-
Notifications
You must be signed in to change notification settings - Fork 8
Expand file tree
/
Copy pathexport_csv.sh
More file actions
executable file
·45 lines (38 loc) · 2.36 KB
/
export_csv.sh
File metadata and controls
executable file
·45 lines (38 loc) · 2.36 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
#!/bin/bash
CURDATE=$(date +%Y-%m-%d_%H)
cd /var/www/mediawiki/w/ || exit 1
echo "[$CURDATE] Exporting studies.."
php extensions/SemanticReports/maintenance/GenerateReport.php \
-q "[[Category:Studies]] |?Study design |?PMID |?DOI |?URI |?Authors list |?Title |?Journal |?Year |?Abstract |?Keyword list=Keywords |?State |?Reviewer" \
-m 'Study page name' \
-v ',' \
-s ',' \
-f "csv" \
-o "/var/www/mediawiki/w/images/csv_reports/studies.$CURDATE.csv"
echo "Done"
echo "Exporting experiments.."
php extensions/SemanticReports/maintenance/GenerateReport.php \
-q "[[Category:Experiments]] |?Original page name=Experiment page name |?Related study=Study |?Location of subjects |?Host species |?Body site |?UBERON ID |?Condition |?EFO ID |?Group 0 name |?Group 1 name |?Group 1 definition |?Group 0 sample size |?Group 1 sample size |?Antibiotics exclusion |?Sequencing type |?16S variable region |?Sequencing platform |?Data transformation |?Statistical test |?Significance threshold |?MHT correction |?LDA Score above |?Matched on |?Confounders controlled for |?Pielou |?Shannon |?Chao1 |?Simpson |?Inverse Simpson |?Richness |?State |?Reviewer" \
-m '-' \
-v ',' \
-s ',' \
-f "csv" \
-o "/var/www/mediawiki/w/images/csv_reports/experiments.$CURDATE.csv"
echo "Done"
echo "Exporting signatures.."
php extensions/SemanticReports/maintenance/GenerateReport.php \
-q "[[Category:Signatures]] |?Original page name=Signature page name |?Related experiment=Experiment |?Related study=Study |?Source data=Source |?Curated date |?Curator |?Revision editor |?Description |?Abundance in Group 1 |?NCBI_export=MetaPhlAn taxon names |?NCBI_export_ids_sc=NCBI Taxonomy IDs |?State |?Reviewer" \
-m '-' \
-v ',' \
-s ',' \
-f "csv" \
-o "/var/www/mediawiki/w/images/csv_reports/signatures.$CURDATE.csv"
echo "Done"
echo "Updating symlinks.."
ln -sf /var/www/mediawiki/w/images/csv_reports/studies.$CURDATE.csv /var/www/mediawiki/w/images/csv_reports/studies.csv
ln -sf /var/www/mediawiki/w/images/csv_reports/experiments.$CURDATE.csv /var/www/mediawiki/w/images/csv_reports/experiments.csv
ln -sf /var/www/mediawiki/w/images/csv_reports/signatures.$CURDATE.csv /var/www/mediawiki/w/images/csv_reports/signatures.csv
echo "Done"
echo "Cleaning up files older than 24 hours.."
find /var/www/mediawiki/w/images/csv_reports/ -maxdepth 1 -name '*.csv' -type f -mtime +0 -delete
echo "Done"