diff --git a/Model/bin/showNewCommentLinks b/Model/bin/showNewCommentLinks
index e85d38f4c..ee2a2bf06 100755
--- a/Model/bin/showNewCommentLinks
+++ b/Model/bin/showNewCommentLinks
@@ -8,7 +8,7 @@ use Data::Dumper;
use Getopt::Long qw(GetOptions);
use ApiCommonData::Load::TuningConfig::Utils;
-my ($propfile, $instance, $schema, $password, $suffix, $prefix, $dblink, $subversionDir, $debug);
+my ($propfile, $instance, $schema, $password, $suffix, $prefix, $remoteUserSchema, $subversionDir, $debug);
Getopt::Long::Configure("pass_through");
GetOptions("propfile=s" => \$propfile,
"instance=s" => \$instance,
@@ -16,7 +16,7 @@ GetOptions("propfile=s" => \$propfile,
"password=s" => \$password,
"suffix=s" => \$suffix,
"prefix=s" => \$prefix,
- "dblink=s" => \$dblink,
+ "remoteUserSchema=s" => \$remoteUserSchema,
"subversionDir=s" => \$subversionDir,
"debug!" => \$debug,
);
@@ -27,7 +27,7 @@ my $dbh = ApiCommonData::Load::TuningConfig::Utils::getDbHandle($instance, $sche
my $csiTable = $prefix . "NewCsi";
my $stmt = $dbh->prepare(<
-
-
+
diff --git a/Model/lib/wdk/model/questions/params/metricsParams.xml b/Model/lib/wdk/model/questions/params/metricsParams.xml
index ef9e0b9f1..5c11942ca 100644
--- a/Model/lib/wdk/model/questions/params/metricsParams.xml
+++ b/Model/lib/wdk/model/questions/params/metricsParams.xml
@@ -76,7 +76,7 @@
CASE when project_id in ('EuPathDB') then 'VEuPathDB'
else project_id
end as display
- FROM metrics.SEARCHESSTATS@USER_DBLINK@)
+ FROM @REMOTE_METRICS_SCHEMA@.SEARCHESSTATS)
ORDER BY display
]]>
@@ -92,7 +92,7 @@
CASE when project_id in ('EuPathDB') then 'VEuPathDB'
else project_id
end as display
- FROM metrics.ORGANISMVIEWSTATS@USER_DBLINK@)
+ FROM @REMOTE_METRICS_SCHEMA@.ORGANISMVIEWSTATS)
ORDER BY display
]]>
@@ -108,7 +108,7 @@
CASE when project_id in ('EuPathDB') then 'VEuPathDB'
else project_id
end as display
- FROM metrics.GENEPAGETABLESTATS@USER_DBLINK@
+ FROM @REMOTE_METRICS_SCHEMA@.GENEPAGETABLESTATS
WHERE project_id is not null)
ORDER BY display
]]>
diff --git a/Model/lib/wdk/model/questions/params/sharedParams.xml b/Model/lib/wdk/model/questions/params/sharedParams.xml
index 0f48be89e..4a61feeb0 100644
--- a/Model/lib/wdk/model/questions/params/sharedParams.xml
+++ b/Model/lib/wdk/model/questions/params/sharedParams.xml
@@ -1518,8 +1518,6 @@ This parameter allows you to apply the minimum number of peptides to each select
-
@@ -2817,22 +2815,6 @@ This parameter allows you to apply the minimum number of peptides to each select
-
-
-
-
-
-
- SELECT term, display, rownum AS internal
- FROM (
- SELECT a.question_name AS term, count(s.step_id) AS display
- FROM @WDK_ENGINE_SCHEMA@answers@USER_DBLINK@ a, @USER_SCHEMA@steps@USER_DBLINK@ s
- WHERE a.answer_id = s.step_id
- GROUP BY a.question_name
- ) t
-
-
-
diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml
index 80d8eec54..5add2b91f 100644
--- a/Model/lib/wdk/model/questions/queries/geneQueries.xml
+++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml
@@ -6444,7 +6444,7 @@ select distinct ta.gene_source_id
SELECT stable_id, substr(headline, 1, 80) as headline, count(*) as comment_count,
min(comment_date) as min_comment_date,
max(comment_date) as max_comment_date
- FROM @COMMENT_SCHEMA@MappedComment@COMMENT_DBLINK@
+ FROM @REMOTE_COMMENT_SCHEMA@MappedComment
WHERE ('@PROJECT_ID@' = 'UniDB' OR project_name = '@PROJECT_ID@')
and is_visible = 1
GROUP BY stable_id, headline
diff --git a/Model/lib/wdk/model/questions/queries/metricsQueries.xml b/Model/lib/wdk/model/questions/queries/metricsQueries.xml
index 75d36d636..310ad8261 100644
--- a/Model/lib/wdk/model/questions/queries/metricsQueries.xml
+++ b/Model/lib/wdk/model/questions/queries/metricsQueries.xml
@@ -32,7 +32,7 @@
to_char(start_date,'YYYY-MM-DD') as start_date, to_char(end_date,'YYYY-MM-DD') as end_date
FROM (
SELECT project_id as project,unique_visitors,visits,page_data_requests,avg_visit_duration,bandwidth_gb,start_date,end_date
- FROM METRICS.AWSTATS@USER_DBLINK@
+ FROM @REMOTE_METRICS_SCHEMA@.AWSTATS
WHERE project_id in ( $$projectIdSelect$$ )
AND start_date >= $$date.min$$
AND end_date <= $$date.max$$ +1
@@ -71,7 +71,7 @@
to_char(start_date,'YYYY-MM-DD') as start_date, to_char(end_date,'YYYY-MM-DD') as end_date
FROM (
SELECT project_id as project, unique_logins, newly_registered, newly_registered_notLogin, total_registered, start_date, end_date
- FROM METRICS.LOGINSTATS@USER_DBLINK@
+ FROM @REMOTE_METRICS_SCHEMA@.LOGINSTATS
WHERE project_id in ( $$projectIdSelect$$ )
AND start_date >= $$date.min$$
AND end_date <= $$date.max$$ + 1
@@ -117,7 +117,7 @@
SELECT project_id as project, registered_users_count, registered_page_count, guest_users_count, guest_page_count,
registered_IP_count, guest_IP_count, guest_users_regPage_pct, guest_IP_regPage_pct, guest_users_regPage_newly_registered_pct,
start_date, end_date
- FROM METRICS.PAGEVIEWSTATS@USER_DBLINK@
+ FROM @REMOTE_METRICS_SCHEMA@.PAGEVIEWSTATS
WHERE project_id in ( $$projectIdSelect$$ )
AND start_date >= $$date.min$$
AND end_date <= $$date.max$$ + 1
@@ -152,7 +152,7 @@
url_segment, count, to_char(start_date,'YYYY-MM-DD') as start_date, to_char(end_date,'YYYY-MM-DD') as end_date
FROM (
SELECT project_id as project, url_segment, count, start_date, end_date
- FROM METRICS.RECORDPAGEVIEWSTATS@USER_DBLINK@
+ FROM @REMOTE_METRICS_SCHEMA@.RECORDPAGEVIEWSTATS
WHERE project_id in ( $$projectIdSelect$$ )
AND start_date >= $$date.min$$
AND end_date <= $$date.max$$ + 1
@@ -192,7 +192,7 @@
to_char(start_date,'YYYY-MM-DD') as start_date, to_char(end_date,'YYYY-MM-DD') as end_date
FROM (
