ricgraph 3.1__tar.gz → 3.2__tar.gz

{ricgraph-3.1/ricgraph.egg-info → ricgraph-3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ricgraph
-Version: 3.1
+Version: 3.2
 Summary: Ricgraph - Research in context graph
 Author: Rik D.T. Janssen
 License-Expression: MIT

{ricgraph-3.1 → ricgraph-3.2}/README.md

@@ -57,6 +57,33 @@ adapted to new application areas.
 Throughout this documentation, we illustrate how Ricgraph works by applying
 it to the application area research information.
 
+## Ricgraph introduction videos
+
+You may want to watch the following videos about Ricgraph. The left one is a
+short video, only including the Ricgraph use cases. The right one is a more
+extensive one (also including the use cases).
+
+<table>
+  <tr>
+    <td style="width:50%;"><b>Ricgraph use cases video (1m30s)</b></td>
+    <td style="width:50%;"><b>Ricgraph introduction video including use cases (2m28s)</b></td>
+  </tr>
+  <tr>
+    <td><video src="docs/videos/ricgraph_usecases.mp4" controls width="90%">Ricgraph use cases video (1m30s)</video></td>
+    <td><video src="docs/videos/ricgraph_intro_usecases.mp4" controls width="90%">Ricgraph introduction video including use cases (2m28s)</video></td>
+  </tr>
+  <tr>
+   <td>
+     <a href="https://docs.ricgraph.eu/docs/videos/ricgraph_usecases.mp4" target="_blank">
+     Click to play or download the Ricgraph use cases video</a>.
+   </td>
+   <td>
+     <a href="https://docs.ricgraph.eu/docs/videos/ricgraph_intro_usecases.mp4" target="_blank">
+     Click to play or download the Ricgraph introduction video</a>.
+   </td>
+  </tr>
+</table>
+
 ## Ricgraph news
 
 Read my recent preprint:
@@ -321,6 +348,8 @@ The following figure shows how three persons have contributed to one research ou
 
 * Explore the full documentation of Ricgraph on
   [https://docs.ricgraph.eu](https://docs.ricgraph.eu).
+* Play the [Ricgraph use cases video](docs/videos/ricgraph_usecases.mp4), or the
+  [Ricgraph introduction video](docs/videos/ricgraph_intro_usecases.mp4).
 * For a gentle introduction in Ricgraph, read the reference publication:
   Rik D.T. Janssen (2024). *Ricgraph: A flexible and extensible graph to explore research in
   context from various systems*. SoftwareX, 26(101736).
@@ -420,4 +449,4 @@ 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 3.1 of Ricgraph - Research in context graph.
+documentation for version 3.2 of Ricgraph - Research in context graph.

{ricgraph-3.1 → ricgraph-3.2}/pyproject.toml

@@ -7,7 +7,7 @@ packages = ["ricgraph"]
 
 [project]
 name = "ricgraph"
-version = "3.1"
+version = "3.2"
 authors = [
   { name="Rik D.T. Janssen" },
 ]

{ricgraph-3.1 → ricgraph-3.2}/ricgraph/ricgraph.py

@@ -6,7 +6,7 @@
 #
 # MIT License
 # 
-# Copyright (c) 2023, 2024, 2025 Rik D.T. Janssen
+# Copyright (c) 2023 - 2026 Rik D.T. Janssen
 # 
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -101,14 +101,18 @@ In the default configuration of Ricgraph, the following properties are included:
 from numpy import nan
 from pandas import DataFrame, concat, set_option
 from typing import Union
-from .ricgraph_utils import timestamp
+
+from .ricgraph_utils import (timestamp, timestamp_posix,
+                             print_records_per_minute,
+                             print_progress)
 from .ricgraph_graphdb import (create_update_node, create_two_nodes_and_edge,
-                               RICGRAPH_NODEADD_MODE,
-                               RICGRAPH_PROPERTIES_STANDARD, RICGRAPH_PROPERTIES_ADDITIONAL)
+                               get_ricgraph_nodeadd_mode,
+                               get_ricgraph_properties_standard,
+                               get_ricgraph_properties_additional)
 
