[med-svn] [Git][med-team/pilercr][master] 3 commits: Add script for fetching data

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / pilercr


Commits:
498271da by Nilesh Patra at 2021-06-18T01:35:48+05:30
Add script for fetching data

- - - - -
5bc3fafa by Nilesh Patra at 2021-06-18T01:40:32+05:30
Install get-test-data script

- - - - -
08d60119 by Nilesh Patra at 2021-06-18T01:40:32+05:30
Interim changelog entry

- - - - -


4 changed files:

- debian/changelog
- debian/docs
- debian/tests/data/example.fasta
- + debian/tests/get-test-data


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,16 @@
 pilercr (1.06+dfsg-5) UNRELEASED; urgency=medium
 
+  [ Shruti Sridhar ]
   * Team upload.
   * Add test data
   * Add autopkgtests
-  * Install docs
+  * Install test docs
 
- -- Shruti Sridhar <shruti.sridhar99 at gmail.com>  Tue, 15 Jun 2021 19:25:25 +0530
+  [ Nilesh Patra ]
+  * d/tests/get-test-data: Add script for fetching data
+  * d/docs: Install get-test-data script
+
+ -- Shruti Sridhar <shruti.sridhar99 at gmail.com>  Fri, 18 Jun 2021 01:29:30 +0530
 
 pilercr (1.06+dfsg-4) unstable; urgency=medium
 


=====================================
debian/docs
=====================================
@@ -1,2 +1,3 @@
 debian/README*
-debian/tests/run-unit-test
\ No newline at end of file
+debian/tests/run-unit-test
+debian/tests/get-test-data


=====================================
debian/tests/data/example.fasta
=====================================
@@ -1,4 +1,4 @@
->CP014688.1:1-39760 Acetobacter persici strain TMW2.1084 plasmid pAC1084_1, complete sequence
+>CP014688.1 Acetobacter persici strain TMW2.1084 plasmid pAC1084_1, complete sequence
 ACGAGGTCGTTTCTGTCGACCCGCTGGCTATATTCAGGCTGGTAGATGTCGGCGTGGTCTGATTATTACC
 ATCACCGCTTGCTGAAGACTGATCCCCGCTGCTGATGATCGGGAGGGCTGACAAATAGTCCCCCTTGTCA
 GTCCGGTCGTCTTCGACACTCCCTACGCTCCCGCTTAGATATACGGCTCCGGTCCCCGTCAGCTTTACGC
@@ -172,4 +172,4 @@ TCATAATCGTGCGGGGGATTGAATCTGGCGTACGCTCAATCAGATCCATCAAACCTTCCCGATCAAATCT
 CTGCTCACACTCATCAATCAGTGGCCTAAGAAGACCGAGCATGTCATCACAAGCACGCTGCAACTCGTTC
 ACAGATTTGCCCCAGTCGCGGAGGACTGCAGCGCGGTCCCAATTGTAAGGTTCCGGCCTTTCGCTCTGCA
 GAATGAGGCGGATATTGCTCTCACCATGCCGGGTTGCGATTTCATACATCTTACTCCCGGCCTCGTAGCG
-CAGGGCACATGGCGGCATAGACTTCAGCAGGGCGCAAGATTTCCAGAAGTCTTTCTTTTCAGCAAACCTA
\ No newline at end of file
+CAGGGCACATGGCGGCATAGACTTCAGCAGGGCGCAAGATTTCCAGAAGTCTTTCTTTTCAGCAAACCTA


=====================================
debian/tests/get-test-data
=====================================
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+# Needs ncbi-entrez-direct
+efetch -db nuccore -id CP014688.1 -format fasta | head -n175 > example.fasta
+mkdir -p data
+
+if [ -f data/example.fasta ]
+then
+diff -u example.fasta data/example.fasta
+
+if [ `echo $?` -ne 0 ]
+then
+	echo "The data has changed, injecting new data, please check manually before upload"
+else
+	echo "The data is same, no changes needed"
+fi
+fi
+
+mv example.fasta data/example.fasta
+
+echo "Done"



View it on GitLab: https://salsa.debian.org/med-team/pilercr/-/compare/8f9b1f2d465443efeb409a24c2ac746eaf840e34...08d60119bae765ddfdbaa7c61cd587b72e28a06b

-- 
View it on GitLab: https://salsa.debian.org/med-team/pilercr/-/compare/8f9b1f2d465443efeb409a24c2ac746eaf840e34...08d60119bae765ddfdbaa7c61cd587b72e28a06b
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