From 423e7a0305d145c7555e94c6760e114a4b66e121 Mon Sep 17 00:00:00 2001 From: Prasad Konka Date: Wed, 29 May 2013 15:32:36 -0400 Subject: [PATCH] Adding gsid repo --- CONTRIBUTING.rst | 86 +++++++++++++ LICENSE | 27 ++++ NOTICE | 316 +++++++++++++++++++++++++++++++++++++++++++++++ README.md | 25 ++++ 4 files changed, 454 insertions(+) create mode 100644 CONTRIBUTING.rst create mode 100644 LICENSE create mode 100644 NOTICE create mode 100644 README.md diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst new file mode 100644 index 0000000..bf14e06 --- /dev/null +++ b/CONTRIBUTING.rst @@ -0,0 +1,86 @@ +================= +How to Contribute +================= + +We welcome community contributions to the caBIO project. +Your contributions back to this repository will allow the broader +research community to benefit from your work and will allow your +enhancements to be integrated with those of others. There are a few +guidelines that we ask contributors to follow so that we can have a +chance of keeping on top of things. + +--------------- +Getting Started +--------------- + +* Make sure you have a `GitHub Account`_. + +* Fork the repository on GitHub to publish any proposed changes + +.. If a project uses a tracker, then: + +* Submit a ticket for your issue at https://tracker.nci.nih.gov/browse/CABIO, + assuming one does not already exist. + + - Click on https://tracker.nci.nih.gov/secure/CreateIssue.jspa?pid=10002&issuetype=8 to get a jira account. + - Clearly describe the issue including steps to reproduce when it is a bug. + - Make sure you fill in the earliest version that you know has the issue. + +.. _`GitHub Account`: https://github.com/signup/free + +-------------- +Making Changes +-------------- + +* Create a topic branch from where you want to base your work. + + - This is usually the master branch. + - Only target release branches if you are certain your fix must be + on that branch. + - To quickly create a topic branch based on master:: + + git checkout -b fix/master/my_contribution master + + Please avoid working directly on the master branch. + +* Make commits of logical units. + +* Please provide tests and documentation with your changes. + +* Check for unnecessary whitespace with ``git diff --check`` before committing. + +* Follow the `NCIP Good Practices for Commit Messages`_. + Start with a one-line summary followed by a blank line followed by a + detailed free-form description. + +.. _`NCIP Good Practices for Commit Messages`: https://github.com/NCIP/ncip.github.com/wiki/Good-Practices#wiki-commit-messages + +------------------ +Submitting Changes +------------------ + +* In general, we require that the OSI-approved `BSD-3-Clause License`_ + be applied to code contributions. There may be cases, however, that + warrant the use of an alternate OSI-approved license and we will + evaluate this situations case-by-case. + +* Push your changes to a topic branch in your fork of the repository. + +* Submit a pull request to the repository in the NCIP organization. + +.. If a project uses a tracker, then: + +* Update your https://tracker.nci.nih.gov/browse/CABIO ticket to mark that you have submitted + code and are ready for it to be reviewed. + + - Include a link to the pull request in the ticket + +.. _`BSD-3-Clause License`: http://opensource.org/licenses/BSD-3-Clause + +-------------------- +Additional Resources +-------------------- + +For help learning Git and Github, see the `NCIP Learning Resources`_. + +.. _`NCIP Learning Resources`: https://github.com/NCIP/ncip.github.com/wiki/Learning-Resources \ No newline at end of file diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..600aa6e --- /dev/null +++ b/LICENSE @@ -0,0 +1,27 @@ +Copyright (c) 2010, Washington University in St. Louis, SemanticBits, Persistent Systems +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 of the National Cancer Institute, SAIC 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/NOTICE b/NOTICE new file mode 100644 index 0000000..ecf1eff --- /dev/null +++ b/NOTICE @@ -0,0 +1,316 @@ +GSID +Copyright (c) 2010, Washington University in St. Louis, SemanticBits, Persistent Systems + + +This project is distributed under the BSD 3-Clause License. +Please see LICENSE file for details. + + +This project was developed as part of the NCI caBIG initiative. + +Applications in clinical and life-science research need to manage information associated with a specimen within an institution as well as across many organizations. For specimen life-cycle tracking, NCI Center for Bioinformatics and Information Technology (CBIIT) has worked with the biorepository and cancer research community to develop a Global Specimen Identifier Service (GSID). GSID can be incorporated by biorepositories involved in multi-site efforts supported by caTissue