SELECT project_id as project, dataset_type, total_complete, total_incomplete, new_complete, new_incomplete, start_date, end_date
- FROM METRICS.USERDATASETSSTATS@USER_DBLINK@
+ FROM @REMOTE_METRICS_SCHEMA@.USERDATASETSSTATS
WHERE project_id in ( $$projectIdNoPortalSelect$$ )
AND start_date >= $$date.min$$
AND end_date <= $$date.max$$ + 1
@@ -233,7 +233,7 @@
to_char(start_date,'YYYY-MM-DD') as start_date, to_char(end_date,'YYYY-MM-DD') as end_date
FROM (
SELECT ovs.project_id as project, organism, IS_REFERENCE_STRAIN as is_reference, oa.project_id as org_project, count, start_date, end_date
- FROM METRICS.ORGANISMVIEWSTATS@USER_DBLINK@ ovs
+ FROM @REMOTE_METRICS_SCHEMA@.ORGANISMVIEWSTATS ovs
LEFT OUTER JOIN apidbtuning.organismattributes oa
ON ovs.organism = oa.ORGANISM_NAME
WHERE ovs.project_id in ( $$projectIdNoAllSelect$$ )
@@ -241,7 +241,7 @@
AND end_date <= $$date.max$$ + 1
UNION
SELECT ovs.project_id as project, organism, IS_REFERENCE_STRAIN as is_reference, oa.project_id as org_project, count, start_date, end_date
- FROM METRICS.ORGANISMVIEWSTATS@USER_DBLINK@ ovs
+ FROM @REMOTE_METRICS_SCHEMA@.ORGANISMVIEWSTATS ovs
LEFT OUTER JOIN apidbtuning.organismattributes oa
ON ovs.organism = oa.ORGANISM_NAME
WHERE ovs.project_id = 'Unknown'
@@ -283,7 +283,7 @@
to_char(start_date,'YYYY-MM-DD') as start_date, to_char(end_date,'YYYY-MM-DD') as end_date
FROM (
SELECT project_id as project, number_of_organisms, steps_count, start_date, end_date
- FROM METRICS.ORGANISMSPERSTEP@USER_DBLINK@
+ FROM @REMOTE_METRICS_SCHEMA@.ORGANISMSPERSTEP
WHERE project_id in ( $$projectIdSelect$$ )
AND start_date >= $$date.min$$
AND end_date <= $$date.max$$ + 1
@@ -320,7 +320,7 @@
to_char(start_date,'YYYY-MM-DD') as start_date, to_char(end_date,'YYYY-MM-DD') as end_date
FROM (
SELECT ovs.project_id as project, ovs.organism, IS_REFERENCE_STRAIN as is_reference, steps_count, oa.project_id as org_project, start_date, end_date
- FROM METRICS.STEPSPERORGANISM@USER_DBLINK@ ovs
+ FROM @REMOTE_METRICS_SCHEMA@.STEPSPERORGANISM ovs
LEFT OUTER JOIN apidbtuning.organismattributes oa
ON ovs.organism = oa.ORGANISM_NAME
WHERE ovs.project_id in ( $$projectIdNoAllSelect$$ )
@@ -360,7 +360,7 @@
to_char(start_date,'YYYY-MM-DD') as start_date, to_char(end_date,'YYYY-MM-DD') as end_date
FROM (
SELECT project_id,RECORD_CLASS_URL_SEGMENT as record_class,table_name,count,start_date,end_date
- FROM METRICS.GENEPAGETABLESTATS@USER_DBLINK@
+ FROM @REMOTE_METRICS_SCHEMA@.GENEPAGETABLESTATS
WHERE start_date >= $$date.min$$
AND end_date <= $$date.max$$ + 1
AND project_id in ( $$projectIdNoPortalSelect$$ )
@@ -397,7 +397,7 @@
tool,count,to_char(start_date,'YYYY-MM-DD') as start_date, to_char(end_date,'YYYY-MM-DD') as end_date
FROM (
SELECT project_id as project,tool,count,start_date,end_date
- FROM METRICS.TOOLSSTATS@USER_DBLINK@