 
 __author__ = 'Rik D.T. Janssen'
-__copyright__ = 'Copyright (c) 2023, 2024, 2025 Rik D.T. Janssen'
+__copyright__ = 'Copyright (c) 2023 - 2026 Rik D.T. Janssen'
 __email__ = ''
 __license__ = 'MIT License'
 __package__ = 'Ricgraph'
@@ -116,7 +120,7 @@ __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__ = '3.1'
+__version__ = '3.2'
 
 
 # ##############################################################################
@@ -148,18 +152,14 @@ def update_nodes_df(nodes: DataFrame) -> None:
     nodes_clean.drop_duplicates(keep='first', inplace=True, ignore_index=True)
 
     print('There are ' + str(len(nodes_clean)) + ' nodes ('
-          + timestamp() + '), updating node: 0  ', end='')
+          + timestamp() + '), updating node:')
     count = 0
+    start_ts = timestamp_posix()
     columns = nodes_clean.columns
     for row in nodes_clean.itertuples():
-        count += 1
-        if count % 250 == 0:
-            print(count, ' ', end='', flush=True)
-        if count % 2500 == 0:
-            print('(' + timestamp() + ')\n', end='', flush=True)
-
+        count = print_progress(count=count, interval=250)
         node_properties = {}
-        for prop_name in RICGRAPH_PROPERTIES_ADDITIONAL:
+        for prop_name in get_ricgraph_properties_additional():
             for other_name in columns:
                 if prop_name == other_name:
                     node_properties[prop_name] = getattr(row, other_name)
@@ -167,7 +167,11 @@ def update_nodes_df(nodes: DataFrame) -> None:
         create_update_node(name=row.name, category=row.category, value=row.value,
                            other_properties=node_properties)
 
-    print(count, '(' + timestamp() + ')\n', end='', flush=True)
+    print_progress(count=count, now=True)
+    end_ts = timestamp_posix()
+    print_records_per_minute(start_ts=start_ts, end_ts=end_ts,
+                             nr_records=count,
+                             what='Updated')
     return
 
 
@@ -184,18 +188,14 @@ def create_nodepairs_and_edges_df(left_and_right_nodepairs: DataFrame) -> None:
     :return: None.
     """
     print('There are ' + str(len(left_and_right_nodepairs)) + ' rows ('
-          + timestamp() + '), creating nodes and edges for row: 0  ', end='')
+          + timestamp() + '), creating nodes and edges for row:')
     count = 0
+    start_ts = timestamp_posix()
     columns = left_and_right_nodepairs.columns
     for row in left_and_right_nodepairs.itertuples():
-        count += 1
-        if count % 250 == 0:
-            print(count, ' ', end='', flush=True)
-        if count % 2500 == 0:
-            print('(' + timestamp() + ')\n', end='', flush=True)
-
+        count = print_progress(count=count, interval=250)
         node_properties = {}
-        for prop_name in RICGRAPH_PROPERTIES_ADDITIONAL:
+        for prop_name in get_ricgraph_properties_additional():
             for other_name in columns:
                 if prop_name + '1' == other_name:
                     node_properties[prop_name + '1'] = getattr(row, other_name)
@@ -206,7 +206,11 @@ def create_nodepairs_and_edges_df(left_and_right_nodepairs: DataFrame) -> None:
         create_two_nodes_and_edge(name1=row.name1, category1=row.category1, value1=row.value1,
                                   name2=row.name2, category2=row.category2, value2=row.value2,
                                   **node_properties)
-    print(count, '(' + timestamp() + ')\n', end='', flush=True)
+    print_progress(count=count, now=True)
+    end_ts = timestamp_posix()
+    print_records_per_minute(start_ts=start_ts, end_ts=end_ts,
+                             nr_records=count,
+                             what='Created')
     return
 
 
@@ -242,7 +246,7 @@ def create_nodepairs_and_edges_params(name1: Union[dict, str], category1: Union[
         left_and_right_nodepairs.rename(columns={value1.name: 'value1'}, inplace=True)
 
     # This makes programming more efficient
-    allowed_properties = RICGRAPH_PROPERTIES_ADDITIONAL + RICGRAPH_PROPERTIES_STANDARD
+    allowed_properties = get_ricgraph_properties_additional() + get_ricgraph_properties_standard()
     ext_other_properties = other_properties.copy()
     ext_other_properties['name1'] = name1
     ext_other_properties['name2'] = name2
@@ -310,7 +314,7 @@ def unify_personal_identifiers(personal_identifiers: DataFrame,
             identifiers.dropna(axis=0, how='any', inplace=True)
             identifiers.drop_duplicates(keep='first', inplace=True, ignore_index=True)
 
