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Improve FAIR report table content #215

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merged 4 commits into from
Oct 15, 2024
Merged

Improve FAIR report table content #215

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08a47f2
Table reports FAIR ID and indicator's purpose
orviz Sep 18, 2024
db0b2b4
Sort indicators in the FAIR order
orviz Sep 18, 2024
ef499f6
Remove duplicated var
orviz Sep 19, 2024
e286af8
Improve --json help
orviz Sep 19, 2024
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232 changes: 224 additions & 8 deletions scripts/fair-eva.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,220 @@
from flask_babel import lazy_gettext as _l
from prettytable import PrettyTable

searching = False
FAIR_PRINCIPLES = ["findable", "accessible", "interoperable", "reusable"]

FAIR_RDA_INDICATORS = {
"RDA_F1_01M": {
"id": "RDA-F1-01M",
"indicator": "Metadata is identified by a persistent identifier",
"priority": "Essential (***)",
},
"RDA_F1_01D": {
"id": "RDA-F1-01D",
"indicator": "Data is identified by a persistent identifier",
"priority": "Essential (***)",
},
"RDA_F1_02M": {
"id": "RDA-F1-02M",
"indicator": "Metadata is identified by a globally unique identifier",
"priority": "Essential (***)",
},
"RDA_F1_02D": {
"id": "RDA-F1-02D",
"indicator": "Data is identified by a persistent identifier",
"priority": "Essential (***)",
},
"RDA_F2_01M": {
"id": "RDA-F2-01M",
"indicator": "Rich metadata is provided to allow discovery",
"priority": "Essential (***)",
},
"RDA_F3_01M": {
"id": "RDA-F3-01M",
"indicator": "Metadata includes the identifier for the data",
"priority": "Essential (***)",
},
"RDA_F4_01M": {
"id": "RDA-F4-01M",
"indicator": "Metadata is offered in such a way that it can be harvested and indexed",
"priority": "Essential (***)",
},
"RDA_A1_01M": {
"id": "RDA-A1-01M",
"indicator": "Metadata contains information to enable the user to get access to the data",
"priority": "Important (**)",
},
"RDA_A1_02M": {
"id": "RDA-A1-02M",
"indicator": "Metadata can be accessed manually (i.e. with human intervention)",
"priority": "Essential (***)",
},
"RDA_A1_02D": {
"id": "RDA-A1-02D",
"indicator": "Data can be accessed manually (i.e. with human intervention)",
"priority": "Essential (***)",
},
"RDA_A1_03M": {
"id": "RDA-A1-03M",
"indicator": "Metadata identifier resolves to a metadata record",
"priority": "Essential (***)",
},
"RDA_A1_02D": {
"id": "RDA-A1-02D",
"indicator": "Data can be accessed manually (i.e. with human intervention)",
"priority": "Essential (***)",
},
"RDA_A1_03D": {
"id": "RDA-A1-03D",
"indicator": "Data identifier resolves to a digital object",
"priority": "Essential (***)",
},
"RDA_A1_04M": {
"id": "RDA-A1-04M",
"indicator": "Metadata is accessed through standardised protocol",
"priority": "Essential (***)",
},
"RDA_A1_04D": {
"id": "RDA-A1-04D",
"indicator": "Data is accessed through standardised protocol",
"priority": "Essential (***)",
},
"RDA_A1_05D": {
"id": "RDA-A1-05D",
"indicator": "Data can be accessed automatically (i.e. by a computer program)",
"priority": "Important (**)",
},
"RDA_A1_1_01M": {
"id": "RDA-A1.1-01M",
"indicator": "Metadata is accessible through a free access protocol",
"priority": "Essential (***)",
},
"RDA_A1_1_01D": {
"id": "RDA-A1.1-01D",
"indicator": "Data is accessible through a free access protocol",
"priority": "Important (**)",
},
"RDA_A1_2_01D": {
"id": "RDA-A1.2-01D",
"indicator": "Data is accessible through an access protocol that supports authentication and authorisation",
"priority": "Useful (*)",
},
"RDA_A2_01M": {
"id": "RDA-A2-01M",
"indicator": "Metadata is guaranteed to remain available after data is no longer available",
"priority": "Essential (***)",
},
"RDA_I1_01M": {
"id": "RDA-I1-01M",
"indicator": "Metadata uses knowledge representation expressed in standardised format",
"priority": "Important (**)",
},
"RDA_I1_01D": {
"id": "RDA-I1-01D",
"indicator": "Data uses knowledge representation expressed in standardised format",
"priority": "Important (**)",
},
"RDA_I1_02M": {
"id": "RDA-I1-02M",
"indicator": "Metadata uses machine-understandable knowledge representation",
"priority": "Important (**)",
},
"RDA_I1_02D": {
"id": "RDA-I1-02D",
"indicator": "Data uses machine-understandable knowledge representation",
"priority": "Important (**)",
},
"RDA_I2_01M": {
"id": "RDA-I2-01M",
"indicator": "Metadata uses FAIR-compliant vocabularies",
"priority": "Important (**)",
},
"RDA_I2_01D": {
"id": "RDA-I2-01D",
"indicator": "Data uses FAIR-compliant vocabularies",
"priority": "Useful (*)",
},
"RDA_I3_01M": {
"id": "RDA-I3-01M",
"indicator": "Metadata includes references to other metadata",
"priority": "Important (**)",
},
"RDA_I3_01D": {
"id": "RDA-I3-01D",
"indicator": "Data includes references to other data",
"priority": "Useful (*)",
},
"RDA_I3_02M": {
"id": "RDA-I3-02M",
"indicator": "Metadata includes references to other data",
"priority": "Important (**)",
},
"RDA_I3_02D": {
"id": "RDA-I3-02D",
"indicator": "Data includes qualified references to other data",
"priority": "Useful (*)",
},
"RDA_I3_03M": {
"id": "RDA-I3-03M",
"indicator": "Metadata includes qualified references to other metadata",
"priority": "Important (**)",
},
"RDA_I3_04M": {
"id": "RDA-I3-04M",
"indicator": "Metadata includes qualified references to other data",
"priority": "Useful (*)",
},
"RDA_R1_01M": {
"id": "RDA-R1-01M",
"indicator": "Plurality of accurate and relevant attributes are provided to allow reuse",
"priority": "Essential (***)",
},
"RDA_R1_1_01M": {
"id": "RDA-R1.1-01M",
"indicator": "Metadata includes information about the licence under which the data can be reused",
"priority": "Essential (***)",
},
"RDA_R1_1_02M": {
"id": "RDA-R1.1-02M",
"indicator": "Metadata refers to a standard reuse licence",
"priority": "Important (**)",
},
"RDA_R1_1_03M": {
"id": "RDA-R1.1-03M",
"indicator": "Metadata refers to a machine understandable reuse licence",
"priority": "Important (**)",
},
"RDA_R1_2_01M": {
"id": "RDA-R1.2-01M",
"indicator": "Metadata includes provenance information according to community-specific standards",
"priority": "Important (**)",
},
"RDA_R1_2_02M": {
"id": "RDA-R1.2-02M",
"indicator": "Metadata includes provenance information according to a cross-community language",
"priority": "Useful (*)",
},
"RDA_R1_3_01M": {
"id": "RDA-R1.3-01M",
"indicator": "Metadata complies with a community standard",
"priority": "Essential (***)",
},
"RDA_R1_3_01D": {
"id": "RDA-R1.3-01D",
"indicator": "Data complies with a community standard",
"priority": "Essential (***)",
},
"RDA_R1_3_02M": {
"id": "RDA-R1.3-02M",
"indicator": "Metadata is expressed in compliance with a machine-understandable community standard",
"priority": "Essential (***)",
},
"RDA_R1_3_02D": {
"id": "RDA-R1.3-02D",
"indicator": "Data is expressed in compliance with a machine-understandable community standard",
"priority": "Important (**)",
},
}