+ FROM @REMOTE_METRICS_SCHEMA@.TOOLSSTATS
WHERE project_id in ( $$projectIdSelect$$ )
AND start_date >= $$date.min$$
AND end_date <= $$date.max$$ + 1
@@ -440,7 +440,7 @@
SELECT project_id as project, steps_count, start_date, end_date,
SUBSTR(search_name, 1, INSTR(search_name, '.')-1) AS record_name,
SUBSTR(search_name, INSTR(search_name, '.')+1) AS singlesearch_name
- FROM METRICS.SEARCHESSTATS@USER_DBLINK@
+ FROM @REMOTE_METRICS_SCHEMA@.SEARCHESSTATS
WHERE project_id in ( $$projectIdSelect$$ )
AND steps_count >= $$step_count.min$$
AND steps_count <= $$step_count.max$$
diff --git a/Model/lib/wdk/model/questions/queries/universalQueries.xml b/Model/lib/wdk/model/questions/queries/universalQueries.xml
index b449c65f0..2dc877cec 100644
--- a/Model/lib/wdk/model/questions/queries/universalQueries.xml
+++ b/Model/lib/wdk/model/questions/queries/universalQueries.xml
@@ -77,7 +77,7 @@
diff --git a/Model/lib/wdk/model/records/commentTableQueries.xml b/Model/lib/wdk/model/records/commentTableQueries.xml
index e95d39a19..b8b13ed30 100644
--- a/Model/lib/wdk/model/records/commentTableQueries.xml
+++ b/Model/lib/wdk/model/records/commentTableQueries.xml
@@ -95,24 +95,24 @@
&&selectReviewed&&
u.first_name || ' ' || u.last_name || ', ' || u.organization as user_name_org
FROM
- @COMMENT_SCHEMA@MappedComment c
+ @REMOTE_COMMENT_SCHEMA@MappedComment c
INNER JOIN apidbtuning.GeneAttributes ga ON c.project_name = ga.project_id AND c.stable_id = ga.source_id
- INNER JOIN @COMMENT_SCHEMA@comment_users u ON c.user_id = u.user_id
+ INNER JOIN @REMOTE_COMMENT_SCHEMA@comment_users u ON c.user_id = u.user_id
INNER JOIN apidbtuning.annotatedgenomesummary ags ON ga.taxon_id = ags.taxon_id
LEFT JOIN (
SELECT comment_id, count(*) as filecount
- FROM @COMMENT_SCHEMA@CommentFile
+ FROM @REMOTE_COMMENT_SCHEMA@CommentFile
GROUP BY comment_id
) files ON c.comment_id = files.comment_id
LEFT JOIN (
SELECT comment_id, string_agg(source_id,',') as pmids
- FROM @COMMENT_SCHEMA@CommentReference
+ FROM @REMOTE_COMMENT_SCHEMA@CommentReference
WHERE database_name='pubmed'
GROUP BY comment_id
) refs ON c.comment_id = refs.comment_id
LEFT JOIN (
SELECT comment_id, COUNT(DISTINCT stable_id) AS geneCount
- FROM @COMMENT_SCHEMA@MappedComment
+ FROM @REMOTE_COMMENT_SCHEMA@MappedComment
WHERE stable_id IN (SELECT source_id FROM apidbTuning.GeneAttributes)
GROUP BY comment_id
) gene_counts ON c.comment_id = gene_counts.comment_id
@@ -194,28 +194,28 @@
u.first_name || ' ' || u.last_name || ', ' || u.organization as user_name_org,
authortable.authors
FROM
- @COMMENT_SCHEMA@MappedComment c
- INNER JOIN @COMMENT_SCHEMA@comment_users u c.user_id = u.user_id
+ @REMOTE_COMMENT_SCHEMA@MappedComment c
+ INNER JOIN @REMOTE_COMMENT_SCHEMA@comment_users u c.user_id = u.user_id
LEFT JOIN (
SELECT comment_id, count(*) as filecount
