diff --git a/.gitignore b/.gitignore index 8d7ab7c..647863d 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ .idea/ test/cover bower_components +node_modules/ diff --git a/README.md b/README.md index 87dce94..fd55f2c 100644 --- a/README.md +++ b/README.md @@ -56,6 +56,12 @@ api as a webservice to (e.g. Changes ------- +### 1.0.4 (2017-07-28) + +- Switch from bower to yarn +- Update dependencies +- Update of biojs-io-biom to version 1.0.9 + ### 1.0.3 (2017-03-29) - Update of biojs-io-biom to version 1.0.7 diff --git a/bower.json b/bower.json deleted file mode 100644 index 60628f9..0000000 --- a/bower.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "name": "biom-conversion-server", - "homepage": "https://github.com/molbiodiv/biom-conversion-server", - "authors": [ - "Markus Ankenbrand " - ], - "description": "Convert between biom version 1 and version 2", - "main": "", - "keywords": [ - "biom", - "converter", - "hdf5", - "json", - "biom-format" - ], - "license": "MIT", - "ignore": [ - "**/.*", - 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"reference": "bb2d123231c095735130cc8f6d31385a44c7b308" + "reference": "2db61e59ff05fe5126d152bd0655c9ea113e550f" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/webmozart/assert/zipball/bb2d123231c095735130cc8f6d31385a44c7b308", - "reference": "bb2d123231c095735130cc8f6d31385a44c7b308", + "url": "https://api.github.com/repos/webmozart/assert/zipball/2db61e59ff05fe5126d152bd0655c9ea113e550f", + "reference": "2db61e59ff05fe5126d152bd0655c9ea113e550f", "shasum": "" }, "require": { - "php": "^5.3.3|^7.0" + "php": "^5.3.3 || ^7.0" }, "require-dev": { "phpunit/phpunit": "^4.6", @@ -2054,7 +2310,7 @@ "type": "library", "extra": { "branch-alias": { - "dev-master": "1.2-dev" + "dev-master": "1.3-dev" } }, "autoload": { @@ -2078,7 +2334,7 @@ "check", "validate" ], - "time": "2016-08-09 15:02:57" + "time": "2016-11-23 20:04:58" } ], "aliases": [], diff --git a/convert.php b/convert.php index 9318b7f..9440e25 100644 --- a/convert.php +++ b/convert.php @@ -20,12 +20,11 @@ require_once __DIR__ . DIRECTORY_SEPARATOR . 'vendor' . DIRECTORY_SEPARATOR . 'autoload.php'; // explicitly set CONTENT_TYPE if empty (required for testing) -if(empty($_SERVER['CONTENT_TYPE'])) -{ +if (empty($_SERVER['CONTENT_TYPE'])) { $_SERVER['CONTENT_TYPE'] = "application/x-www-form-urlencoded"; } // load json data into $_REQUEST if content type is application/json -if($_SERVER["CONTENT_TYPE"] === 'application/json'){ +if ($_SERVER["CONTENT_TYPE"] === 'application/json') { $_REQUEST = json_decode(file_get_contents('php://input'), true); } $to = isset($_REQUEST["to"]) ? $_REQUEST["to"] : false; diff --git a/docker/Dockerfile b/docker/Dockerfile index 5947c6c..396ac48 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -18,7 +18,7 @@ RUN curl -sS https://getcomposer.org/installer | php -- --install-dir=/usr/local # Install bower RUN ln -s /usr/bin/nodejs /usr/bin/node -RUN npm install -g bower +RUN npm install -g yarn # Prepare apache RUN rm -rf /var/www/html @@ -37,7 +37,7 @@ RUN echo "export LANG=C.UTF-8" >>/etc/apache2/envvars RUN git clone https://github.com/molbiodiv/biom-conversion-server.git /var/www/html RUN cd /var/www/html && conda install --yes --file explicit-conda-spec.txt RUN cd /var/www/html && composer install -RUN cd /var/www/html && bower install --allow-root +RUN cd /var/www/html && yarn install # Add custom php ini ADD php.ini /etc/php/7.0/apache2/php.ini diff --git a/index.html b/index.html index 709d026..7d5d629 100644 --- a/index.html +++ b/index.html @@ -6,17 +6,17 @@ BiomCS - biom conversion server - + - - + + - + - +
-

