):
                     left_and_right_nodepairs[prop_name + '1'] = other_value
                 else:
-                    left_and_right_nodepairs = pandas.concat([left_and_right_nodepairs, other_value], axis='columns')
+                    left_and_right_nodepairs = concat([left_and_right_nodepairs, other_value], axis='columns')
                     left_and_right_nodepairs.rename(columns={other_value.name: prop_name + '1'}, inplace=True)
 
             if prop_name + '2' == other_name:
                 if isinstance(other_value, str):
                     left_and_right_nodepairs[prop_name + '2'] = other_value
                 else:
-                    left_and_right_nodepairs = pandas.concat([left_and_right_nodepairs, other_value], axis='columns')
+                    left_and_right_nodepairs = concat([left_and_right_nodepairs, other_value], axis='columns')
                     left_and_right_nodepairs.rename(columns={other_value.name: prop_name + '2'}, inplace=True)
 
     # Reorder a bit, starting with the last, only the name-category-value property, since they will surely exist
@@ -280,7 +280,7 @@ def create_nodepairs_and_edges_params(name1: Union[dict, str], category1: Union[
     return
 
 
-def unify_personal_identifiers(personal_identifiers: pandas.DataFrame,
+def unify_personal_identifiers(personal_identifiers: DataFrame,
                                source_event: Union[dict, str], history_event: Union[dict, str]) -> None:
     """Unify a collection of personal identifiers (e.g. ORCID, ISNI, etc.).
     That means that every column is unified to every other column.
@@ -305,7 +305,7 @@ def unify_personal_identifiers(personal_identifiers: pandas.DataFrame,
             identifiers = personal_identifiers[[column1, column2]].copy(deep=True)
 
             # Ensure that all '' values are NaN, so that those rows can be easily removed with dropna()
-            identifiers.replace('', numpy.nan, inplace=True)
+            identifiers.replace('', nan, inplace=True)
             # dropna(how='any'): drop row if one or more row values contain NaN
             identifiers.dropna(axis=0, how='any', inplace=True)
             identifiers.drop_duplicates(keep='first', inplace=True, ignore_index=True)
@@ -350,10 +350,10 @@ def unify_personal_identifiers(personal_identifiers: pandas.DataFrame,
 # This will be executed on module initialization
 
 # Make sure DataFrames are printed with all columns on full width
-pandas.set_option('display.max_columns', None)
-pandas.set_option('display.width', 500)
+set_option('display.max_columns', None)
+set_option('display.width', 500)
 # To prevent warning
 # "FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed
 # in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`.
 # To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`"
-pandas.set_option('future.no_silent_downcasting', True)
+set_option('future.no_silent_downcasting', True)

{ricgraph-2.12 → ricgraph-2.13}/ricgraph/ricgraph_cache.py

@@ -42,7 +42,7 @@
 # ########################################################################
 
 
-import sys
+from sys import getsizeof
 from typing import Union
 from neo4j.graph import Node
 from .ricgraph_constants import MAX_NODES_CACHE_NODELINK, MAX_NODES_CACHE_KEY_ID
@@ -193,5 +193,5 @@ def nodes_cache_nodelink_size() -> tuple[int, float]:
     global _nodes_cache_nodelink
 
     length = len(_nodes_cache_nodelink)
-    size_kb = round(sys.getsizeof(_nodes_cache_nodelink) / 1000, 1)
+    size_kb = round(getsizeof(_nodes_cache_nodelink) / 1000, 1)
     return length, size_kb

{ricgraph-2.12 → ricgraph-2.13}/ricgraph/ricgraph_constants.py

@@ -104,11 +104,13 @@ MAX_NR_HISTORYITEMS_TO_ADD = 50
 #
 # Call the function lookup_resout_type() to do this mapping.
 # If you add a type, also add it to ROTYPE_ALL.
+# If you add a type that is a publication, also add it to ROTYPE_PUBLICATION.
 #
 # This list is inspired by the Strategy Evaluation Protocol 2021-2027
 # https://www.universiteitenvannederland.nl/files/documenten/Domeinen/Onderzoek/SEP_2021-2027.pdf,
 # Appendix E2.
 ROTYPE_ABSTRACT = 'abstract'
+ROTYPE_ARTEFACT = 'artefact'
 ROTYPE_BOOK = 'book'
 ROTYPE_BOOKCHAPTER = 'book chapter'
 ROTYPE_CONFERENCE_ARTICLE = 'conference article'
@@ -138,6 +140,7 @@ ROTYPE_THESIS = 'thesis'
 ROTYPE_WEBSITE = 'website or web publication'
 
 ROTYPE_ALL = [ROTYPE_ABSTRACT,
+              ROTYPE_ARTEFACT,
               ROTYPE_BOOK,
               ROTYPE_BOOKCHAPTER,
               ROTYPE_CONFERENCE_ARTICLE,
@@ -165,3 +168,25 @@ ROTYPE_ALL = [ROTYPE_ABSTRACT,
               ROTYPE_SOFTWARE,
               ROTYPE_THESIS,
               ROTYPE_WEBSITE]
+
+
+ROTYPE_PUBLICATION = [ROTYPE_ABSTRACT,
+                      ROTYPE_BOOK,
+                      ROTYPE_BOOKCHAPTER,
+                      ROTYPE_CONFERENCE_ARTICLE,
+                      ROTYPE_EDITORIAL,
+                      ROTYPE_ENTRY,
+                      ROTYPE_JOURNAL_ARTICLE,
+                      ROTYPE_LETTER,
+                      ROTYPE_MEMORANDUM,
+                      ROTYPE_METHOD_DESCRIPTION,
+                      ROTYPE_PATENT,
+                      ROTYPE_PHDTHESIS,
+                      ROTYPE_POSTER,
+                      ROTYPE_PREPRINT,
+                      ROTYPE_PRESENTATION,
+                      ROTYPE_REGISTERED_REPORT,
+                      ROTYPE_REPORT,
+                      ROTYPE_RETRACTION,
+                      ROTYPE_REVIEW,
+                      ROTYPE_THESIS]