Merge branch 'release-v0.7.0' into 'main'

Release v0.7.0

See merge request !69

.gitignore

@@ -17,3 +17,4 @@ build/
 
 # documentation
 _apidoc
+/dist/

.gitlab/issue_templates/Default.md

+## Summary
+
+*Please give a short summary of what the issue is.*
+
+## Expected Behavior
+
+*What did you expect how the software should behave?*
+
+## Actual Behavior
+
+*What did the software actually do?*
+
+## Steps to Reproduce the Problem
+
+*Please describe, step by step, how others can reproduce the problem.  Please try these steps for yourself on a clean system.*
+
+1.
+2.
+3.
+
+## Specifications
+
+- Version: *Which version of this software?*
+- Platform: *Which operating system, which other relevant software versions?*
+
+## Possible fixes
+
+*Do you have ideas how the issue can be resolved?*

.gitlab/merge_request_templates/Default.md

+# Summary
+
+*Insert a meaningful description for this merge request here:  What is the new/changed behavior?
+Which bug has been fixed? Are there related issues?*
+
+
+# Focus
+
+*Point the reviewer to the core of the code change. Where should they start reading? What should
+they focus on (e.g. security, performance, maintainability, user-friendliness, compliance with the
+specs, finding more corner cases, concrete questions)?*
+
+
+# Test Environment
+
+*How to set up a test environment for manual testing?*
+
+
+# Check List for the Author
+
+Please, prepare your MR for a review. Be sure to write a summary and a focus and create gitlab
+comments for the reviewer. They should guide the reviewer through the changes, explain your changes
+and also point out open questions. For further good practices have a look at [our review
+guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md)
+
+- [ ] All automated tests pass
+- [ ] Reference related issues
+- [ ] Up-to-date CHANGELOG.md (or not necessary)
+- [ ] Up-to-date JSON schema (or not necessary)
+- [ ] Appropriate user and developer documentation (or not necessary)
+  - How do I use the software?  Assume "stupid" users.
+  - How do I develop or debug the software?  Assume novice developers.
+- [ ] Annotations in code (Gitlab comments)
+  - Intent of new code
+  - Problems with old code
+  - Why this implementation?
+
+
+# Check List for the Reviewer
+
+- [ ] I understand the intent of this MR
+- [ ] All automated tests pass
+- [ ] Up-to-date CHANGELOG.md (or not necessary)
+- [ ] Appropriate user and developer documentation (or not necessary)
+- [ ] The test environment setup works and the intended behavior is reproducible in the test
+  environment
+- [ ] In-code documentation and comments are up-to-date.
+- [ ] Check: Are there specifications? Are they satisfied?
+
+For further good practices have a look at [our review guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md).
+
+
+/assign me
+/target_branch dev

CHANGELOG.md

@@ -4,6 +4,14 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.7.0] - 2023-03-09 ##
+(Florian Spreckelsen)
+
+### Added ###
+
+- `create_entity_link` function to create html links to entities; useful for
+  logging
+
 ## [0.6.1] - 2023-01-20##
 
 ### Added ###

CITATION.cff

@@ -20,6 +20,6 @@ authors:
     given-names: Stefan
     orcid: https://orcid.org/0000-0001-7214-8125
 title: CaosDB - Advanced User Tools
-version: 0.6.1
+version: 0.7.0
 doi: 10.3390/data4020083
 date-released: 2023-01-20
\ No newline at end of file

setup.py

@@ -46,8 +46,8 @@ from setuptools import find_packages, setup
 ########################################################################
 
 MAJOR = 0
-MINOR = 6
-MICRO = 1
+MINOR = 7
+MICRO = 0
 PRE = ""  # e.g. rc0, alpha.1, 0.beta-23
 ISRELEASED = True
 

src/caosadvancedtools/crawler.py

@@ -58,6 +58,7 @@ from .guard import RETRIEVE, ProhibitedException
 from .guard import global_guard as guard
 from .serverside.helper import send_mail as main_send_mail
 from .suppressKnown import SuppressKnown
+from .utils import create_entity_link
 
 logger = logging.getLogger(__name__)
 
@@ -103,15 +104,8 @@ def apply_list_of_updates(to_be_updated, update_flags={},
 
     info = "UPDATE: updating the following entities\n"
 
-    baseurl = db.configuration.get_config()["Connection"]["url"]
-
-    def make_clickable(txt, id):
-        return "<a href='{}/Entity/{}'>{}</a>".format(baseurl, id, txt)
-
     for el in to_be_updated:
-        info += str("\t" + make_clickable(el.name, el.id)
-                    if el.name is not None
-                    else "\t" + make_clickable(str(el.id), el.id))
+        info += str("\t" + create_entity_link(el))
         info += "\n"
     logger.info(info)
 

src/caosadvancedtools/loadFiles.py

@@ -175,8 +175,6 @@ def loadpath(path, include, exclude, prefix, dryrun, forceAllowSymlinks, caosdbi
         for f in files:
             totalsize += f.size
 