Welcome to the biom conversion server 1.0.3

+

Welcome to the biom conversion server 1.0.4

To use the API call convert.php with parameters "to" and "content".
Parameter "to" can be "json" or "hdf5" while parameter "content" is the content of the file to convert in base64 encoding. diff --git a/package.json b/package.json new file mode 100644 index 0000000..7d632fe --- /dev/null +++ b/package.json @@ -0,0 +1,23 @@ +{ + "name": "biom-conversion-server", + "repository": { + "type": "git", + "url": "https://github.com/molbiodiv/biom-conversion-server.git" + }, + "author": "Markus Ankenbrand", + "description": "Convert between biom version 1 and version 2", + "keywords": [ + "biom", + "converter", + "hdf5", + "json", + "biom-format" + ], + "license": "MIT", + "dependencies": { + "biojs-io-biom": "^1.0.9", + "bootstrap": "^3.3.7", + "file-saver": "^1.3.3", + "jquery": "^3.2.1" + } +} diff --git a/test/ConvertTest.php b/test/ConvertTest.php index c3711cb..7d1c830 100644 --- a/test/ConvertTest.php +++ b/test/ConvertTest.php @@ -4,7 +4,7 @@ require_once __DIR__.'/overload_header_function.php'; -class ConvertTest extends \PHPUnit_Framework_TestCase +class ConvertTest extends \PHPUnit\Framework\TestCase { public function testConvertWithMissingTo() { diff --git a/test/biomcs/BiomCSTest.php b/test/biomcs/BiomCSTest.php index 9ccba26..7ee9c1f 100644 --- a/test/biomcs/BiomCSTest.php +++ b/test/biomcs/BiomCSTest.php @@ -4,7 +4,7 @@ require_once __DIR__.'/../overload_header_function.php'; -class BiomCSTest extends \PHPUnit_Framework_TestCase +class BiomCSTest extends \PHPUnit\Framework\TestCase { public function testConvertToJSON() { diff --git a/yarn.lock b/yarn.lock new file mode 100644 index 0000000..ed9e8b8 --- /dev/null +++ b/yarn.lock @@ -0,0 +1,381 @@ +# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY. +# yarn lockfile v1 + + +ajv@^4.9.1: + version "4.11.8" + resolved "https://registry.yarnpkg.com/ajv/-/ajv-4.11.8.tgz#82ffb02b29e662ae53bdc20af15947706739c536" + dependencies: + co "^4.6.0" + json-stable-stringify "^1.0.1" + +asn1@~0.2.3: + version "0.2.3" + resolved "https://registry.yarnpkg.com/asn1/-/asn1-0.2.3.tgz#dac8787713c9966849fc8180777ebe9c1ddf3b86" + +assert-plus@1.0.0, assert-plus@^1.0.0: + version "1.0.0" + resolved "https://registry.yarnpkg.com/assert-plus/-/assert-plus-1.0.0.tgz#f12e0f3c5d77b0b1cdd9146942e4e96c1e4dd525" + +assert-plus@^0.2.0: + version "0.2.0" + resolved "https://registry.yarnpkg.com/assert-plus/-/assert-plus-0.2.0.tgz#d74e1b87e7affc0db8aadb7021f3fe48101ab234" + +asynckit@^0.4.0: + version "0.4.0" + resolved "https://registry.yarnpkg.com/asynckit/-/asynckit-0.4.0.tgz#c79ed97f7f34cb8f2ba1bc9790bcc366474b4b79" + +aws-sign2@~0.6.0: + version "0.6.0" + resolved 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