diff options
author | Christoph Helma <helma@in-silico.de> | 2009-08-14 10:33:51 +0200 |
---|---|---|
committer | Christoph Helma <helma@in-silico.de> | 2009-08-14 10:33:51 +0200 |
commit | 7d19f5562f3f59f7a14a4d6f7d8da6f24fdabd8c (patch) | |
tree | 3a2a1cfcb746fc44162a9ceed492ecf5f7047230 | |
parent | 9d9ed94fb136262ed072d61c07b94b90c243646d (diff) |
Initial version of opentox-lazar
-rw-r--r-- | .gitignore | 1 | ||||
-rw-r--r-- | LICENSE | 674 | ||||
-rw-r--r-- | README | 74 | ||||
-rw-r--r-- | Rakefile | 15 | ||||
-rw-r--r-- | application.rb | 216 | ||||
-rw-r--r-- | config.ru | 5 | ||||
-rw-r--r-- | environment.rb | 21 | ||||
-rw-r--r-- | lazar.rb | 92 | ||||
-rw-r--r-- | models.rb | 47 | ||||
-rw-r--r-- | views/model.builder | 7 |
10 files changed, 1053 insertions, 99 deletions
@@ -1 +1,2 @@ +tmp/* *.sqlite3 @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + + Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the manufacturer +can do so. This is fundamentally incompatible with the aim of +protecting users' freedom to change the software. The systematic +pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we +have designed this version of the GPL to prohibit the practice for those +products. If such problems arise substantially in other domains, we +stand ready to extend this provision to those domains in future versions +of the GPL, as needed to protect the freedom of users. + + Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish to +avoid the special danger that patents applied to a free program could +make it effectively proprietary. To prevent this, the GPL assures that +patents cannot be used to render the program non-free. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based +on the Program. + + To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + + A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + + The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + + The Corresponding Source for a work in source code form is that +same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + + When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + + A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + + If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + + The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + + All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + + If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + + A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + <one line to give the program's name and a brief idea of what it does.> + Copyright (C) <year> <name of author> + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + <program> Copyright (C) <year> <name of author> + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +<http://www.gnu.org/licenses/>. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +<http://www.gnu.org/philosophy/why-not-lgpl.html>. @@ -0,0 +1,74 @@ +OpenTox Fminer +============= + +* An OpenTox REST Webservice (http://www.opentox.org) +* Ruby implementation of the lazar algorithm +* Implements a subset of the OpenTox algorithm/model API (http://opentox.org/wiki/opentox/Structure). +* Runs at http://webservices.in-silico.ch/lazar + +REST API + +Description Method URI Parameters Result Status codes + +Get index of all GET /models List of model URIs 200, 500 +models + +Get model description GET /model{id} XML with model 200, 202, 404, 500 + representation + +Create a prediction POST / name, file or Model URI 200, 500 +model dataset_uri + +Delete a model DELETE /{id} 200, 404, 500 + +Create a prediction POST /{id} compound_uri Prediction URI 200, 404, 500 + +Get index of all GET /predictions List of prediction 200, 500 +predictions URIs + +Show a prediction GET /prediction/{id} XML with prediction 200, 202, 404, 500 + result + +Show neighbors for a GET /prediction/{id} XML with neighbors 200, 404, 500 +prediction /neighbors + +Show relevant features GET /prediction/{id} XML with relevant 200, 404, 500 +for a prediction /features features + +Delete a prediction DELETE /prediction/{id} 200, 404, 500 + +EXAMPLES + +Create a prediction model from a tab/whitespace delimited file (smiles activity): + + curl -X POST -d name="Hamster carcinogenicity" -d file=@hamster_carcinogenicity http://webservices.in-silico.ch/lazar/models + +Create a