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ecrin-github / MDR_Aggregator

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Phase 2: ***ERROR*** In ExecuteSQL; Exception while reading from stream, SQL was: INSERT INTO st.study_conditions(study_id, original_value, original_ct_type_id, original_ct_code, icd_code, icd_name) #11

Open michelescarlato opened 1 month ago

michelescarlato commented 1 month ago 
08/09/2024 : 10:25 :   Transferred euctr_ad.study_conditions (new studies) data, ids 100001 to 105769
08/09/2024 : 10:25 :   Loaded 39567 study_conditions, for new studies

+++++++++++++++++++++++++++++++++++++++
08/09/2024 : 10:26 :   ***ERROR*** In ExecuteSQL; Exception while reading from stream, 
SQL was: INSERT INTO st.study_conditions(study_id, original_value, original_ct_type_id, original_ct_code, 
        icd_code, icd_name)
                   SELECT s.study_id, s.original_value, s.original_ct_type_id, s.original_ct_code, 
        s.icd_code, s.icd_name
                   FROM nk.source_data s
                   LEFT JOIN nk.existing_coded_data e1
                   ON s.sd_sid = e1.sd_sid
                   AND s.icd_code = e1.icd_code
                   WHERE s.icd_code is not null and e1.sd_sid is null  and  s.id >= 1 and s.id < 50001 
+++++++++++++++++++++++++++++++++++++++

08/09/2024 : 10:26 :   Transferred euctr_ad.study_conditions (existing studies) data, ids 1 to 50000

+++++++++++++++++++++++++++++++++++++++
08/09/2024 : 10:27 :   ***ERROR*** In ExecuteSQL; Exception while reading from stream, 
SQL was: INSERT INTO st.study_conditions(study_id, original_value, original_ct_type_id, original_ct_code, 
        icd_code, icd_name)
                   SELECT s.study_id, s.original_value, s.original_ct_type_id, s.original_ct_code, 
        s.icd_code, s.icd_name
                   FROM nk.source_data s
                   LEFT JOIN nk.existing_coded_data e1
                   ON s.sd_sid = e1.sd_sid
                   AND s.icd_code = e1.icd_code
                   WHERE s.icd_code is not null and e1.sd_sid is null  and  s.id >= 50001 and s.id < 100001 
+++++++++++++++++++++++++++++++++++++++

08/09/2024 : 10:27 :   Transferred euctr_ad.study_conditions (existing studies) data, ids 50001 to 100000

+++++++++++++++++++++++++++++++++++++++
08/09/2024 : 10:27 :   ***ERROR*** In ExecuteSQL; Exception while reading from stream, 
SQL was: INSERT INTO st.study_conditions(study_id, original_value, original_ct_type_id, original_ct_code, 
        icd_code, icd_name)
                   SELECT s.study_id, s.original_value, s.original_ct_type_id, s.original_ct_code, 
        s.icd_code, s.icd_name
                   FROM nk.source_data s
                   LEFT JOIN nk.existing_coded_data e1
                   ON s.sd_sid = e1.sd_sid
                   AND s.icd_code = e1.icd_code
                   WHERE s.icd_code is not null and e1.sd_sid is null  and  s.id >= 100001 and s.id < 150001 
+++++++++++++++++++++++++++++++++++++++

08/09/2024 : 10:27 :   Transferred euctr_ad.study_conditions (existing studies) data, ids 100001 to 105769
08/09/2024 : 10:27 :   Loaded 0 icd coded study conditions, for existing studies
08/09/2024 : 10:27 :   Transferred euctr_ad.study_conditions (existing studies) data, ids 1 to 50000
08/09/2024 : 10:27 :   Transferred euctr_ad.study_conditions (existing studies) data, ids 50001 to 100000
michelescarlato commented 1 month ago

AG -D 2024-09-08 100000.log

michelescarlato commented 1 month ago

After increasing the timeout as suggested in #12,

16/09/2024 : 18:25 :   **** TRANSFER OBJECT DATA ****

+++++++++++++++++++++++++++++++++++++++
16/09/2024 : 18:25 :   ***ERROR*** In ExecuteSQL; 23505: duplicate key value violates unique constraint "data_objects_pkey"

DETAIL: Key (id)=(381344) already exists., 
SQL was: INSERT INTO ob.data_objects(id, title, version, display_title, doi, doi_status_id, publication_year,
        object_class_id, object_type_id, managing_org_id, managing_org, managing_org_ror_id, 
        lang_code, access_type_id, access_details, access_details_url, url_last_checked, 
        eosc_category, add_study_contribs, add_study_topics)
                SELECT t.object_id, s.title, s.version, s.display_title, s.doi, s.doi_status_id, s.publication_year,
        s.object_class_id, s.object_type_id, s.managing_org_id, s.managing_org, s.managing_org_ror_id, 
        s.lang_code, s.access_type_id, s.access_details, s.access_details_url, s.url_last_checked, 
        s.eosc_category, s.add_study_contribs, s.add_study_topics
                FROM biolincc_ad.data_objects s
                INNER JOIN nk.temp_objects_to_add t
                on s.sd_oid = t.sd_oid 
+++++++++++++++++++++++++++++++++++++++

16/09/2024 : 18:25 :   Transferred biolincc_ad.data_objects (new objects) data, as a single batch

which is probably a minor issue.

But I notice that the error was there also on the previous execution:


15/09/2024 : 10:44 :   **** TRANSFER OBJECT DATA ****

+++++++++++++++++++++++++++++++++++++++
15/09/2024 : 10:44 :   ***ERROR*** In ExecuteSQL; 23505: duplicate key value violates unique constraint "data_objects_pkey"

DETAIL: Key (id)=(381344) already exists., 
SQL was: INSERT INTO ob.data_objects(id, title, version, display_title, doi, doi_status_id, publication_year,
        object_class_id, object_type_id, managing_org_id, managing_org, managing_org_ror_id, 
        lang_code, access_type_id, access_details, access_details_url, url_last_checked, 
        eosc_category, add_study_contribs, add_study_topics)
                SELECT t.object_id, s.title, s.version, s.display_title, s.doi, s.doi_status_id, s.publication_year,
        s.object_class_id, s.object_type_id, s.managing_org_id, s.managing_org, s.managing_org_ror_id, 
        s.lang_code, s.access_type_id, s.access_details, s.access_details_url, s.url_last_checked, 
        s.eosc_category, s.add_study_contribs, s.add_study_topics
                FROM biolincc_ad.data_objects s
                INNER JOIN nk.temp_objects_to_add t
                on s.sd_oid = t.sd_oid 
+++++++++++++++++++++++++++++++++++++++

15/09/2024 : 10:44 :   Transferred biolincc_ad.data_objects (new objects) data, as a single batch
15/09/2024 : 10:44 :   Loaded 0 data_objects

15/09/2024 : 10:44 :   Transferred biolincc_ad.object_titles (new objects) data, as a single batch
15/09/2024 : 10:44 :   Loaded 1234 object titles
michelescarlato commented 1 month ago

AG -D 2024-09-16 172730.log