From d23270465945bd0bca0098faceb8aaf98942002d Mon Sep 17 00:00:00 2001 From: geoffjentry Date: Mon, 25 Jan 2016 10:37:11 -0500 Subject: [PATCH] code review --- LICENSE.txt | 27 +++++++++++++++++++++++++++ README.md | 16 ++++++++-------- src/.DS_Store | Bin 6148 -> 0 bytes src/main/.DS_Store | Bin 6148 -> 0 bytes src/test/.DS_Store | Bin 6148 -> 0 bytes 5 files changed, 35 insertions(+), 8 deletions(-) create mode 100644 LICENSE.txt delete mode 100644 src/.DS_Store delete mode 100644 src/main/.DS_Store delete mode 100644 src/test/.DS_Store diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..6acd685 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,27 @@ +Copyright (c) 2015, Broad Institute, Inc. +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +* Neither the name Broad Institute, Inc. nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE \ No newline at end of file diff --git a/README.md b/README.md index 4f21840..2035334 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ java -jar cromwell.jar Actions: parse - Compares a WDL file against the grammar and prints out an + Compares a WDL file against the grammar and writes out an abstract syntax tree if it is valid, and a syntax error otherwise. Note that higher-level AST checks are not done via this sub-command and the 'validate' subcommand should @@ -65,12 +65,12 @@ highlight ## validate -Given a WDL file, this runs the full syntax checker over the file and resolves imports in the process. If any syntax errors are found, they are printed out. Otherwise the program exits. +Given a WDL file, this runs the full syntax checker over the file and resolves imports in the process. If any syntax errors are found, they are written out. Otherwise the program exits. Error if a `call` references a task that doesn't exist: ``` -$ java -jar cromwell.jar validate 2.wdl +$ java -jar wdltool.jar validate 2.wdl ERROR: Call references a task (BADps) that doesn't exist (line 22, col 8) call BADps @@ -81,7 +81,7 @@ ERROR: Call references a task (BADps) that doesn't exist (line 22, col 8) Error if namespace and task have the same name: ``` -$ java -jar cromwell.jar validate 5.wdl +$ java -jar wdltool.jar validate 5.wdl ERROR: Task and namespace have the same name: Task defined here (line 3, col 6): @@ -100,7 +100,7 @@ import "ps.wdl" as ps Examine a WDL file with one workflow in it, compute all the inputs needed for that workflow and output a JSON template that the user can fill in with values. The keys in this document should remain unchanged. The values tell you what type the parameter is expecting. For example, if the value were `Array[String]`, then it's expecting a JSON array of JSON strings, like this: `["string1", "string2", "string3"]` ``` -$ java -jar cromwell.jar inputs 3step.wdl +$ java -jar wdltool.jar inputs 3step.wdl { "three_step.cgrep.pattern": "String" } @@ -110,10 +110,10 @@ This inputs document is used as input to the `run` subcommand. ## parse -Given a WDL file input, this does grammar level syntax checks and prints out the resulting abstract syntax tree. +Given a WDL file input, this does grammar level syntax checks and writes out the resulting abstract syntax tree. ``` -$ echo "workflow wf {}" | java -jar cromwell.jar parse /dev/stdin +$ echo "workflow wf {}" | java -jar wdltool.jar parse /dev/stdin (Document: imports=[], definitions=[ @@ -149,7 +149,7 @@ workflow wf { This WDL file can be formatted in HTML as follows: ``` -$ java -jar cromwell.jar highlight test.wdl html +$ java -jar wdltool.jar highlight test.wdl html task abc { String in command { diff --git a/src/.DS_Store b/src/.DS_Store deleted file mode 100644 index 9604c915d7b8d2e3c47081ab1bfbca343bb98a7e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHKJ5EC}5S)cqM50Ma=__ypD+(vb1^9#lDUc$ee--EAXqo*KiJqR6h6ZM(_1Nnj zTb|3 z&ZCzgHV+Vc;h4w>&5}w?s#S|&NoTxOUN0OIlMaiUc~0GI)uCA2&UlM-SWna_1*E{G z0=Kzbdi{T-&-DM7B(0=?6!=pL*s$KLSA0^{*2&|%);9VR-E)5EZkz{&LzH7;lw&Tu f9N$M$<~5&lzZZ^)L1#SZMEwl7E;1?b+X|cjR1+BX diff --git a/src/main/.DS_Store b/src/main/.DS_Store deleted file mode 100644 index c108b7bb8ceabeaec9e3c5cb4909fe0fefaca413..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHKyH3ME5S)b|MbMBhx1z7=&y9o`J}sX9uy8y lj)_r@x$ts)A4!?le9q^6;g}e7#)D4O&w%S9lLCLOz!z6g8t?!B diff --git a/src/test/.DS_Store b/src/test/.DS_Store deleted file mode 100644 index 6a866169fd8a92125ad113e5d0f17df9202febc4..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHK%SyyR5Ukb+t6ui#aehD{enD8)FYpIkvtA?+*kwKE=5Jg55EFv1c<>Oqp{Hhg zx{^#CrqcjqbK2Ly8o-LKh)*5nru*tMyNF0d6n)12*mkdd-*IuSDYwEqcKE<<%)iC~ zZ#bgIiL+McH+gy zsX!|5X9e_rD0IapaB#G%gM+mIME#97