Merge pull request #12 from IQSS/master

Beta build, 6/5, version diffs

Vagrantfile

@@ -18,10 +18,11 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
 
   config.vm.provision "shell", path: "scripts/setup/asadmin-setup.sh"
   config.vm.provision "shell", path: "scripts/vagrant/deploy.sh"
+  config.vm.provision "shell", path: "scripts/vagrant/test.sh"
 
   # Create a forwarded port mapping which allows access to a specific port
   # within the machine from a port on the host machine. In the example below,
-  # accessing "localhost:8080" will access port 80 on the guest machine.
+  # accessing "localhost:8888" will access port 8080 on the guest machine.
   config.vm.network "forwarded_port", guest: 8080, host: 8888
 
   # Create a private network, which allows host-only access to the machine
@@ -41,10 +42,13 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
   # the path on the host to the actual folder. The second argument is
   # the path on the guest to mount the folder. And the optional third
   # argument is a set of non-required options.
+  # FIXME: use /dataverse/downloads instead
   config.vm.synced_folder "downloads", "/downloads"
-  config.vm.synced_folder "target", "/builds"
+  # FIXME: use /dataverse/conf instead
   config.vm.synced_folder "conf", "/conf"
+  # FIXME: use /dataverse/scripts instead
   config.vm.synced_folder "scripts", "/scripts"
+  config.vm.synced_folder ".", "/dataverse"
 
   # Provider-specific configuration so you can fine-tune various
   # backing providers for Vagrant. These expose provider-specific options.

conf/httpd/conf.d/dataverse.conf

@@ -0,0 +1,19 @@
+ProxyPass / ajp://localhost:8009/
+
+# From https://wiki.apache.org/httpd/RewriteHTTPToHTTPS
+
+RewriteEngine On
+# This will enable the Rewrite capabilities
+
+RewriteCond %{HTTPS} !=on
+# This checks to make sure the connection is not already HTTPS
+
+#RewriteRule ^/?(.*) https://%{SERVER_NAME}/$1 [R,L]
+RewriteRule ^/dvn/api/data-deposit/?(.*) https://%{SERVER_NAME}/dvn/api/data-deposit/$1 [R,L]
+# This rule will redirect users from their original location, to the same location but using HTTPS.
+# i.e.  http://www.example.com/foo/ to https://www.example.com/foo/
+# The leading slash is made optional so that this will work either in httpd.conf
+# or .htaccess context
+
+# [#GLASSFISH-20694] Glassfish 4.0 and jk Unable to populate SSL attributes - Java.net JIRA - https://java.net/jira/browse/GLASSFISH-20694
+#SSLOptions +StdEnvVars +ExportCertData

doc/Sphinx/source/Developers/tools.rst

@@ -18,3 +18,14 @@ created. You can edit this file to configure PageKite to serve up port 8080
 (the default GlassFish HTTP port) or the port of your choosing.
 
 According to https://pagekite.net/support/free-for-foss/ PageKite (very generously!) offers free accounts to developers writing software the meets http://opensource.org/docs/definition.php such as Dataverse.
+
+Vagrant
++++++++
+
+Vagrant allows you to spin up a virtual machine running Dataverse on
+your development workstation.
+
+From the root of the git repo, run ``vagrant up`` and eventually you
+should be able to reach an installation of Dataverse at
+http://localhost:8888 (or whatever forwarded_port indicates in the
+Vagrantfile)

doc/Sphinx/source/index.rst

@@ -41,7 +41,7 @@ Other Resources
 Additional information about the Dataverse Project itself
 including presentations, information about upcoming releases, data
 management and citation, and announcements can be found at
-`http://thedata.org <http://thedata.org/>`__
+`http://datascience.iq.harvard.edu/ <http://datascience.iq.harvard.edu/>`__
 
