Hello 
I have a CDM compliant postgresql database, and i’m trying to launch Achilles atop it.
I had some bad starts with using docker to do this, and decided to switch to using R given that it was better at showing me errors, plus more widely used.
I worked my way down to step 5 of the getting started section of the [github]/OHDSI/Achilles page
When I try to execute exportToJson to generate Achilles statistics, I get an error, which runs,
exportToJson(connectionDetails, "odhsi", "odhsi", "/Users/snkasthu/Downloads/achillies_output"); Warning: folder /Users/snkasthu/Downloads/achillies_output already exists Connecting using PostgreSQL driver Generating condition treemap | | 0%Error executing SQL: Error in rJava::.jcall(s, "Ljava/sql/ResultSet;", "executeQuery", as.character(query)[1]): org.postgresql.util.PSQLException: ERROR: relation "achilles_results" does not exist Position: 587
An error report has been created at /Users/snkasthu/Achilles/errorReport.txt Error in value[[3L]](cond) : no loop for break/next, jumping to top level
The detailed error report reads,
DBMS:
postgresql
Error:
org.postgresql.util.PSQLException: ERROR: relation “achilles_results” does not exist
Position: 587
SQL:
select concept_hierarchy.concept_id,
COALESCE(concept_hierarchy.soc_concept_name,‘NA’) || ‘||’ || COALESCE(concept_hierarchy.hlgt_concept_name,‘NA’) || ‘||’ || COALESCE(concept_hierarchy.hlt_concept_name,‘NA’) || ‘||’ || COALESCE(concept_hierarchy.pt_concept_name,‘NA’) || ‘||’ || COALESCE(concept_hierarchy.snomed_concept_name,‘NA’) concept_path,
ar1.count_value as num_persons,
ROUND(CAST(1.0ar1.count_value / denom.count_value AS NUMERIC),5) as percent_persons,
ROUND(CAST(1.0ar2.count_value / ar1.count_value AS NUMERIC),5) as records_per_person
from (select * from ACHILLES_results where analysis_id = 400) ar1
inner join
(select * from ACHILLES_results where analysis_id = 401) ar2
on ar1.stratum_1 = ar2.stratum_1
inner join
(
select snomed.concept_id,
snomed.concept_name as snomed_concept_name,
pt_to_hlt.pt_concept_name,
hlt_to_hlgt.hlt_concept_name,
hlgt_to_soc.hlgt_concept_name,
soc.concept_name as soc_concept_name
from
(
select concept_id, concept_name
from odhsi.concept
where vocabulary_id = 1
) snomed
left join
(select c1.concept_id as snomed_concept_id, max(c2.concept_id) as pt_concept_id
from
odhsi.concept c1
inner join
odhsi.concept_ancestor ca1
on c1.concept_id = ca1.descendant_concept_id
and c1.vocabulary_id = 1
inner join
odhsi.concept c2
on ca1.ancestor_concept_id = c2.concept_id
and c2.vocabulary_id = 15
and c2.concept_class = ‘Preferred Term’
group by c1.concept_id
) snomed_to_pt
on snomed.concept_id = snomed_to_pt.snomed_concept_id
left join (select c1.concept_id as pt_concept_id, c1.concept_name as pt_concept_name, max(c2.concept_id) as hlt_concept_id from odhsi.concept c1 inner join odhsi.concept_ancestor ca1 on c1.concept_id = ca1.descendant_concept_id and c1.vocabulary_id = 15 and c1.concept_class = 'Preferred Term' inner join odhsi.concept c2 on ca1.ancestor_concept_id = c2.concept_id and c2.vocabulary_id = 15 and c2.concept_class = 'High Level Term' group by c1.concept_id, c1.concept_name ) pt_to_hlt on snomed_to_pt.pt_concept_id = pt_to_hlt.pt_concept_id
left join (select c1.concept_id as hlt_concept_id, c1.concept_name as hlt_concept_name, max(c2.concept_id) as hlgt_concept_id from odhsi.concept c1 inner join odhsi.concept_ancestor ca1 on c1.concept_id = ca1.descendant_concept_id and c1.vocabulary_id = 15 and c1.concept_class = 'High Level Term' inner join odhsi.concept c2 on ca1.ancestor_concept_id = c2.concept_id and c2.vocabulary_id = 15 and c2.concept_class = 'High Level Group Term' group by c1.concept_id, c1.concept_name ) hlt_to_hlgt on pt_to_hlt.hlt_concept_id = hlt_to_hlgt.hlt_concept_id
left join (select c1.concept_id as hlgt_concept_id, c1.concept_name as hlgt_concept_name, max(c2.concept_id) as soc_concept_id from odhsi.concept c1 inner join odhsi.concept_ancestor ca1 on c1.concept_id = ca1.descendant_concept_id and c1.vocabulary_id = 15 and c1.concept_class = 'High Level Group Term' inner join odhsi.concept c2 on ca1.ancestor_concept_id = c2.concept_id and c2.vocabulary_id = 15 and c2.concept_class = 'System Organ Class' group by c1.concept_id, c1.concept_name ) hlgt_to_soc on hlt_to_hlgt.hlgt_concept_id = hlgt_to_soc.hlgt_concept_id
left join odhsi.concept soc on hlgt_to_soc.soc_concept_id = soc.concept_id
) concept_hierarchy
on CAST(ar1.stratum_1 AS INT) = concept_hierarchy.concept_id
,
(select count_value from ACHILLES_results where analysis_id = 1) denom
order by ar1.count_value desc
R version:
R version 3.2.0 (2015-04-16)
Platform:
x86_64-apple-darwin13.4.0
Attached base packages:
- stats
- graphics
- grDevices
- utils
- datasets
- methods
- base
Other attached packages:
- Achilles (1.0)
- rjson (0.2.15)
- SqlRender (1.1.2)
- DatabaseConnector (1.2.1)
- RJDBC (0.2-5)
- rJava (0.9-6)
- DBI (0.3.1)
- devtools (1.8.0)
Any suggestions on why i’m missing this relation would be very much appreciated