TST: end to end test for license check

end-to-end-tests/test_crawler.py

@@ -18,6 +18,7 @@
 tests the crawling of ELN files
 """
 import os
+import re
 from pathlib import Path
 
 from ruqad.crawler import trigger_crawler
@@ -30,5 +31,18 @@ def test_crawl():
     crawl a directory as it would be created by export from kadi and running a data quality check
     """
     print(os.listdir(DATADIR))
-    retval = trigger_crawler(os.fspath(DATADIR))
+    retval, ent_qc = trigger_crawler(os.fspath(DATADIR))
+
+    # Check that validation of metadata was successful:
     assert retval
+
+    # Check that license was present in 1223 and absent in 1222:
+    qc = {}
+    for ent in ent_qc:
+        pth = ent.get_property("ELNFile").value.path
+        match = re.match("/.*/.*/(?P<folder>[0-9]+)/.*\.eln", pth)
+        assert match is not None
+        qc[match.group("folder")] = ent
+
+    assert qc["1223"].get_property("FAIRLicenseCheck").value
+    assert not qc["1222"].get_property("FAIRLicenseCheck").value

src/ruqad/crawler.py

@@ -18,7 +18,7 @@ from caoscrawler.validator import (load_json_schema_from_datamodel_yaml,
 ruqad_crawler_settings = resources.files('ruqad').joinpath('resources/crawler-settings')
 
 
-def trigger_crawler(target_dir: str) -> bool:
+def trigger_crawler(target_dir: str) -> tuple[bool, list[db.Entity]]:
     """
     Trigger a standard crawler run equivalent to the command line:
 
@@ -26,7 +26,10 @@ def trigger_crawler(target_dir: str) -> bool:
     caosdb-crawler -i crawler/identifiables.yaml -s update crawler/cfood.yaml <target_dir>
     ```
 
-    Return False in case of unsuccessful metadata validation and True otherwise.
+    A tuple:
+    - 1st element of tuple: Return False in case of unsuccessful metadata validation
+      and True otherwise.
+    - 2nd element of tuple: list of quality check records.
     """
 
     # insert all .zip and .eln files, if they do not yet exist
@@ -53,6 +56,17 @@ def trigger_crawler(target_dir: str) -> bool:
     entities = scan_directory(target_dir,
                               ruqad_crawler_settings.joinpath('cfood.yaml'))
 
+    ent_qc = []
+
+    # Show warning if license is not present in an eln file:
+    for ent in entities:
+        if not (len(ent.parents) == 1 and ent.parents[0].name == "QualityCheck"):
+            continue
+        ent_qc.append(ent)
+
+        if not ent.get_property("FAIRLicenseCheck").value:
+            print("{} does not contain a license.".format(ent.get_property("ELNFile").value.path))
+
     # Remove files from entities:
     records = [r for r in entities if r.role == "Record"]
     validation = validate(records, schemas)
@@ -62,7 +76,7 @@ def trigger_crawler(target_dir: str) -> bool:
         for v, recordtype in zip(validation, schemas.keys()):
             if not v[0]:
                 print("{}: {}".format(recordtype, v[1]))
-        return False
+        return (False, ent_qc)
 
     print("crawl", target_dir)
     crawler_main(crawled_directory_path=target_dir,
@@ -71,4 +85,4 @@ def trigger_crawler(target_dir: str) -> bool:
                      'identifiables.yaml'),
                  remove_prefix="/"+os.path.basename(target_dir))
 
-    return True
+    return (True, ent_qc)