Suite open source, home-grown, and commercial biospecimen management systems. The Cancer Genome Atlas (TCGA) program has evaluated and provided input into this GSID for their use to associate a unique identifier to each specimen and each derivative. + +The Global Specimen Identifier (GSID) Service is a NCI Enterprise Service. Global Specimen Identifer (GSID) is defined as the entity that contains a Globally Unique Idenitifer (UUID) and associated attributes that consists of a name value pair. A UUID is defined as a 16 byte identifier that is intended to be globally unique. There are 3 x 10^38 unique identifiers that can be obtained through the service + +The project was initially developed by Washington University in St. Louis, SemanticBits and Persistent Systems under funding from the CBIIT office of the National Cancer Institute. + +In 2013, as part of the National Cancer Informatics Program (NCIP) Open Development Initiative, +the GSID source code was migrated to GitHub to allow further development by the broader community. + +This project includes as sub-components other projects that are copyrighted by third parties and that distributed under various licenses. Please find a summary in the list below: + +1) jquery.dimensions.js: + Copyright by Paul Bakaus and Brandon Aaron + Distributed under the MIT and GPL licenses +2) jquery.js: + Copyright by John Resig (jquery.com) + Distributed under the MIT and GPL licenses +3) util.js: + Copyright by Thomas Fuchs + Distributed under the MIT licenses +4) WS-Addressing.xsd + Copyright by BEA Systems Inc. and IBM Corporation and Microsoft Corporation + Distributed under W3C Document License +5) policy.xsd: + Copyright by BEA Systems Inc. and IBM Corporation and Microsoft Corporation and SAP AG + Distributed under W3C Document License +6) utility.xsd: + Copyright by IBM Corporation and Microsoft Corporation + Distributed under W3C Document License +7) ws-secureconversation.xsd: + Copyright by BEA Systems, Inc., Computer Associates International, + Inc., International Business Machines Corporation, Layer 7 + Technologies, Microsoft Corporation, Netegrity, Inc., Oblix Inc., + OpenNetwork Technologies Inc., Ping Identity Corporation, Reactivity Inc., + RSA Security Inc., VeriSign Inc., and Westbridge Technology, Inc. + Distributed under W3C Document License +8) oasis-200401-wss-wssecurity-secext-1.0.xsd + oasis-200401-wss-wssecurity-utility-1.0.xsd + xmldsig-core-schema.xsd + WS-BaseFaults.wsdl + WS-BaseFaults.xsd + WS-ResourceLifetime.wsdl + WS-ResourceLifetime.xsd + WS-BaseN.wsdl + WS-BaseN.xsd + WS-Topics.xsd + WS-ResourceProperties.wsdl + WS-ResourceProperties.xsd + WS-ServiceGroup.wsdl + WS-ServiceGroup.xsd + Copyright by OASIS Open + Distributed under W3C Document License +9) ws-trust.wsdl, ws-trust.xsd: + Copyright by BEA Systems, Inc., Computer Associates International, + Inc., International Business Machines Corporation, Layer 7 + Technologies, Microsoft Corporation, Netegrity, Inc., Oblix Inc., + OpenNetwork Technologies Inc., Ping Identity Corporation, Reactivity Inc., + RSA Security Inc., VeriSign Inc., and Westbridge Technology, Inc. + Distributed under W3C Document License +10) build-stubs.xml + Copyright by University of Chicago, The University of Southern California + Distributed under The Globus Toolkit Public License + + +==================== Copyright notice by BEA Systems Inc. and IBM Corporation and Microsoft Corporation ========================= + + +==================== Copyright notice by BEA Systems Inc. and IBM Corporation and Microsoft Corporation and SAP AG ========================= + + + +==================== Copyright notice by IBM Corporation and Microsoft Corporation ========================= + + + +==================== Copyright notice by BEA Systems, Inc., Computer Associates International, +Inc., International Business Machines Corporation, Layer 7 +Technologies, Microsoft Corporation, Netegrity, Inc., Oblix Inc., +OpenNetwork Technologies Inc., Ping Identity Corporation, Reactivity Inc., +RSA Security Inc., VeriSign Inc., and Westbridge Technology, Inc. ========================= + + +Copyright Notice + +(c) 2001-2004 BEA Systems, Inc., Computer Associates International, +Inc., International Business Machines Corporation, Layer 7 +Technologies, Microsoft Corporation, Netegrity, Inc., Oblix Inc., +OpenNetwork Technologies Inc., Ping Identity Corporation, Reactivity Inc., +RSA Security Inc., VeriSign Inc., and Westbridge Technology, Inc. +All rights reserved. + +BEA, Computer Associates, IBM, Layer 7, Microsoft, Netegrity, Oblix, +OpenNetwork, Ping Identity, Reactivity, RSA Security, VeriSign, and Westbridge +(collectively, the "Authors") hereby grant you permission to copy and +display the WS-SecureConversation Schema Document, in any medium