-            if RICGRAPH_NODEADD_MODE == 'strict':
+            if get_ricgraph_nodeadd_mode() == 'strict':
                 # Remove rows which have a cell value that occurs more than once.
                 # There are two situations: (1) nodes with unique value; (2) nodes with non-unique value.
                 # (1) We assume that in one source system, always the same ID is used to connect to

{ricgraph-3.1 → ricgraph-3.2}/ricgraph/ricgraph_cache.py

@@ -46,7 +46,7 @@ from sys import getsizeof
 from typing import Optional
 from pymemcache.client.base import Client
 from .ricgraph_constants import MAX_NODES_CACHE_KEY_ID
-from .ricgraph_utils import (get_configfile_key,
+from .ricgraph_utils import (get_configfile_key_memcached_parameters,
                              serialize_value, deserialize_value)
 
 
@@ -70,19 +70,21 @@ def memcached_open_connection() -> None:
     If Memcached is not available, then return None.
     Set the Memcached client in a global variable.
     """
-    global _MEMCACHED_HOST, _MEMCACHED_PORT
     global _memcached_available, _memcached_client
 
-    if _MEMCACHED_TO_BE_USED != 'True':
+    memcached_to_be_used, memcached_host, memcached_port = get_configfile_key_memcached_parameters()
+    if memcached_to_be_used:
+        _memcached_available = True
+    else:
         _memcached_available = False
         return
 
-    if _MEMCACHED_HOST == '' or _MEMCACHED_PORT == '':
+    if memcached_host == '':
         _memcached_available = False
         return
 
     try:
-        memcached_client = Client(server=(_MEMCACHED_HOST, int(_MEMCACHED_PORT)),
+        memcached_client = Client(server=(memcached_host, memcached_port),
                                   allow_unicode_keys=True)
 
         # Test connection by setting and deleting a test key.
@@ -93,6 +95,8 @@ def memcached_open_connection() -> None:
         _memcached_client = memcached_client
         return
     except:
+        print('memcached_open_connection(): Warning: could not reach Memcached cache daemon,')
+        print('     it is probably not running, continuing with local cache.')
         _memcached_available = False
         _memcached_client = None
         return
@@ -271,16 +275,3 @@ def nodes_cache_key_id_type_size() -> str:
     result += 'This cache has ' + str(items) + ' elements, and its size is '
     result += str(size_kb) + ' kB.'
     return result
-
-
-# ############################################
-# ################### main ###################
-# ############################################
-# This will be executed on module initialization
-_MEMCACHED_HOST = get_configfile_key(section='Memcached',
-                                     key='memcached_host')
-# This returns a str, will be converted to int later on.
-_MEMCACHED_PORT = get_configfile_key(section='Memcached',
-                                     key='memcached_port')
-_MEMCACHED_TO_BE_USED = get_configfile_key(section='Memcached',
-                                           key='ricgraph_explorer_uses_memcached')

