[ARVADOS] updated: 156f7186528045a58628c58f3b4b48fcb3825cd5

Git user git at public.curoverse.com
Wed Jun 14 11:27:59 EDT 2017


Summary of changes:
 .licenseignore                              |  46 +++++++
 build/check-copyright-notices               | 201 ++++++++++++++++++++++++++++
 build/{libcloud-pin => libcloud-pin.sh}     |   0
 build/run-build-packages-python-and-ruby.sh |   2 +-
 build/run-build-packages.sh                 |   2 +-
 build/run-tests.sh                          |   2 +-
 doc/start/index.html.textile.liquid.bkup    |  50 -------
 7 files changed, 250 insertions(+), 53 deletions(-)
 create mode 100644 .licenseignore
 create mode 100755 build/check-copyright-notices
 rename build/{libcloud-pin => libcloud-pin.sh} (100%)
 delete mode 100644 doc/start/index.html.textile.liquid.bkup

       via  156f7186528045a58628c58f3b4b48fcb3825cd5 (commit)
       via  0bd8810e6ea29ab242472b9dae11c621cf50953c (commit)
      from  3c44c82acb3dbf50acd75f0c979d8a18ee11dbd0 (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit 156f7186528045a58628c58f3b4b48fcb3825cd5
Merge: 3c44c82 0bd8810
Author: Tom Clegg <tom at curoverse.com>
Date:   Wed Jun 14 11:26:27 2017 -0400

    Merge branch '2411-check-copyright'
    
    refs #2411
    
    Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curoverse.com>


commit 0bd8810e6ea29ab242472b9dae11c621cf50953c
Author: Tom Clegg <tom at curoverse.com>
Date:   Thu Jun 1 14:50:17 2017 -0400

    2411: Add build/check-copyright-notices.
    
    Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curoverse.com>

diff --git a/.licenseignore b/.licenseignore
new file mode 100644
index 0000000..ee5e5fd
--- /dev/null
+++ b/.licenseignore
@@ -0,0 +1,46 @@
+*agpl-3.0.txt
+apps/workbench/app/assets/javascripts/list.js
+build/package-test-dockerfiles/centos7/localrepo.repo
+build/package-test-dockerfiles/ubuntu1604/etc-apt-preferences.d-arvados
+*by-sa-3.0.txt
+*COPYING
+doc/fonts/*
+*/docker_image
+docker/jobs/apt.arvados.org.list
+*.gif
+.gitignore
+*/.gitignore
+*/.gitkeep
+*/.gitstub
+*.gz
+*.gz.report
+*.ico
+*.jpg
+*.json
+*LICENSE*.txt
+*.lock
+*.log
+*.map
+*.png
+*/proc_stat
+*/README
+*/robots.txt
+*/runit-docker/*
+*/script/rails
+sdk/cwl/tests/input/blorp.txt
+sdk/cwl/tests/tool/blub.txt
+sdk/go/manifest/testdata/*_manifest
+sdk/java/.classpath
+sdk/java/pom.xml
+sdk/java/.project
+sdk/java/.settings/org.eclipse.jdt.core.prefs
+sdk/java/src/main/resources/log4j.properties
+sdk/pam/examples/shellinabox
+sdk/pam/pam-configs/arvados
+sdk/python/tests/data/*
+services/api/config/unbound.template
+services/arv-web/sample-cgi-app/public/.htaccess
+services/arv-web/sample-cgi-app/public/index.cgi
+services/keepproxy/pkg-extras/etc/default/keepproxy
+*.tar
+tools/crunchstat-summary/tests/crunchstat_error_messages.txt
diff --git a/build/check-copyright-notices b/build/check-copyright-notices
new file mode 100755
index 0000000..aef14fa
--- /dev/null
+++ b/build/check-copyright-notices
@@ -0,0 +1,201 @@
+#!/bin/bash
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+set -e
+
+fix=false
+while [[ "${@}" != "" ]]
+do
+    arg=${1}
+    shift
+    case ${arg} in
+        --help)
+            cat <<EOF
+Usage: $0 [--fix] [-- git-ls-args...]
+
+Options:
+
+--fix   Insert missing copyright notices where possible.
+
+Git arguments:
+
+Arguments after "--" are passed to \`git ls-files\`; this can be used to
+restrict the set of files to check.
+
+EOF
+            exit 2
+            ;;
+        --fix)
+            fix=true
+            ;;
+        --)
+            break
+            ;;
+        *)
+            echo >&2 "Unrecognized argument '${arg}'. Try $0 --help"
+            exit 2
+            ;;
+    esac
+done
+
+fixer() {
+    want="${want}" perl -pi~ -e 'if ($. == 1) { s{^(\#\!.*\n)?}{${1}$ENV{want}\n\n} }' "${1}"
+}
+
+IFS=$'\n' read -a ignores -r -d $'\000' <.licenseignore || true
+result=0
+git ls-files -z ${@} | \
+    while read -rd $'\000' fnm
+    do
+        grepAfter=2
+        grepBefore=0
+        cs=
+        cc=
+        ce=
+        fixer=
+        if [[ ! -f ${fnm} ]] || [[ -L ${fnm} ]] || [[ ! -s ${fnm} ]]
+        then
+            continue
+        fi
+
+        ignore=
+        for pattern in "${ignores[@]}"
+        do
+            if [[ ${fnm} == ${pattern} ]]
+            then
+                ignore=1
+            fi
+        done
+        if [[ ${ignore} = 1 ]]; then continue; fi
+
+        case ${fnm} in
+            Makefile | */Makefile \
+                | *.dockerfile | */Dockerfile.* | */Dockerfile | *.dockerignore \
+                | */MANIFEST.in | */fuse.conf | */gitolite.rc \
+                | *.pl | *.pm | *.PL \
+                | *.rb | *.rb.example | *.rake | *.ru \
+                | *.gemspec | */Gemfile | */Rakefile \
+                | services/login-sync/bin/* \
+                | sdk/cli/bin/* \
+                | *.py \
+                | sdk/python/bin/arv-* \
+                | sdk/cwl/bin/* \
+                | services/nodemanager/bin/* \
+                | services/fuse/bin/* \
+                | tools/crunchstat-summary/bin/* \
+                | crunch_scripts/* \
+                | *.yaml | *.yml | *.yml.example | *.cwl \
+                | *.sh | *.service \
+                | */run | */run-service | */restart-dns-server \
+                | */nodemanager/doc/*.cfg \
+                | */nginx.conf \
+                | build/build.list)
+                fixer=fixer
+                cc="#"
+                ;;
+            *.md)
+                fixer=fixer
+                cc="[//]: #"
+                ;;
+            *.rst)
+                fixer=fixer
+                cc=".."
+                ;;
+            *.erb)
+                fixer=fixer
+                cs="<%#"
+                cc=""
+                ce=" %>"
+                ;;
+            *.liquid)
+                fixer=fixer
+                cs=$'{% comment %}\n'
+                cc=
+                ce=$'\n%{% endcomment %}'
+                grepAfter=3
+                grepBefore=1
+                ;;
+            *.textile)
+                fixer=fixer
+                cs="###."
+                cc="...."
+                ce=
+                ;;
+            *.css)
+                fixer=fixer
+                cs="/*"
+                cc=""
+                ce=" */"
+                ;;
+            *.go | *.scss | *.java | *.js | *.coffee)
+                fixer=fixer
+                cc="//"
+                ;;
+            *.sql)
+                fixer=fixer
+                cc="--"
+                ;;
+            *.html | *.svg)
+                fixer=fixer
+                cs="<!-- "
+                cc=
+                ce=" -->"
+                ;;
+            *)
+                cc="#"
+                hashbang=$(head -n1 ${fnm})
+                if [[ ${hashbang} = "#!/bin/sh" ]] ||  [[ ${hashbang} = "#!/bin/bash" ]]
+                then
+                    fixer=fixer
+                fi
+                ;;
+        esac
+        wantGPL="${cs:-${cc}} Copyright (C) The Arvados Authors. All rights reserved.
+${cc}
+${cc}${cc:+ }SPDX-License-Identifier: AGPL-3.0${ce}"
+        wantApache="${cs:-${cc}} Copyright (C) The Arvados Authors. All rights reserved.
+${cc}
+${cc}${cc:+ }SPDX-License-Identifier: Apache-2.0${ce}"
+        wantBYSA="${cs:-${cc}} Copyright (C) The Arvados Authors. All rights reserved.
+${cc}
+${cc}${cc:+ }SPDX-License-Identifier: CC-BY-SA-3.0${ce}"
+        found=$(head "$fnm" | egrep -A${grepAfter} -B${grepBefore} 'Copyright.*Arvados' || true)
+        case ${fnm} in
+            Makefile | build/* | lib/* | tools/* | apps/* | services/*)
+                want=${wantGPL}
+                ;;
+            crunch_scripts/* | backports/* | docker/* | sdk/*)
+                want=${wantApache}
+                ;;
+            README.md | doc/*)
+                want=${wantBYSA}
+                ;;
+            *)
+                want=
+                ;;
+        esac
+        case "$found" in
+            "$wantGPL")
+                ;;
+            "$wantApache")
+                ;;
+            "$wantBYSA")
+                ;;
+            "")
+                if [[ -z ${found} ]] && [[ -n ${want} ]] && [[ $fix = true ]] && [[ $fixer != "" ]]
+                then
+                    ${fixer} ${fnm}
+                else
+                    echo "missing copyright notice: $fnm"
+                    result=1
+                fi
+                ;;
+            *)
+                echo "nonstandard copyright notice: $fnm '${found}'"
+                result=1
+                ;;
+        esac
+    done
+exit $result
diff --git a/build/libcloud-pin b/build/libcloud-pin.sh
similarity index 100%
rename from build/libcloud-pin
rename to build/libcloud-pin.sh
diff --git a/build/run-build-packages-python-and-ruby.sh b/build/run-build-packages-python-and-ruby.sh
index 13aa687..b7c642a 100755
--- a/build/run-build-packages-python-and-ruby.sh
+++ b/build/run-build-packages-python-and-ruby.sh
@@ -3,7 +3,7 @@
 COLUMNS=80
 