- FROM @COMMENT_SCHEMA@CommentFile
+ FROM @REMOTE_COMMENT_SCHEMA@CommentFile
GROUP BY comment_id
) files ON c.comment_id = files.comment_id
LEFT JOIN (
SELECT comment_id, string_agg(source_id,',') as pmids
- FROM @COMMENT_SCHEMA@CommentReference
+ FROM @REMOTE_COMMENT_SCHEMA@CommentReference
WHERE database_name='pubmed'
GROUP BY comment_id
) refs ON c.comment_id = refs.comment_id
LEFT JOIN (
SELECT comment_id, string_agg(source_id,',') as authors
- FROM @COMMENT_SCHEMA@CommentReference
+ FROM @REMOTE_COMMENT_SCHEMA@CommentReference
WHERE database_name='author'
GROUP BY comment_id
) authortable ON c.comment_id = authortable.comment_id
LEFT JOIN (
SELECT comment_id, count(stable_id) as geneCount
- FROM @COMMENT_SCHEMA@MappedComment
+ FROM @REMOTE_COMMENT_SCHEMA@MappedComment
GROUP BY comment_id
) gene_counts c.comment_id = gene_counts.comment_id
WHERE ('@PROJECT_ID@' = 'UniDB' OR c.project_name = '@PROJECT_ID@')
@@ -252,22 +252,22 @@
SELECT c.comment_target_id, c.project_name as project_id, c.comment_id, c.stable_id, c.comment_date, c.headline,
files.filecount, refs.pmids, gene_counts.geneCount,
u.first_name || ' ' || u.last_name || ', ' || u.organization as user_name_org
- FROM @COMMENT_SCHEMA@MappedComment c
- INNER JOIN @COMMENT_SCHEMA@comment_users u ON c.user_id = u.user_id
+ FROM @REMOTE_COMMENT_SCHEMA@MappedComment c
+ INNER JOIN @REMOTE_COMMENT_SCHEMA@comment_users u ON c.user_id = u.user_id
LEFT JOIN (
SELECT comment_id, count(*) as filecount
- FROM @COMMENT_SCHEMA@CommentFile
+ FROM @REMOTE_COMMENT_SCHEMA@CommentFile
GROUP BY comment_id
) files ON c.comment_id = files.comment_id
LEFT JOIN (
SELECT comment_id, string_agg(source_id,',') as pmids
- FROM @COMMENT_SCHEMA@CommentReference
+ FROM @REMOTE_COMMENT_SCHEMA@CommentReference
WHERE database_name='pubmed'
GROUP BY comment_id
) refs ON c.comment_id = refs.comment_id
LEFT JOIN (
SELECT comment_id, count(stable_id) as geneCount
- FROM @COMMENT_SCHEMA@mappedComment
+ FROM @REMOTE_COMMENT_SCHEMA@mappedComment
GROUP BY comment_id
) gene_counts ON c.comment_id = gene_counts.comment_id
WHERE ('@PROJECT_ID@' = 'UniDB' OR c.project_name = '@PROJECT_ID@')
@@ -297,9 +297,9 @@
= 1
- -- THEN 'View '
- -- || comm.num_user_comments || ' user comment'
- -- || CASE WHEN comm.num_user_comments = 1
- -- THEN ''
- -- ELSE 's'
- -- END
- -- ELSE 'Add the first User Comment'
- -- END AS user_comment_link_text,
- -- coalesce(comm.num_user_comments, 0) AS num_user_comments,
- 'TODO' as user_comment_link_text,
- 0 as num_user_comments,
+ CASE WHEN comm.num_user_comments >= 1
+ THEN 'View '
+ || comm.num_user_comments || ' user comment'
+ || CASE WHEN comm.num_user_comments = 1
+ THEN ''
+ ELSE 's'
+ END
+ ELSE 'Add the first User Comment'
+ END AS user_comment_link_text,
+ coalesce(comm.num_user_comments, 0) AS num_user_comments,