 **User Group**
 

scripts/api/data-deposit/create-dataset

@@ -3,5 +3,5 @@ USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
 DATAVERSE_ALIAS=peteTop
-curl --insecure --data-binary "@scripts/api/data-deposit/data/atom-entry-study.xml" -H "Content-Type: application/atom+xml" https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/collection/dataverse/$DATAVERSE_ALIAS \
+curl -s --insecure --data-binary "@scripts/api/data-deposit/data/atom-entry-study.xml" -H "Content-Type: application/atom+xml" https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/collection/dataverse/$DATAVERSE_ALIAS \
 | xmllint -format -

scripts/api/data-deposit/delete-dataset

@@ -2,8 +2,13 @@
 USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
-#GLOBAL_ID=hdl:TEST/12345
-GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12`
+if [ -z "$1" ]; then
+  GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12,13`
+else
+  GLOBAL_ID=$1
+  # https://redmine.hmdc.harvard.edu/issues/3993
+  #GLOBAL_ID=doi:10.5072/FK2/5555
+fi
 #curl --insecure -X DELETE https://$DVN_SERVER/api/datasets/$DATABASE_ID?key=$USERNAME
 curl --insecure -i -X DELETE https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit/study/$GLOBAL_ID
 #| xmllint -format -

scripts/api/data-deposit/delete-file

@@ -0,0 +1,14 @@
+#!/bin/bash -x
+USERNAME=pete
+PASSWORD=pete
+DVN_SERVER=localhost:8181
+if [ -z "$1" ]; then
+  FILE_ID=`scripts/api/data-deposit/show-files | cut -d'/' -f1`
+  #echo $FILE_ID
+  #exit
+else
+  FILE_ID=$1
+fi
+#curl --insecure -X DELETE https://$DVN_SERVER/api/datasets/$DATABASE_ID?key=$USERNAME
+curl --insecure -i -X DELETE https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit-media/file/$FILE_ID
+#| xmllint -format -

scripts/api/data-deposit/list-datasets

@@ -2,6 +2,11 @@
 USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
-DATAVERSE_ALIAS=peteTop
-curl --insecure https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/collection/dataverse/$DATAVERSE_ALIAS \
+if [ -z "$1" ]; then
+  DATAVERSE_ALIAS=peteTop
+  #DATAVERSE_ALIAS=root
+else
+  DATAVERSE_ALIAS=$1
+fi
+curl --insecure -s https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/collection/dataverse/$DATAVERSE_ALIAS \
 | xmllint -format -

scripts/api/data-deposit/pipeline

@@ -0,0 +1,11 @@
+#!/usr/bin/env ruby
+require "rexml/document"
+include REXML
+service_document = Document.new `scripts/api/data-deposit/service-document`
+collection = XPath.first(service_document, "//collection/@href")
+puts collection
+
+puts "Getting first title from #{collection}"
+feed_of_studies = Document.new `scripts/api/data-deposit/show-collection #{collection}`
+title = XPath.first(feed_of_studies, "//title")
+puts title

scripts/api/data-deposit/publish-dataset

@@ -0,0 +1,14 @@
+#!/bin/sh
+USERNAME=pete
+PASSWORD=pete
+DVN_SERVER=localhost:8181
+if [ -z "$1" ]; then
+  GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12,13`
+else
+  GLOBAL_ID=$1
+  #GLOBAL_ID=doi:10.5072/FK2/5555
+fi
+# We cat /dev/null so that contentLength is zero. This makes headersOnly true:: https://github.com/swordapp/JavaServer2.0/blob/sword2-server-1.0/src/main/java/org/swordapp/server/ContainerAPI.java#L338
+# 'to tell curl to read the format from stdin you write "@-"' -- http://curl.haxx.se/docs/manpage.html
+cat /dev/null | curl -s --insecure -X POST -H "In-Progress: false" --data-binary @- https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit/study/$GLOBAL_ID \
+| xmllint --format -

scripts/api/data-deposit/publish-dataverse

@@ -0,0 +1,13 @@
+#!/bin/sh
+USERNAME=pete
+PASSWORD=pete
+DVN_SERVER=localhost:8181
+if [ -z "$1" ]; then
+  echo "Please supply a dataverse alias"
+  exit 1
+else
+  DATAVERSE_ALIAS=$1
+  #DATAVERSE_ALIAS=peteTop
+fi
+cat /dev/null | curl -s --insecure -X POST -H "In-Progress: false" --data-binary @- https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit/dataverse/$DATAVERSE_ALIAS \
+| xmllint --format -