prediction model from an existing dataset: + + curl -X POST -d dataset_uri=http://webservices.in-silico.ch/datasets/1 http://webservices.in-silico.ch/lazar/models + +Get model information: + + curl http://webservices.in-silico.ch/lazar/model/1 (returns status code 202, if model is still under construction) + +Predict a compound: + + curl -X POST -d compound_uri=http://webservices.in-silico.ch/compound/N%23%5BN%2B%5Dc1ccccc1%2EF%5BB%2D%5D%28F%29%28F%29F http://webservices.in-silico.ch/lazar/model/1 + +Show a prediction: + + curl http://webservices.in-silico.ch/lazar/prediction/1 (returns status code 202, if prediction is still running) + +Show prediction neighbors: + + curl http://webservices.in-silico.ch/lazar/prediction/neighbors + +Show relevant features for a prediction: + + curl http://webservices.in-silico.ch/lazar/prediction/features + +INSTALLATION + +Run 'rake install' to install the required gems + +Copyright (c) 2009 Christoph Helma. See LICENSE for details. diff --git a/Rakefile b/Rakefile new file mode 100644 index 0000000..931410f --- /dev/null +++ b/Rakefile @@ -0,0 +1,15 @@ +require 'rubygems' +require 'rake' + +desc "Install required gems and openbabel" +task :install do + `sudo gem sources -a http://gems.github.com` + `sudo gem install sinatra dm-core dm-more builder helma-opentox-ruby-api` +end + +desc "Run tests" +task :test do + puts "No tests for lazar." + #load 'test.rb' +end + diff --git a/application.rb b/application.rb new file mode 100644 index 0000000..172db06 --- /dev/null +++ b/application.rb @@ -0,0 +1,216 @@ +load 'environment.rb' + +# MODELS +get '/models?' do # get index of models + Model.all.collect{ |m| m.uri }.join("\n") +end + +get '/model/:id' do + begin + model = Model.get(params[:id]) + rescue + status 404 + "Model #{params[:id]} not found" + end + if model.finished + xml model + else + status 202 + "Model #{params[:id]} under construction" + end +end + +post '/models' do # create a model + + if params[:dataset_uri] + training_dataset = OpenTox::Dataset.new :uri => params[:dataset_uri] + else + training_dataset = OpenTox::Dataset.new :name => params[:name] + end + model = Model.create(:name => params[:name], :training_dataset_uri => training_dataset.uri) + model.update_attributes(:uri => url_for("/model/", :full) + model.id.to_s) + + pid = fork do #Spork.spork do + unless params[:dataset_uri] # create model from a tab delimited file + File.open(params[:file][:tempfile].path).each_line do |line| + items = line.chomp.split(/\s+/) + compound = OpenTox::Compound.new :smiles => items[0] + feature = OpenTox::Feature.new :name => params[:name], :values => { 'classification' => items[1] } + training_dataset.add(compound, feature) + end + end + + feature_generation = OpenTox::Fminer.new(training_dataset) + feature_dataset = feature_generation.dataset + model.feature_dataset_uri = feature_dataset.uri.chomp + model.finished = true + model.save + end + Process.detach(pid) + model.uri.to_s +end + +delete '/model/:id' do + begin + model = Model.get params[:id] + rescue + status 404 + "Model #{params[:id]} not found" + end + model.predictions.each do |p| + p.neighbors.each { |n| n.destroy } + p.features.each { |n| f.destroy } + p.destroy + end + model.destroy + "Model #{params[:id]} succesfully deleted." + # TODO: what happens with datasets, avoid stale datasets, but other components might need them +end + +post '/model/:id' do # create prediction + + begin + model = Model.get params[:id] + rescue + status 404 + "Model #{params[:id]} not found" + end + query_compound = OpenTox::Compound.new :uri => params[:compound_uri] + activity_dataset = OpenTox::Dataset.new :uri => model.training_dataset_uri + + database_activities = activity_dataset.features(query_compound) + + if database_activities.size > 0 # return database values + database_activities.collect{ |f| f.uri }.join('\n') + + else # make prediction + prediction = Prediction.find_or_create(:model_uri => model.uri, :compound_uri => params[:compound_uri]) + + unless prediction.finished # present cached prediction if finished + + #Spork.spork do + pid = fork do + prediction.update_attributes(:uri => url_for("/prediction/", :full) + prediction.id.to_s) + feature_dataset = OpenTox::Dataset.new :uri => model.feature_dataset_uri + compound_descriptors = feature_dataset.all_compounds_and_features + training_features = feature_dataset.all_features + compound_activities = activity_dataset.all_compounds_and_features + query_features = query_compound.match(training_features) + query_features.each do |f| + puts f.uri + Feature.find_or_create(:feature_uri => f.uri, :prediction_uri => prediction.uri) + end + + conf = 0.0 + + compound_descriptors.each do |compound_uri,features| + sim = similarity(features,query_features,model) + if sim > 0.0 + Neighbor.find_or_create(:compound_uri => compound_uri, :similarity => sim, :prediction_uri => prediction.uri) + compound_activities[compound_uri].each do |a| + case a.value('classification').to_s + when 'true' + conf += sim #TODO gaussian + when 'false' + conf -= sim #TODO gaussian + end + end + end + end + + if conf > 0.0 + classification = true + elsif conf < 0.0 + classification = false + end + prediction.update_attributes(:confidence => conf, :classification => classification, :finished => true) + prediction.save! + puts prediction.to_yaml + + end + Process.detach(pid) + end + + prediction.uri + end +end + +# PREDICTIONS +get '/predictions?' do # get index of predictions + Prediction.all.collect{ |p| p.uri }.join("\n") +end + +get '/prediction/:id' do # display prediction + begin + prediction = Prediction.get(params[:id]) + rescue + status 404 + "Prediction #{params[:id]} not found." + end + if prediction.finished + xml prediction + else + status 202 + "Prediction #{params[:id]} not yet finished." + end +end + +get '/prediction/:id/neighbors' do + begin + prediction = Prediction.get(params[:id]) + rescue + status 404 + "Prediction #{params[:id]} not found." + end + xml Neighbor.all(:prediction_uri => prediction.uri) +end + +get '/prediction/:id/features' do + begin + prediction = Prediction.get(params[:id]) + rescue + status 404 + "Prediction #{params[:id]} not found." + end + xml Feature.all(:prediction_uri => prediction.uri) +end + +delete '/prediction/:id' do + begin + p = Prediction.get(params[:id]) + rescue + status 404 + "Prediction #{params[:id]} not found." + end + p.neighbors.each { |n| n.destroy } + p.features.each { |f| f.destroy } + p.destroy + "Prediction #{params[:id]} succesfully deleted." +end + +# Utility functions +def similarity(neighbor_features, query_features, model) + + nf = neighbor_features.collect{|f| f.uri } + qf = query_features.collect{|f| f.uri } + #common_features = neighbor_features & query_features + #all_features = neighbor_features | query_features + common_features = nf & qf + all_features = nf | qf + + sum_p_common = 0.0 + sum_p_all = 0.0 + + #all_features.each { |f| sum_p_all += f.value.to_f } + #common_features.each { |f| sum_p_common += f.value.to_f } + #sum_p_common/sum_p_all + common_features.size.to_f/all_features.size.to_f + +end + +def xml(object) + builder do |xml| + xml.instruct! + object.to_xml + end +end diff --git a/config.ru b/config.ru new file mode 100644 index 0000000..0cc3dc6 --- /dev/null +++ b/config.ru @@ -0,0 +1,5 @@ +require 'rubygems' +require 'sinatra' +require 'application.rb' + +run Sinatra::Application diff --git a/environment.rb b/environment.rb new file mode 100644 index 0000000..b525c45 --- /dev/null +++ b/environment.rb @@ -0,0 +1,21 @@ +require 'rubygems' + +['sinatra', 'sinatra/url_for', 'dm-core', 'dm-more', 'builder', 'opentox-ruby-api'].each do |lib| + require lib +end + +require "openbabel" + +sqlite = "#{File.expand_path(File.dirname(__FILE__))}/#{Sinatra::Base.environment}.sqlite3" +DataMapper.setup(:default, "sqlite3:///#{sqlite}") +DataMapper::Logger.new(STDOUT, 0) + +load 'models.rb' + +unless File.exists?(sqlite) + Model.auto_migrate! + Prediction.auto_migrate! + Neighbor.auto_migrate! + Feature.auto_migrate! +end + diff --git a/lazar.rb b/lazar.rb deleted file mode 100644 index fc69573..0000000 --- a/lazar.rb +++ /dev/null @@ -1,92 +0,0 @@ -#['rubygems', 'sinatra', 'rest_client', 'sinatra/url_for', 'crack/xml', 'dm-core', 'spork'].each do |lib| -['rubygems', 'sinatra', 'rest_client', 'sinatra/url_for', 'crack/xml', 'dm-core', 'builder', 'logger'].each do |lib| - require lib -end - -DataMapper.setup(:default, "sqlite3://#{Dir.pwd}/lazar.sqlite3") - -class Model - include DataMapper::Resource - property :id, Serial - property :name, String - property :feature_dataset_uri, String - property :training_dataset_uri, String -end - -Model.auto_migrate! unless File.exists?