 . `dirname "$(readlink -f "$0")"`/run-library.sh
-#. `dirname "$(readlink -f "$0")"`/libcloud-pin
+#. `dirname "$(readlink -f "$0")"`/libcloud-pin.sh
 
 read -rd "\000" helpmessage <<EOF
 $(basename $0): Build Arvados Python packages and Ruby gems
diff --git a/build/run-build-packages.sh b/build/run-build-packages.sh
index 777cd3c..7763ca5 100755
--- a/build/run-build-packages.sh
+++ b/build/run-build-packages.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 . `dirname "$(readlink -f "$0")"`/run-library.sh
-. `dirname "$(readlink -f "$0")"`/libcloud-pin
+. `dirname "$(readlink -f "$0")"`/libcloud-pin.sh
 
 read -rd "\000" helpmessage <<EOF
 $(basename $0): Build Arvados packages
diff --git a/build/run-tests.sh b/build/run-tests.sh
index 352d05b..e637dac 100755
--- a/build/run-tests.sh
+++ b/build/run-tests.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname "$(readlink -f "$0")"`/libcloud-pin
+. `dirname "$(readlink -f "$0")"`/libcloud-pin.sh
 
 COLUMNS=80
 . `dirname "$(readlink -f "$0")"`/run-library.sh
diff --git a/doc/start/index.html.textile.liquid.bkup b/doc/start/index.html.textile.liquid.bkup
deleted file mode 100644
index 339a84a..0000000
--- a/doc/start/index.html.textile.liquid.bkup
+++ /dev/null
@@ -1,50 +0,0 @@
----
-layout: default
-navsection: start 
-title: Welcome to Arvados!
-...
-
-This guide provides an introduction to using Arvados to solve big data bioinformatics problems.
-
-
-h2. Typographic conventions
-
-This manual uses the following typographic conventions:
-
-<notextile>
-<ul>
-<li>Code blocks which are set aside from the text indicate user input to the system.  Commands that should be entered into a Unix shell are indicated by the directory where you should  enter the command ('~' indicates your home directory) followed by '$', followed by the highlighted <span class="userinput">command to enter</span> (do not enter the '$'), and possibly followed by example command output in black.  For example, the following block indicates that you should type <code>ls foo.*</code> while in your home directory and the expected output will be "foo.input" and "foo.output".
-</notextile>
-
-<div class="custom-container key-features">
-<a class="prev" href="#">‹</a>
-
-<div class="carousel">
-    <ul>
-        <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/dashboard2.png" style="width:909px; height:503px;" title="[START] After logging in, you see Workbench's dashboard."></li>
-        <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/running2.png" style="width:909px; height:503px;" title="Pipelines describe a set of computational tasks (jobs)."></li>
-        <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/log.png" style="width:909px; height:503px;" title="The output of all jobs is logged and stored automatically."></li>
-        <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/graph.png" style="width:909px; height:503px;" title="Pipelines can be also viewed in auto-generated graph form."></li>
-        <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/rerun.png" style="width:909px; height:503px;" title="Pipelines can easily be re-run..."></li>
-        <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/chooseinputs.png" style="width:909px; height:503px;" title="...by changing parameters or picking new datasets..."></li>
-        <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/webupload.png" style="width:909px; height:503px;" title="...which can be uploaded right in Workbench."></li>
-        <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/collectionpage.png" style="width:909px; height:503px;" title="Collections allow sharing datasets and job outputs easily."></li>
-        <li><img class="hascaption" src="{{ site.baseurl }}/images/keyfeatures/provenance.png" style="width:909px; height:503px;" title="Data provenance is tracked automatically. [END]"></li>
-    </ul>
-</div>
-<a class="next" href="#">›</a>
-<div class="clear"></div>
-</div>
-
-<script type="text/javascript">
-(function() {
-    $(".key-features .carousel").jCarouselLite({
-        btnNext: ".key-features .next",
-        btnPrev: ".key-features .prev",
-        visible: 1,
-    });
-});
-('.hascaption').each(function() {
-    $(this).after( "<div style='background: rgba(0,0,0,0.6); color: white; padding: 1.4em;'>" + $(this).attr('title') + "</div>" ); 
-});
-</script>

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