{ricgraph-3.1 → ricgraph-3.2}/ricgraph/ricgraph_constants.py

@@ -82,7 +82,7 @@ MAX_NODES_CACHE_KEY_ID = 2000000
 MAX_NR_HISTORYITEMS_TO_ADD = 50
 
 # The maximum length of the organization abbreviation.
-MAX_ORG_ABBREVIATION_LENGTH = 3
+MAX_ORG_ABBREVIATION_LENGTH = 4
 
 
 # ########################################################################
@@ -95,96 +95,116 @@ MAX_ORG_ABBREVIATION_LENGTH = 3
 #
 # An example mapping may look like this:
 # mapping = {
-#    'book': ROTYPE_BOOK,
-#    'data set': ROTYPE_DATASET,
-#    'software': ROTYPE_SOFTWARE
+#    'book': ROCATEGORY_BOOK,
+#    'data set': ROCATEGORY_DATASET,
+#    'software': ROCATEGORY_SOFTWARE
 # }
 #
-# 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.
+# Call the function lookup_resout_category() to do this mapping.
+# If you add a type, also add it to ROCATEGORY_ALL.
+# If you add a type that is a publication, also add it to ROCATEGORY_PUBLICATION.
+#
+# ROCATEGORY_* are used in the Ricgraph 'category' field.
 #
 # 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'
-ROTYPE_DATASET = 'data set'
-ROTYPE_DESIGN = 'design'
-ROTYPE_DIGITAL_VISUAL_PRODUCT = 'digital or visual product'
-ROTYPE_EDITORIAL = 'editorial'
-ROTYPE_ENTRY = 'entry for encyclopedia or dictionary'
-ROTYPE_EXHIBITION_PERFORMANCE = 'exhibition or performance'
-ROTYPE_JOURNAL_ARTICLE = 'journal article'
-ROTYPE_LETTER = 'letter to the editor'
-ROTYPE_MEMORANDUM = 'memorandum'
-ROTYPE_METHOD_DESCRIPTION = 'method description'
-ROTYPE_MODEL = 'model'
-ROTYPE_OTHER_CONTRIBUTION = 'other contribution'
-ROTYPE_PATENT = 'patent'
-ROTYPE_PHDTHESIS = 'PhD thesis'
-ROTYPE_POSTER = 'poster'
-ROTYPE_PREPRINT = 'preprint'
-ROTYPE_PRESENTATION = 'presentation'
-ROTYPE_REGISTERED_REPORT = 'registered report'
-ROTYPE_REPORT = 'report'
-ROTYPE_RETRACTION = 'retraction'
-ROTYPE_REVIEW = 'review'
-ROTYPE_SOFTWARE = 'software'
-ROTYPE_THESIS = 'thesis'
-ROTYPE_WEBSITE = 'website or web publication'
-
-ROTYPE_ALL = [ROTYPE_ABSTRACT,
-              ROTYPE_ARTEFACT,
-              ROTYPE_BOOK,
-              ROTYPE_BOOKCHAPTER,
-              ROTYPE_CONFERENCE_ARTICLE,
-              ROTYPE_DATASET,
-              ROTYPE_DESIGN,
-              ROTYPE_DIGITAL_VISUAL_PRODUCT,
-              ROTYPE_EDITORIAL,
-              ROTYPE_ENTRY,
-              ROTYPE_EXHIBITION_PERFORMANCE,
-              ROTYPE_JOURNAL_ARTICLE,
-              ROTYPE_LETTER,
-              ROTYPE_MEMORANDUM,
-              ROTYPE_METHOD_DESCRIPTION,
-              ROTYPE_MODEL,
-              ROTYPE_OTHER_CONTRIBUTION,
-              ROTYPE_PATENT,
-              ROTYPE_PHDTHESIS,
-              ROTYPE_POSTER,
-              ROTYPE_PREPRINT,
-              ROTYPE_PRESENTATION,
-              ROTYPE_REGISTERED_REPORT,
-              ROTYPE_REPORT,
-              ROTYPE_RETRACTION,
-              ROTYPE_REVIEW,
-              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]
+ROCATEGORY_ABSTRACT = 'abstract'
+ROCATEGORY_ARTEFACT = 'artefact'
+ROCATEGORY_BOOK = 'book'
+ROCATEGORY_BOOKCHAPTER = 'book chapter'
+ROCATEGORY_CONFERENCE_ARTICLE = 'conference article'
+ROCATEGORY_DATASET = 'data set'
+ROCATEGORY_DESIGN = 'design'
+ROCATEGORY_DIGITAL_VISUAL_PRODUCT = 'digital or visual product'
+ROCATEGORY_EDITORIAL = 'editorial'
+ROCATEGORY_ENTRY = 'entry for encyclopedia or dictionary'
+ROCATEGORY_EXHIBITION_PERFORMANCE = 'exhibition or performance'
+ROCATEGORY_JOURNAL_ARTICLE = 'journal article'
+ROCATEGORY_LETTER = 'letter to the editor'
+ROCATEGORY_MEMORANDUM = 'memorandum'
+ROCATEGORY_METHOD_DESCRIPTION = 'method description'