("lazar.sqlite3") - -COMPOUNDS_URI = 'http://webservices.in-silico.ch/compounds/' -FEATURES_URI = 'http://webservices.in-silico.ch/features/' -DATASET_URI = 'http://localhost:4567/' -FEATURE_GENERATION_URI = 'http://localhost:9394/' -@similarity_prediction = RestClient::Resource.new 'http://webservices.in-silico.ch/weighted_similarity_classification' - -get '/?' do # get index of models - Model.all.collect{ |m| url_for("/", :full) + m.id.to_s }.join("\n") -end - -get '/:id' do - @model = Model.get(params[:id]) - builder :model -end - -get '/:id/:inchikey' do # show prediction - @prediction = Prediction.first(:model_id => params[:id], :compound_uri => params[:compound_uri]) - builder :prediction -end - -post '/:id' do # create prediction - unless prediction = Prediction.first(:model_id => params[:id], :compound_uri => params[:compound_uri]) - Spork.spork do - Prediction.create(@similarity_prediction.post, :compound_uri => params[:compound_uri], :feature_dataset_uri => Model.get(params[:id]).feature_dataset_uri) - end - end - inchikey = @compounds.get "#{params[:compound_uri]}.inchikey" - # or redirect? - url_for("/#{params[:id]}/#{inchikey}", :full) -end - -post '/' do # create model - - training_dataset_uri = RestClient.post DATASET_URI, :name => params[:name] - dataset = RestClient::Resource.new training_dataset_uri - model = Model.create(:name => params[:name], :training_dataset_uri => training_dataset_uri) - - #Spork.spork do - pid = fork do - - # create model from a tab delimited file - File.open(params[:file][:tempfile].path).each_line do |line| - items = line.split(/\s+/) - begin - compound_uri = COMPOUNDS_URI + URI.encode(items[0]) - #compound_uri = RestClient.post COMPOUNDS_URI, :smiles => items[0] - rescue - puts "Failed to get InChI key for #{items[0]}" - end - feature_uri = RestClient.post FEATURES_URI, :name => params[:name], :value => items[1] - dataset.put :compound_uri => compound_uri, :feature_uri => feature_uri - model.training_dataset_uri = training_dataset_uri - model.save - #rescue - #puts "Creation of feature #{params[:name]}:#{items[1]} for compound #{items[0]} failed." - #end - end - - - feature_dataset_uri = RestClient.post FEATURE_GENERATION_URI, :dataset_uri => training_dataset_uri - model.feature_dataset_uri = feature_dataset_uri.chomp - model.save - - # create features - #feature_dataset_uri = @feature_generation.post :dataset_uri => params[:dataset_uri] - #model = Model.create(:name => params[:name], :training_dataset_uri => training_dataset_uri, :feature_dataset_uri => feature_dataset_uri) - #model.save - # validate - # or redirect? - - end - - Process.detach(pid) - url_for("/", :full) + model.id.to_s -end diff --git a/models.rb b/models.rb new file mode 100644 index 0000000..118253a --- /dev/null +++ b/models.rb @@ -0,0 +1,47 @@ +class Model + include DataMapper::Resource + property :id, Serial + property :name, String + property :uri, URI + property :feature_dataset_uri, URI + property :training_dataset_uri, URI + property :finished, Boolean, :default => false + + def predictions + Prediction.all(:model_uri => uri) + end +end + +class Prediction + include DataMapper::Resource + property :id, Serial + property :uri, URI + property :model_uri, URI + property :compound_uri, URI + property :classification, Boolean + property :confidence, Float + property :finished, Boolean, :default => false + + def neighbors + Neighbor.all(:prediction_uri => uri) + end + + def features + Feature.all(:prediction_uri => uri) + end +end + +class Neighbor + include DataMapper::Resource + property :id, Serial + property :compound_uri, URI + property :prediction_uri, URI + property :similarity, Float +end + +class Feature + include DataMapper::Resource + property :id, Serial + property :feature_uri, URI + property :prediction_uri, URI +end diff --git a/views/model.builder b/views/model.builder deleted file mode 100644 index b3832a3..0000000 --- a/views/model.builder +++ /dev/null @@ -1,7 +0,0 @@ -xml.instruct! -xml.model do - xml.uri url_for("/", :full) + @model.id.to_s - xml.name @model.name - xml.training_dataset_uri @model.training_dataset_uri - xml.feature_dataset_uri @model.feature_dataset_uri -end |