[med-svn] [Git][med-team/ncbi-entrez-direct][master] 4 commits: Start work on ncbi-entrez-direct 13.7.20200615+dfsg-2.

[Aaron M. Ucko]

Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct


Commits:
94ca7b92 by Aaron M. Ucko at 2020-06-28T21:00:44-04:00
Start work on ncbi-entrez-direct 13.7.20200615+dfsg-2.

- - - - -
146d078d by Aaron M. Ucko at 2020-06-28T21:08:52-04:00
Install ftp-cp, ftp-ls, nquire, and transmute as simple wrappers.

debian/rules: Install ftp-cp, ftp-ls, nquire, and transmute as simple
wrappers for edirect (with no .pl suffix) now that they're no longer
independent Perl scripts (as of 12.3.20191024[+ds]), fixing a
regression caught by autopkgtest.

- - - - -
a124a1f4 by Aaron M. Ucko at 2020-06-28T21:11:04-04:00
d/tests/run-unit-test: Correct invocation of filter-stop-words

filter-stop-words ignores its arguments and reads from standard input.

- - - - -
36914b99 by Aaron M. Ucko at 2020-06-28T21:11:51-04:00
Finalize ncbi-entrez-direct 13.7.20200615+dfsg-2 for unstable.

- - - - -


3 changed files:

- debian/changelog
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+ncbi-entrez-direct (13.7.20200615+dfsg-2) unstable; urgency=medium
+
+  * debian/rules: Install ftp-cp, ftp-ls, nquire, and transmute as simple
+    wrappers for edirect (with no .pl suffix) now that they're no longer
+    independent Perl scripts (as of 12.3.20191024[+ds]), fixing a
+    regression caught by autopkgtest.
+  * debian/tests/run-unit-test: Correct invocation of filter-stop-words
+    (which ignores its arguments and reads from standard input).
+
+ -- Aaron M. Ucko <ucko at debian.org>  Sun, 28 Jun 2020 21:11:51 -0400
+
 ncbi-entrez-direct (13.7.20200615+dfsg-1) unstable; urgency=medium
 
   * New upstream release.


=====================================
debian/rules
=====================================
@@ -15,7 +15,8 @@ LIB_DIR = /usr/lib/$(PACKAGE)
 MODES = address blast citmatch contact filter link notify post proxy search \
         spell
 STD_WRAPPERS = $(MODES:%=bin/e%)
-WRAPPERS = $(STD_WRAPPERS) bin/esummary
+OTHER_WRAPPERS = esummary ftp-cp ftp-ls nquire transmute
+WRAPPERS = $(STD_WRAPPERS) $(OTHER_WRAPPERS:%=bin/%)
 AS_IS_SCRIPTS = amino-acid-composition archive-pubmed between-two-genes \
                 enquire entrez-phrase-search esample exclude-uid-lists \
                 expand-current fetch-extras fetch-pubmed filter-stop-words \
@@ -26,8 +27,7 @@ BASH_SCRIPTS = index-extras index-themes
 BIN_BASH_SCRIPTS = $(BASH_SCRIPTS:%=bin/%)
 DL_SCRIPTS = download-ncbi-data download-pubmed download-sequence
 BIN_DL_SCRIPTS = $(DL_SCRIPTS:%=bin/%)
-PERL_SCRIPTS = edirutil ftp-cp ftp-ls gbf2xml nquire run-ncbi-converter \
-               transmute
+PERL_SCRIPTS = edirutil gbf2xml run-ncbi-converter
 BIN_PERL_SCRIPTS = $(PERL_SCRIPTS:%=bin/%)
 # Only bt-link and xplore need this treatment at present,
 # but list all bt-* scripts to be safe.
@@ -82,6 +82,26 @@ bin/esummary: bin/edirect
 	echo 'exec /usr/bin/edirect -fetch -format docsum "$$@"' >> $@
 	chmod +x $@
 
+bin/ftp-cp: bin/edirect
+	echo '#!/bin/sh' > $@
+	echo 'exec /usr/bin/edirect -ftpcp "$$@"' >> $@
+	chmod +x $@
+
+bin/ftp-ls: bin/edirect
+	echo '#!/bin/sh' > $@
+	echo 'exec /usr/bin/edirect -ftpls "$$@"' >> $@
+	chmod +x $@
+
+bin/nquire: bin/edirect
+	echo '#!/bin/sh' > $@
+	echo 'exec /usr/bin/edirect -nquir "$$@"' >> $@
+	chmod +x $@
+
+bin/transmute: bin/edirect
+	echo '#!/bin/sh' > $@
+	echo 'exec /usr/bin/edirect -tmute "$$@"' >> $@
+	chmod +x $@
+
 $(BIN_BASH_SCRIPTS): bin/%: %
 	mkdir -p bin
 	sed -e '$(FIX_BASH_SHEBANG)' $< > $@


=====================================
debian/tests/run-unit-test
=====================================
@@ -38,7 +38,7 @@ echo -e "\e[92m\e[1mPassed\e[0m"
 echo
 
 echo -e "\e[93m\e[1mTest 4: filter-stop-words\e[0m"
-filter-stop-words stopwords
+filter-stop-words < stopwords
 echo -e "\e[92m\e[1mPassed\e[0m"
 echo 
 echo -e "\e[93m\e[1mTest 5: gbf2xml\e[0m"



View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/14173f9c25d4b41220fb0566b89266390037131c...36914b997fe7b6f71dbe208a0f2e29e2ca47f056

-- 
View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/14173f9c25d4b41220fb0566b89266390037131c...36914b997fe7b6f71dbe208a0f2e29e2ca47f056
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