[FIX] OASIS-to-BIDS is not up to date with online data (aramis-lab#1321)

* First pass

* Small fix

* Update bids_utils test

* Changes 1'
'

* Make change in oasis utils

* Remove duplicate function

clinica/iotools/bids_utils.py

@@ -360,6 +360,7 @@ def create_participants_df(
 
     fields_bids = ["participant_id"]
     prev_location = ""
+    prev_sheet = 0
     index_to_drop = []
     subjects_to_drop = []
     study_name = StudyName(study_name)
@@ -387,7 +388,7 @@ def create_participants_df(
             tmp = field_location[i].split("/")
             location = tmp[0]
             # If a sheet is available
-            sheet = tmp[1] if len(tmp) > 1 else ""
+            sheet = tmp[1] if len(tmp) > 1 else 0
             # Check if the file to open for a certain field is the same of the previous field
             if location == prev_location and sheet == prev_sheet:
                 pass

clinica/iotools/converters/oasis_to_bids/oasis_to_bids_utils.py

@@ -59,11 +59,7 @@ def create_sessions_dict(
             # Load the file
             tmp = field_location[i].split("/")
             location = tmp[0]
-            if len(tmp) > 1:
-                sheet = tmp[1]
-            else:
-                sheet = ""
-
+            sheet = tmp[1] if len(tmp) > 1 else 0
             file_to_read_path = clinical_data_dir / location
             file_ext = os.path.splitext(location)[1]
             if file_ext == ".xlsx":