without fee or +royalty, provided that you include the following on ALL copies of the +WS-SecureConversation Schema Document that you make: + +1. A link or URL to the Specification at this location. + +2. The copyright notice as shown in the WS-SecureConversation Specification. + +BEA, Computer Associates, IBM, Layer7, Microsoft, Netegrity, Oblix, +OpenNetwork, Ping Identity, Reactivity, RSA Security, VeriSign, and Westbridge +(collectively, the "Authors") each agree to grant you a license, under +royalty-free and otherwise reasonable, non-discriminatory terms and +conditions, to their respective essential patent claims that they deem +necessary to implement the WS-SecureConversation Schema Document. + +THE WS-SecureConversation SCHEMA DOCUMENT IS PROVIDED "AS IS," AND THE AUTHORS MAKE +NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED, INCLUDING, BUT +NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A +PARTICULAR PURPOSE, NON-INFRINGEMENT, OR TITLE; THAT THE CONTENTS OF +THE WS-SecureConversation SCHEMA DOCUMENT ARE SUITABLE FOR ANY PURPOSE; NOR THAT THE +IMPLEMENTATION OF SUCH CONTENTS WILL NOT INFRINGE ANY THIRD PARTY +PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. + +THE AUTHORS WILL NOT BE LIABLE FOR ANY DIRECT, INDIRECT, SPECIAL, +INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF OR RELATING TO ANY +USE OR DISTRIBUTION OF THE WS-SecureConversation SPECIFICATION. + +The WS-SecureConversation Schema Document may change before final release and you are +cautioned against relying on the content of this specification. + +The name and trademarks of the Authors may NOT be used in any manner, +including advertising or publicity pertaining to the Specification or +its contents without specific, written prior permission. Title to +copyright in the WS-SecureConversation Schema Document will at all times remain with +the Authors. + +No other rights are granted by implication, estoppel or otherwise. + +==================== Copyright notice by OASIS Open ========================= + + + +==================== Copyright notice by BEA Systems, Inc., Computer Associates International, +Inc., International Business Machines Corporation, Layer 7 +Technologies, Microsoft Corporation, Netegrity, Inc., Oblix Inc., +OpenNetwork Technologies Inc., Ping Identity Corporation, Reactivity Inc., +RSA Security Inc., VeriSign Inc., and Westbridge Technology, Inc. ========================= + + \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..2edb41d --- /dev/null +++ b/README.md @@ -0,0 +1,25 @@ +Welcome to the Global Specimen Identifier (GSID) Project! +===================================== + +Applications in clinical and life-science research need to manage information associated with a specimen within an institution as well as across many organizations. For specimen life-cycle tracking, NCI Center for Bioinformatics and Information Technology (CBIIT) has worked with the biorepository and cancer research community to develop a Global Specimen Identifier Service (GSID). GSID can be incorporated by biorepositories involved in multi-site efforts supported by caTissue Suite open source, home-grown, and commercial biospecimen management systems. The Cancer Genome Atlas (TCGA) program has evaluated and provided input into this GSID for their use to associate a unique identifier to each specimen and each derivative. + +GSID will enable biorepositories to: +* Support the individual researcher by providing a framework for cross referencing a specimen to the specimen’s history and other findings on that specimen +* Provide a source of certified globally unique identifier +* Certify externally generated IDs are globally unique +* Maintain relations between GSIDs, such as source to aliquot, or children to multiple parents. + +The Global Specimen Identifier (GSID) Service is a NCI Enterprise Service. Global Specimen Identifer (GSID) is defined as the entity that contains a Globally Unique Idenitifer (UUID) and associated attributes that consists of a name value pair. A UUID is defined as a 16 byte identifier that is intended to be globally unique. There are 3 x 10^38 unique identifiers that can be obtained through the service + +The Global Specimen Identifier is distributed under the BSD 3-Clause License. +Please see the NOTICE and LICENSE files for details. + +You will find more details about the GSID in the following links: + * [Home Page] (https://wiki.nci.nih.gov/display/caTissue/Global+Specimen+Identifier+(GSID)) + * [NCI OSDI] (https://wiki.nci.nih.gov/display/caBIGCommunityCode/CBIIT+Open+Source+Development+Initiative) + * [Issue Tracker] (https://bugzilla.wustl.edu/bugzilla/) + * [Code Repository] (https://github.com/NCIP/gsid) + +Please join us in further developing and improving Global Specimen Identifier (GSID). + +