scripts/api/data-deposit/service-document

@@ -1,2 +1,12 @@
 #!/bin/bash
-curl --insecure https://pete:pete@localhost:8181/dvn/api/data-deposit/v1/swordv2/service-document | xmllint -format -
+USERNAME=pete
+PASSWORD=$USERNAME
+if [ -z "$1" ]; then
+  HOSTNAME=localhost:8181
+else
+  HOSTNAME=$1
+fi
+URL=https://$HOSTNAME/dvn/api/data-deposit/v1/swordv2/service-document
+echo Retrieving service document from $URL >&2
+curl --insecure -u $USERNAME:$PASSWORD $URL \
+| xmllint -format -

scripts/api/data-deposit/show-atom-entry

@@ -2,7 +2,11 @@
 USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
-#GLOBAL_ID=hdl:TEST/12345
-GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12`
+if [ -z "$1" ]; then
+  GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12,13`
+else
+  GLOBAL_ID=$1
+  #GLOBAL_ID=doi:10.5072/FK2/5555
+fi
 curl --insecure -s https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit/study/$GLOBAL_ID \
 | xmllint -format -

scripts/api/data-deposit/show-collection

@@ -0,0 +1,10 @@
+#!/bin/bash
+USERNAME=pete
+PASSWORD=pete
+if [ -z "$1" ]; then
+  echo "Please provide a URL"
+else
+  URL=$1
+fi
+curl --insecure -s -u $USERNAME:$PASSWORD $URL
+#| xmllint -format -

scripts/api/data-deposit/show-files

@@ -1,3 +1,3 @@
 #!/bin/sh
 #scripts/api/data-deposit/show-statement | xpath "//entry/content/@*[name()='type' or name()='src']"
-scripts/api/data-deposit/show-statement | xpath '//entry/id/text()' | cut -d'/' -f11,12
+scripts/api/data-deposit/show-statement | xpath '//entry/id/text()' | cut -d'/' -f11,12,13

scripts/api/data-deposit/show-statement

@@ -2,7 +2,12 @@
 USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
-GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12`
+if [ -z "$1" ]; then
+  GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12,13`
+else
+  GLOBAL_ID=$1
+  #GLOBAL_ID=doi:10.5072/FK2/5555
+fi
 curl --insecure -s https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/statement/study/$GLOBAL_ID \
 | xmllint -format - \
 #| xpath '//entry/title'

scripts/api/data-deposit/unsupported-download-files

@@ -0,0 +1,12 @@
+#!/bin/sh
+USERNAME=pete
+PASSWORD=pete
+DVN_SERVER=localhost:8181
+if [ -z "$1" ]; then
+  GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12,13`
+else
+  GLOBAL_ID=$1
+  #GLOBAL_ID=doi:10.5072/FK2/5555
+fi
+curl -s --insecure https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit-media/study/$GLOBAL_ID \
+| xmllint -format -

scripts/api/data-deposit/upload-file

@@ -2,6 +2,13 @@
 USERNAME=pete
 PASSWORD=pete
 DVN_SERVER=localhost:8181
-GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12`
+if [ -z "$1" ]; then
+  GLOBAL_ID=`scripts/api/data-deposit/list-datasets | xpath '//id/text()' | cut -d'/' -f11,12,13`
+else
+  GLOBAL_ID=$1
+  #GLOBAL_ID=doi:10.5072/FK2/5555
+fi
 curl -s --insecure --data-binary @scripts/api/data-deposit/data/example.zip -H "Content-Disposition: filename=example.zip" -H "Content-Type: application/zip" -H "Packaging: http://purl.org/net/sword/package/SimpleZip" https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit-media/study/$GLOBAL_ID \
 | xmllint -format -
+#curl -s --insecure --data-binary @scripts/search/data/binary/trees.zip -H "Content-Disposition: filename=trees.zip" -H "Content-Type: application/zip" -H "Packaging: http://purl.org/net/sword/package/SimpleZip" https://$USERNAME:$PASSWORD@$DVN_SERVER/dvn/api/data-deposit/v1/swordv2/edit-media/study/$GLOBAL_ID \
+#| xmllint -format -

scripts/api/data/dataset-bad-missingInitialVersion.json

@@ -1,5 +1,6 @@
 {
-  "authority":"anAuthority",
-  "identifier":"dataset-one",
-  "protocol":"chadham-house-rule"
+  "authority": "anAuthority",
+  "identifier": "dataset-one",
+  "persistentUrl": "http://dx.doi.org/10.5072/FK2/9",
+  "protocol": "chadham-house-rule"
 }