first implementation of all indicators for the CSH

app/celery/automated_tasks/__init__.py

@@ -1,12 +1,18 @@
 from .f1_model_persistent_identifier_task import f1_model_persistent_identifier
 from .f4_model_metadata_harvestable_task import f4_model_metadata_harvestable
-from .csh_fair import csh_f1_2_globally_unique_identifier, csh_a1_contains_access_information
+from .csh_fair import csh_f1_2_globally_unique_identifier, csh_a1_contains_access_information, csh_i3_01_ref_other_metadata, csh_i3_02_ref_other_data, csh_i3_03_qual_ref_other_metadata, csh_i3_04_qual_ref_other_data, csh_r1_1_01_has_reuse_license, csh_r1_1_02_has_standard_reuse_license
 
 
 
 __all__ = [
     f1_model_persistent_identifier,
     f4_model_metadata_harvestable,
     csh_f1_2_globally_unique_identifier,
-    csh_a1_contains_access_information
+    csh_a1_contains_access_information,
+    csh_i3_01_ref_other_metadata,
+    csh_i3_02_ref_other_data,
+    csh_i3_03_qual_ref_other_metadata,
+    csh_i3_04_qual_ref_other_data,
+    csh_r1_1_01_has_reuse_license,
+    csh_r1_1_02_has_standard_reuse_license
 ]

app/celery/automated_tasks/csh_fair.py

@@ -11,10 +11,15 @@
 
 config = get_settings()
 
-def is_doi(identifier):
+def is_doi(identifier: str):
     doi_pattern = r'^10\.\d{4,9}/[-._;()/:A-Z0-9]+$'
     # Use the re.match function to check if the string matches the pattern
-    return bool(re.match(doi_pattern, identifier))
+    print("identifier: ", identifier)
+    match = re.match(doi_pattern, identifier)
+    print("?? match")
+    print("doi match: ", match)
+    return False
+    #return bool(re.match(doi_pattern, identifier))
 
 
 
@@ -49,13 +54,9 @@ def incoperate_results(task_dict: dict, result: 'app.models.TaskStatus', test: b
     # Works, but does not trigger updating of children
     # redis_app.json().set(f"session:{session_id}", f".tasks.{task_id}.status", obj=result)
 
-
-
 @app.task
-def csh_f1_2_globally_unique_identifier(
-    task_dict: dict, data: dict, test: bool = False
-):
-        print("f1_2_glob")
+def csh_f1_2_globally_unique_identifier(task_dict: dict, data: dict, test: bool = False):
+        print(" ")
         """
         Representation of celery task to evaluate an assessment.
         These celery tasks should be in the format:
@@ -80,15 +81,18 @@ def assessment_task(task_dict: dict, data: dict) -> None:
 
 
         identifier = check_route(data, ["resource", "resource_identifier"])
-
+        print("grabbed identifier: ", identifier)
         #could also retrive "type" from data instead of using .startswith
-
-        if(is_doi(identifier)):
+        if(identifier is False):
+            result = "failed"
+        elif(is_doi(identifier)):
             result = "success"
         elif(identifier.startswith("DRKS")):
             result = "success"    
         else:
             result = "failed"
+
+        print("!!!!!!!!!!!!! ---- ", result)
 
         incoperate_results(task_dict, result, test)
 
@@ -153,4 +157,94 @@ def csh_a1_contains_access_information(task_dict: dict, data: dict, test: bool =
     else:
         result = "failed"
 
-    incoperate_results(task_dict, result, test)
+    incoperate_results(task_dict, result, test)
+    print("working?")
+
+@app.task
+def csh_i3_01_ref_other_metadata(task_dict: dict, data: dict, test: bool = False):
+    #check if other metadata is referenced
+    ref_resources = check_route(data, ["resource", "ids"])
+    print("INFO - csh-i3-01")
+    result = "not_applicable"
+    if(ref_resources != False):
+        print("IDs: ", ref_resources, type(ref_resources))
+        for res in ref_resources:
+            print(res, type(res))
+            print(res.get('typeGeneral'))
+            if(res.get('typeGeneral') != 'Dataset'):
+                result = "success"
+    incoperate_results(task_dict, result, test)
+
+@app.task
+def csh_i3_02_ref_other_data(task_dict: dict, data: dict, test: bool = False):
+    #check if other data is referenced
+    ref_resources = check_route(data, ["resource", "ids"])
+    print("INFO - csh-i3-02")
+    result = "not_applicable"
+    if(ref_resources != False):
+        for res in ref_resources:
+            print(res)
+            print(res.get('typeGeneral'))
+            if(res.get('typeGeneral') == 'Dataset'):
+                result = "success"
+    incoperate_results(task_dict, result, test)
+
+@app.task
+def csh_i3_03_qual_ref_other_metadata(task_dict: dict, data: dict, test: bool = False):
+    #check if other metadata is referenced
+    ref_resources = check_route(data, ["resource", "ids"])
+    print("INFO - csh-i3-03")
+    result = "not_applicable"
+    if(ref_resources != False):
+        for res in ref_resources:
+            if(res.get('typeGeneral') != 'Dataset'):
+                #set to fail if ONE refed metadata has no relationType
+                if(result == "not_applicable"):
+                    result = "success"
+                if(res.get('relationType') == None):
+                    result = "failed"
+    incoperate_results(task_dict, result, test)
+
+@app.task
+def csh_i3_04_qual_ref_other_data(task_dict: dict, data: dict, test: bool = False):
+    #check if other data is referenced
+    ref_resources = check_route(data, ["resource", "ids"])
+    print("INFO - csh-i3-04")
+    result = "not_applicable"
+    if(ref_resources != False):
+        for res in ref_resources:
+            if(res.get('typeGeneral') == 'Dataset'):
+                #set to fail if ONE refed metadata has no relationType
+                if(result == "not_applicable"):
+                    result = "success"
+                if(res.get('relationType') == None):
+                    result = "failed"
+    incoperate_results(task_dict, result, test)
+
+##### Reusability
+@app.task
+def csh_r1_1_01_has_reuse_license(task_dict: dict, data: dict, test: bool = False):
+    resource_type = check_route(data, ["resource", "classification", "type"])
+    if(resource_type == False): resource_type = check_route(data, ["resource", "resource_classification", "resource_type"])
+    if(resource_type in ["Study", "Substudy/Data collection event"]):
+        result = "warning" #TODO: Ask others to specify how this can be checked
+    else:
+        license_info = check_route(data, ["resource", "nonStudyDetails", "useRights"])
+        if(license_info != False):
+            result = "success"
+        else:
+            result = "failed"
+    incoperate_results(task_dict, result, test)
+
+@app.task #TODO: verify if this automated task really works since it depends on a parent task
+def csh_r1_1_02_has_standard_reuse_license(task_dict: dict, data: dict, test: bool = False):
+    #check if userights label is a fitting license
+    license_label  = check_route(data,["resource", "nonStudyDetails", "nonStudyDetails", "useRights"])
+    if(license_label in ["Creative Commons Zero v1.0 Universal", "Creative Commons Attribution 4.0 International", "Creative Commons Attribution Non Commercial 4.0 International", "Creative Commons Attribution Share Alike 4.0 International", "Creative Commons Attribution Non Commercial Share Alike 4.0 International"]):
+        result = "success"
+    elif(license_label == "Other"):
+        result = "warning"
+    else:
+        result = "failed"
+    incoperate_results(task_dict, result, test)
+