CASE WHEN (ga.project_id NOT IN ('HostDB')
AND aid.apolloid IS NOT NULL
AND ga.organism NOT IN ('Candida dubliniensis CD36')
@@ -401,21 +399,12 @@ GROUP BY source_id
apidbtuning.geneattributes ga
INNER JOIN apidbtuning.annotatedgenomesummary gsum ON gsum.taxon_id = ga.taxon_id
LEFT JOIN apidbtuning.ApolloID aid ON ga.organism = aid.organism
- -- LEFT JOIN (
- -- SELECT stable_id AS gene_id, project_name, count(distinct comment_id) AS num_user_comments
- -- FROM (
- -- SELECT *
- -- FROM dblink('dbname=apicommS options=-csearch_path=',
- -- 'select * from userlogins5.mappedcomment')
- -- AS t1(COMMENT_ID NUMERIC(10), USER_ID NUMERIC(12), EMAIL VARCHAR(255), COMMENT_DATE TIMESTAMP, COMMENT_TARGET_ID VARCHAR(20), STABLE_ID VARCHAR(200)
- -- , CONCEPTUAL NUMERIC(1), PROJECT_NAME VARCHAR(200), PROJECT_VERSION VARCHAR(100), HEADLINE VARCHAR(2000), REVIEW_STATUS_ID VARCHAR(20)
- -- , ACCEPTED_VERSION VARCHAR(100), LOCATION_STRING VARCHAR(1000), ORGANISM VARCHAR(100), IS_VISIBLE NUMERIC(1)
- -- )
- -- ) t
- -- FROM @COMMENT_SCHEMA@MappedComment@COMMENT_DBLINK@
- -- WHERE is_visible = 1
- -- GROUP BY stable_id, project_name
- -- ) comm ON ga.source_id = comm.gene_id AND ga.project_id = comm.project_name
+ LEFT JOIN (
+ SELECT stable_id AS gene_id, project_name, count(distinct comment_id) AS num_user_comments
+ FROM @REMOTE_COMMENT_SCHEMA@MappedComment
+ WHERE is_visible = 1
+ GROUP BY stable_id, project_name
+ ) comm ON ga.source_id = comm.gene_id AND ga.project_id = comm.project_name
]]>
diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml
index bcdf99863..e8d3477dd 100644
--- a/Model/lib/wdk/model/records/geneTableQueries.xml
+++ b/Model/lib/wdk/model/records/geneTableQueries.xml
@@ -2526,7 +2526,7 @@ from (
WITH comments AS (
SELECT DISTINCT
stable_id
- FROM @COMMENT_SCHEMA@MappedComment@COMMENT_DBLINK@
+ FROM @REMOTE_COMMENT_SCHEMA@MappedComment
WHERE comment_target_id = 'gene'
AND review_status_id != 'rejected'
AND is_visible = 1
diff --git a/Model/lib/wdk/model/records/userfileRecords.xml b/Model/lib/wdk/model/records/userfileRecords.xml
index 62f67cab0..4369532e8 100644
--- a/Model/lib/wdk/model/records/userfileRecords.xml
+++ b/Model/lib/wdk/model/records/userfileRecords.xml
@@ -60,13 +60,13 @@
' ||
rtrim(max(case when key = 'organization' then value end)) as provider
- FROM useraccounts.account_properties@ACCT_DBLINK@
+ FROM @REMOTE_USERACCOUNTS_SCHEMA@.account_properties
GROUP BY user_id
) ap ON a.user_id = ap.user_id
)
@@ -74,7 +74,7 @@
f.filename, f.title, f.notes,
to_char(f.uploadtime,'YYYY-MM-DD HH24:MI:SS') AS uploadtime,
f.filesize, f.format, u.provider
- FROM uploads.UserFile@USER_DBLINK@ f, users u
+ FROM @REMOTE_UPLOADS_SCHEMA@.UserFile f, users u
WHERE f.owneruserid = u.signature (+)
AND projectname = '@PROJECT_ID@'
]]>