clinica/iotools/converters/specifications/participant.tsv

@@ -1,40 +1,40 @@
 Field	BIDS CLINICA	BIDS format	BIDS type	AIBL	AIBL location	OASIS	OASIS location	OASIS3	OASIS3 location
-BIDS id of the participant	participant_id	Keyword 'sub-' followed by one of the original subject IDs without special characters or symbols	string						
-Second participant id	alternative_id_1		string	RID	aibl_ptdemog_*.csv	ID	oasis_cross-sectional.csv	Subject	oasis3_participants.csv
-Third participant id	alternative_id_2		string						
-Fourth participant id	alternative_id_3		string						
-Type of subj in PrevDemAls dataset	prevdemals_status	A or R (A = patients, R = relatives)	char						
-Date of birth	date_of_birth	YYYY-MM-DD HH:MM:SS	string	PTDOB	aibl_ptdemog_*.csv				
-Sex	sex	M or F	char	PTGENDER	aibl_ptdemog_*.csv	M/F	oasis_cross-sectional.csv	M/F	oasis3_participants.csv
-Educational level	education_level	Free format	string			Educ	oasis_cross-sectional.csv	Education	oasis3_participants.csv
-Deceased	deceased	Y or N							
-Age in years	age_bl	In years with, possibly, decimals	float			Age	oasis_cross-sectional.csv	ageAtEntry	oasis3_participants.csv
-Civil status	marital_status	Free format	string						
-	adni_rid								
-Site in which the patient was studied	site	Free format	string	SITEID	aibl_ptdemog_*.csv				
-	original_study								
-	cdr					CDR	oasis_cross-sectional.csv	cdr	oasis3_participants.csv
-Diagnosis at baseline	diagnosis_bl	AD=Alzheimer's disease - bvFTD=behavioral variant Fronto Temporal Dementia	string			CDR	oasis_cross-sectional.csv	cdr	oasis3_participants.csv
-Score of mmse test at the baseline	mmse_bl								
-APOE (number of E4 alleles)	apoe4	0, 1 or 2 (number of E4 alleles)	int						
-	apoe_gen1			APGEN1	aibl_apoeres_*.csv				
-	apoe_gen2			APGEN2	aibl_apoeres_*.csv				
-	prevdemals_age_at_onset_patients	In years with, possibly, decimals	float						
-Laterality of the subject	laterality					Hand	oasis_cross-sectional.csv	Hand	oasis3_participants.csv
-	inclusion_date	YYYY-MM-DD HH:MM:SS	string						
-									
-	prevdemals_parent_transmitting_ftd	Y or N	char						
-	prevdemals_parent_transmitting_als	Y or N	char						
-	prevdemals_parent_transmitting	father or mother	string						
-Indicate if the genotype is mutated or not	prevdemals_genetic_status_mutated	Y (mutated) or N (not mutated)	bool						
-									
-	prevdemals_aoo_transmitting_parent	in years							
-	prevdemals_family_phenotype_als	Y or N							
-	prevdemals_family_phenotype_ftd	Y or N							
-Average age onset disease in all the family member	prevdemals_aoo_mean_family		float						
-	prevdemals_expected_years_aoo_bl		signed float						
-	age_first_symptoms								
-	clinad_inclusion								
-	clinad_final_inclusion								
-	prevdemals_distance_aoo_transmitting_parent								
-	prevdemals_family_code								
+BIDS id of the participant	participant_id	Keyword 'sub-' followed by one of the original subject IDs without special characters or symbols	string
+Second participant id	alternative_id_1		string	RID	aibl_ptdemog_*.csv	ID	oasis_cross-sectional-5708aa0a98d82080.xlsx	Subject	oasis3_participants.csv
+Third participant id	alternative_id_2		string
+Fourth participant id	alternative_id_3		string
+Type of subj in PrevDemAls dataset	prevdemals_status	A or R (A = patients, R = relatives)	char
+Date of birth	date_of_birth	YYYY-MM-DD HH:MM:SS	string	PTDOB	aibl_ptdemog_*.csv
+Sex	sex	M or F	char	PTGENDER	aibl_ptdemog_*.csv	M/F	oasis_cross-sectional-5708aa0a98d82080.xlsx	M/F	oasis3_participants.csv
+Educational level	education_level	Free format	string			Educ	oasis_cross-sectional-5708aa0a98d82080.xlsx	Education	oasis3_participants.csv
+Deceased	deceased	Y or N
+Age in years	age_bl	In years with, possibly, decimals	float			Age	oasis_cross-sectional-5708aa0a98d82080.xlsx	ageAtEntry	oasis3_participants.csv
+Civil status	marital_status	Free format	string
+	adni_rid
+Site in which the patient was studied	site	Free format	string	SITEID	aibl_ptdemog_*.csv
+	original_study
+	cdr					CDR	oasis_cross-sectional-5708aa0a98d82080.xlsx	cdr	oasis3_participants.csv
+Diagnosis at baseline	diagnosis_bl	AD=Alzheimer's disease - bvFTD=behavioral variant Fronto Temporal Dementia	string			CDR	oasis_cross-sectional-5708aa0a98d82080.xlsx	cdr	oasis3_participants.csv
+Score of mmse test at the baseline	mmse_bl
+APOE (number of E4 alleles)	apoe4	0, 1 or 2 (number of E4 alleles)	int
+	apoe_gen1			APGEN1	aibl_apoeres_*.csv
+	apoe_gen2			APGEN2	aibl_apoeres_*.csv
+	prevdemals_age_at_onset_patients	In years with, possibly, decimals	float
+Laterality of the subject	laterality					Hand	oasis_cross-sectional-5708aa0a98d82080.xlsx	Hand	oasis3_participants.csv
+	inclusion_date	YYYY-MM-DD HH:MM:SS	string
+
+	prevdemals_parent_transmitting_ftd	Y or N	char
+	prevdemals_parent_transmitting_als	Y or N	char
+	prevdemals_parent_transmitting	father or mother	string
+Indicate if the genotype is mutated or not	prevdemals_genetic_status_mutated	Y (mutated) or N (not mutated)	bool
+
+	prevdemals_aoo_transmitting_parent	in years
+	prevdemals_family_phenotype_als	Y or N
+	prevdemals_family_phenotype_ftd	Y or N
+Average age onset disease in all the family member	prevdemals_aoo_mean_family		float
+	prevdemals_expected_years_aoo_bl		signed float
+	age_first_symptoms
+	clinad_inclusion
+	clinad_final_inclusion
+	prevdemals_distance_aoo_transmitting_parent
+	prevdemals_family_code