app/celery/automated_tasks/csh_helpers.py

@@ -2,12 +2,11 @@
 
 def check_route(metadata, route_keys):
     current_position = json.loads(metadata)
-
     for key in route_keys:
         if key in current_position:
-
             current_position = current_position[key]
         else:
+            print("the key {} form the route{} is not in the dict".format(key, route_keys), )
             #if a key is missing return false
             return False
     #if the route exists return the value

app/main.py

@@ -10,7 +10,7 @@
 tags_metadata = [
     {
         "name": "Indicators",
-        "description": "FAIR Combine assessments. Endpoints to retrieve the descriptions of the assessments done by "
+        "description": "FAIR assessments. Endpoints to retrieve the descriptions of the assessments done by "
         "the application "
         "to evaluate how FAIR a resource is/",
     },
@@ -29,22 +29,23 @@
 ]
 
 description = """
-FAIR Combine is a web application designed to help users assess how FAIR their
-their Combine resources are.
+FAIR Eval is a web application designed to help users assess how FAIR their
+their scientific resources are. Currently supported are FAIR Combine and CSH resources.
 
 Users may submit their Combine model, and the application will create a list
 of assessments following the FAIR principle. Some of these assessments will run
 in the background while others will need to be filled by the users.
+Users may also make API requests to evalutate the metadata of a CSH resource.
 
 Once all assessments are completed, the application returns a set of scores
-describing how FAIR their model is.
+describing how FAIR their resource is.
 """
 
 
 app = FastAPI(
-    title="FAIR Combine API",
+    title="FAIR Eval API",
     description=description,
-    version="0.0.1",
+    version="0.1.0",
     openapi_tags=tags_metadata,
     lifespan=get_tasks_definitions,
 )

app/metrics/metrics.csv

@@ -93,4 +93,19 @@
 "CSH-RDA-A1-03M","Essential","Metadata identifier resolves to a metadata record","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
 "CSH-RDA-A1-04M","Essential","Metadata is accessed through standardised protocol","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
 "CSH-RDA-A1.1-01M","Essential","Metadata is accessible through a free access protocol","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
-"CSH-RDA-A2-01M","Essential","Metadata is guaranteed to remain available after data is no longer available","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-A2-01M","Essential","Metadata is guaranteed to remain available after data is no longer available","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-I1-01M","Important","Metadata uses knowledge representation expressed in standardised format","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-I1-02M","Important","Metadata uses machine-understandable knowledge representation","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-I2-01M","Important","Metadata uses FAIR-compliant vocabularies","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-I3-01M","Important","Metadata includes references to other metadata","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-I3-02M","Useful","Metadata includes references to other data","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-I3-03M","Important","Metadata includes qualified references to other metadata","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-I3-04M","Useful","Metadata includes qualified references to other data","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-R1-01M","Essential","Plurality of accurate and relevant attributes are provided to allow reuse","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-R1.1-01M","Essential","Metadata includes information about the licence under which the data can be reused","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-R1.1-02M","Important","Metadata refers to a standard reuse licence","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-R1.1-03M","Important","Metadata refers to a machine-understandable reuse licence","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-R1.2-01M","Important","Metadata includes provenance information according to community-specific standards","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-R1.2-02M","Useful","Metadata includes provenance information according to a cross-community language","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-R1.3-01M","Essential","Metadata complies with a community standard","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"
+"CSH-RDA-R1.3-02M","Essential","Metadata is expressed in compliance with a machine-understandable community standard","---Add a description about the indicator (probably adapt from RDA schema)---","Add an explanation on how this indicator is technically evaluated"