class Formatter(logging.Formatter):
Expand Down Expand Up @@ -85,7 +298,7 @@ def get_input_args():
),
)
parser.add_argument(
"-j", "--json", action="store_true", help=("Flag to print the json results")
"-j", "--json", action="store_true", help=("Flag to print the results in JSON format")
)
parser.add_argument(
"--totals",
Expand Down Expand Up @@ -124,7 +337,7 @@ def is_port_open():


def calcpoints(result):
keys = ["findable", "accessible", "interoperable", "reusable", "total"]
keys = FAIR_PRINCIPLES + ["total"]
values = [0, 0, 0, 0, 0]
result_points = 0
weight_of_tests = 0
Expand Down Expand Up @@ -178,7 +391,8 @@ def format_msg_for_table(message_data):
def collect_score_data(fair_results):
# Split by principle: required for setting dividers in the resultant table
indicators_by_principle = {}
for principle, principle_result in fair_results.items():
for principle in FAIR_PRINCIPLES:
principle_result = fair_results[principle]
indicators_by_principle[principle] = list(principle_result.values())

rows = []
Expand All @@ -190,9 +404,11 @@ def collect_score_data(fair_results):
points = indicator_result["points"]
if isinstance(points, float):
points = "%.2f" % points
indicator_id_internal = indicator_result["name"].upper()
indicator_rda_data = FAIR_RDA_INDICATORS[indicator_id_internal]
row = [
indicator_result["name"].upper(),
principle,
indicator_rda_data["id"],
indicator_rda_data["indicator"],
points,
output_message,
]
Expand All @@ -203,9 +419,9 @@ def collect_score_data(fair_results):

def print_table(indicator_rows, totals={}):
table = PrettyTable()
table.field_names = ["FAIR indicator", "FAIR principle", "Score", "Output"]
table.field_names = ["ID", "Indicator", "Score", "Output"]
table.align = "l"
table._max_width = {"Output": 100}
table._max_width = {"Indicator": 40, "Output": 60}
table.add_rows([row for row in indicator_rows])

# Printing out totals
Expand Down
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