+ROCATEGORY_MODEL = 'model'
+ROCATEGORY_OTHER_CONTRIBUTION = 'other contribution'
+ROCATEGORY_PATENT = 'patent'
+ROCATEGORY_PHDTHESIS = 'PhD thesis'
+ROCATEGORY_POSTER = 'poster'
+ROCATEGORY_PREPRINT = 'preprint'
+ROCATEGORY_PRESENTATION = 'presentation'
+ROCATEGORY_REGISTERED_REPORT = 'registered report'
+ROCATEGORY_REPORT = 'report'
+ROCATEGORY_RETRACTION = 'retraction'
+ROCATEGORY_REVIEW = 'review'
+ROCATEGORY_SOFTWARE = 'software'
+ROCATEGORY_THESIS = 'thesis'
+ROCATEGORY_WEBSITE = 'website or web publication'
+
+# ########################################################################
+# This is a special research output type allowing to select all publication
+# types.
+ROCATEGORY_PUBLICATION_ALL = 'publication_all'
+
+
+ROCATEGORY_ALL = [ROCATEGORY_ABSTRACT,
+                  ROCATEGORY_ARTEFACT,
+                  ROCATEGORY_BOOK,
+                  ROCATEGORY_BOOKCHAPTER,
+                  ROCATEGORY_CONFERENCE_ARTICLE,
+                  ROCATEGORY_DATASET,
+                  ROCATEGORY_DESIGN,
+                  ROCATEGORY_DIGITAL_VISUAL_PRODUCT,
+                  ROCATEGORY_EDITORIAL,
+                  ROCATEGORY_ENTRY,
+                  ROCATEGORY_EXHIBITION_PERFORMANCE,
+                  ROCATEGORY_JOURNAL_ARTICLE,
+                  ROCATEGORY_LETTER,
+                  ROCATEGORY_MEMORANDUM,
+                  ROCATEGORY_METHOD_DESCRIPTION,
+                  ROCATEGORY_MODEL,
+                  ROCATEGORY_OTHER_CONTRIBUTION,
+                  ROCATEGORY_PATENT,
+                  ROCATEGORY_PHDTHESIS,
+                  ROCATEGORY_POSTER,
+                  ROCATEGORY_PREPRINT,
+                  ROCATEGORY_PRESENTATION,
+                  ROCATEGORY_REGISTERED_REPORT,
+                  ROCATEGORY_REPORT,
+                  ROCATEGORY_RETRACTION,
+                  ROCATEGORY_REVIEW,
+                  ROCATEGORY_SOFTWARE,
+                  ROCATEGORY_THESIS,
+                  ROCATEGORY_WEBSITE]
+
+# A resout_type_all is defined in initialize_ricgraph_explorer().
+# These are elements of ROCATEGORY_ALL that are present in your Ricgraph.
+# I.e., those have been harvested from the source systems that you chose to harvest.
+
+ROCATEGORY_PUBLICATION = [ROCATEGORY_ABSTRACT,
+                          ROCATEGORY_BOOK,
+                          ROCATEGORY_BOOKCHAPTER,
+                          ROCATEGORY_CONFERENCE_ARTICLE,
+                          ROCATEGORY_EDITORIAL,
+                          ROCATEGORY_ENTRY,
+                          ROCATEGORY_JOURNAL_ARTICLE,
+                          ROCATEGORY_LETTER,
+                          ROCATEGORY_MEMORANDUM,
+                          ROCATEGORY_METHOD_DESCRIPTION,
+                          ROCATEGORY_PATENT,
+                          ROCATEGORY_PHDTHESIS,
+                          ROCATEGORY_POSTER,
+                          ROCATEGORY_PREPRINT,
+                          ROCATEGORY_PRESENTATION,
+                          ROCATEGORY_REGISTERED_REPORT,
+                          ROCATEGORY_REPORT,
+                          ROCATEGORY_RETRACTION,
+                          ROCATEGORY_REVIEW,
+                          ROCATEGORY_THESIS]
+
+# A resout_type_pub is defined in initialize_ricgraph_explorer().
+# These are elements of ROCATEGORY_PUBLICATION that are present in your Ricgraph.
+# I.e., those have been harvested from the source systems that you chose to harvest.
+
+
+# ########################################################################
+# Other types used in Ricgraph.
+CATEGORY_PRESS_MEDIA = 'press media'