-        print("Made in total {} new files with a combined size of {} "
-              "accessible.".format(len(files), convert_size(totalsize)))
         logger.info("Made in total {} new files with a combined size of {} "
                     "accessible.".format(len(files), convert_size(totalsize)))
 
@@ -249,6 +247,10 @@ exclude is given preference over include.
         raise ValueError(
             "Do not use a localpath and in- or exclude simultaneously!")
 
+    # configure logging
+    logger.addHandler(logging.StreamHandler(stream=sys.stdout))
+    logger.setLevel(logging.INFO)
+
     con = db.get_connection()
     con.timeout = float(args.timeout)
     con._login()

src/caosadvancedtools/utils.py

@@ -55,6 +55,26 @@ def replace_path_prefix(path, old_prefix, new_prefix):
     return os.path.join(new_prefix, path)
 
 
+def create_entity_link(entity: db.Entity, base_url: str = ""):
+    """
+    creates a string that contains the code for an html link to the provided entity.
+
+    The text of the link is the entity name if one exists and the id otherwise.
+
+    Args:
+        entity (db.Entity): the entity object to which the link will point
+        base_url (str): optional, by default, the url starts with '/Entity' and thus is relative.
+                        You can provide a base url that will be prefixed.
+    Returns:
+        str: the string containing the html code
+
+    """
+    return "<a href='{}/Entity/{}'>{}</a>".format(
+        base_url,
+        entity.id,
+        entity.name if entity.name is not None else entity.id)
+
+
 def string_to_person(person):
     """
     Creates a Person Record from a string.

src/doc/conf.py

@@ -27,9 +27,9 @@ copyright = '2021, IndiScale GmbH'
 author = 'Daniel Hornung'
 
 # The short X.Y version
-version = '0.6.1'
+version = '0.7.0'
 # The full version, including alpha/beta/rc tags
-release = '0.6.1'
+release = '0.7.0'
 
 
 # -- General configuration ---------------------------------------------------

unittests/test_json_schema_model_parser.py

@@ -164,7 +164,7 @@ def test_enum():
         assert isinstance(model[name], db.Record)
         assert model[name].name == name
         assert len(model[name].parents) == 1
-        assert model[name].has_parent(model["license"])
+        assert model[name].has_parent(model["license"], retrieve=False)
 
     # Also allow enums with non-string types
     number_enums = ["1.1", "2.2", "3.3"]
@@ -181,7 +181,7 @@ def test_enum():
         assert isinstance(model[name], db.Record)
         assert model[name].name == name
         assert len(model[name].parents) == 1
-        assert model[name].has_parent(model["number_enum"])
+        assert model[name].has_parent(model["number_enum"], retrieve=False)
 
 
 @pytest.mark.xfail(reason="Don't allow integer enums until https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/issues/224 has been fixed")
@@ -207,7 +207,7 @@ def test_int_enum():
         assert isinstance(model[name], db.Record)
         assert model[name].name == name
         assert len(model[name].parents) == 1
-        assert model[name].has_parent(model["int_enum"])
+        assert model[name].has_parent(model["int_enum"], retrieve=False)
 
 
 def test_references():
@@ -339,7 +339,7 @@ def test_list():
         assert isinstance(model[name], db.Record)
         assert model[name].name == name
         assert len(model[name].parents) == 1
-        assert model[name].has_parent(model["license"])
+        assert model[name].has_parent(model["license"], retrieve=False)
 
 
 def test_name_property():

unittests/test_utils.py

@@ -26,7 +26,7 @@ from tempfile import NamedTemporaryFile
 
 import caosdb as db
 from caosadvancedtools.utils import (check_win_path, get_referenced_files,
-                                     string_to_person)
+                                     string_to_person, create_entity_link)
 from caosdb import RecordType, configure_connection, get_config
 from caosdb.connection.mockup import MockUpResponse, MockUpServerConnection
 from caosdb.exceptions import TransactionError
@@ -140,3 +140,8 @@ class PathTest(unittest.TestCase):
         assert check_win_path(r"C:\hallo")
         assert check_win_path(r"\hallo")
         assert not check_win_path("/hallo")
+
+
+class EntityLinkTest(unittest.TestCase):
+    def test_link(self):
+        assert "<a href='/Entity/1'>a</a>" == create_entity_link(db.Entity(id=1, name='a'))