forked from chenyian-nibio/targetmine
-
Notifications
You must be signed in to change notification settings - Fork 0
/
LICENSE.intermine
452 lines (373 loc) · 24.9 KB
/
LICENSE.intermine
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
InterMine is an open source project distributed under the GNU Lesser
General Public Licence.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library 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
Lesser General Public License for more details.
The following comment should appear in all source code files:
/*
* Copyright (C) 2002-2017 FlyMine
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. See the LICENSE file for more
* information or http://www.gnu.org/copyleft/lesser.html.
*
*/
InterMine
Department of Genetics
Downing Street
Cambridge, CB2 3EH, UK
www.intermine.org
The LGPL is defined as follows:
GNU LESSER GENERAL PUBLIC LICENSE
Version 2.1, February 1999
Copyright (C) 1991, 1999 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
[This is the first released version of the Lesser GPL. It also counts
as the successor of the GNU Library Public License, version 2, hence
the version number 2.1.]
Preamble
The licenses for most software are designed to take away your freedom to share
and change it. By contrast, the GNU General Public Licenses are intended to
guarantee your freedom to share and change free software--to make sure the
software is free for all its users.
This license, the Lesser General Public License, applies to some specially
designated software packages--typically libraries--of the Free Software
Foundation and other authors who decide to use it. You can use it too, but we
suggest you first think carefully about whether this license or the ordinary
General Public License is the better strategy to use in any particular case,
based on the explanations below.
When we speak of free software, we are referring to freedom of use, 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 this service if you wish);
that you receive source code or can get it if you want it; that you can change
the software and use pieces of it in new free programs; and that you are
informed that you can do these things.
To protect your rights, we need to make restrictions that forbid distributors to
deny you these rights or to ask you to surrender these rights. These
restrictions translate to certain responsibilities for you if you distribute
copies of the library or if you modify it.
For example, if you distribute copies of the library, whether gratis or for a
fee, you must give the recipients all the rights that we gave you. You must make
sure that they, too, receive or can get the source code. If you link other code
with the library, you must provide complete object files to the recipients, so
that they can relink them with the library after making changes to the library
and recompiling it. And you must show them these terms so they know their
rights.
We protect your rights with a two-step method: (1) we copyright the library, and
(2) we offer you this license, which gives you legal permission to copy,
distribute and/or modify the library.
To protect each distributor, we want to make it very clear that there is no
warranty for the free library. Also, if the library is modified by someone else
and passed on, the recipients should know that what they have is not the
original version, so that the original author's reputation will not be affected
by problems that might be introduced by others.
Finally, software patents pose a constant threat to the existence of any free
program. We wish to make sure that a company cannot effectively restrict the
users of a free program by obtaining a restrictive license from a patent holder.
Therefore, we insist that any patent license obtained for a version of the
library must be consistent with the full freedom of use specified in this
license.
Most GNU software, including some libraries, is covered by the ordinary GNU
General Public License. This license, the GNU Lesser General Public License,
applies to certain designated libraries, and is quite different from the
ordinary General Public License. We use this license for certain libraries in
order to permit linking those libraries into non-free programs.
When a program is linked with a library, whether statically or using a shared
library, the combination of the two is legally speaking a combined work, a
derivative of the original library. The ordinary General Public License
therefore permits such linking only if the entire combination fits its criteria
of freedom. The Lesser General Public License permits more lax criteria for
linking other code with the library.
We call this license the "Lesser" General Public License because it does Less to
protect the user's freedom than the ordinary General Public License. It also
provides other free software developers Less of an advantage over competing
non-free programs. These disadvantages are the reason we use the ordinary
General Public License for many libraries. However, the Lesser license provides
advantages in certain special circumstances.
For example, on rare occasions, there may be a special need to encourage the
widest possible use of a certain library, so that it becomes a de-facto
standard. To achieve this, non-free programs must be allowed to use the library.
A more frequent case is that a free library does the same job as widely used
non-free libraries. In this case, there is little to gain by limiting the free
library to free software only, so we use the Lesser General Public License.
In other cases, permission to use a particular library in non-free programs
enables a greater number of people to use a large body of free software. For
example, permission to use the GNU C Library in non-free programs enables many
more people to use the whole GNU operating system, as well as its variant, the
GNU/Linux operating system.
Although the Lesser General Public License is Less protective of the users'
freedom, it does ensure that the user of a program that is linked with the
Library has the freedom and the wherewithal to run that program using a modified
version of the Library.
The precise terms and conditions for copying, distribution and modification
follow. Pay close attention to the difference between a "work based on the
library" and a "work that uses the library". The former contains code derived
from the library, whereas the latter must be combined with the library in order
to run.
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License Agreement applies to any software library or other program which
contains a notice placed by the copyright holder or other authorized party
saying it may be distributed under the terms of this Lesser General Public
License (also called "this License"). Each licensee is addressed as "you".
A "library" means a collection of software functions and/or data prepared so as
to be conveniently linked with application programs (which use some of those
functions and data) to form executables.
The "Library", below, refers to any such software library or work which has been
distributed under these terms. A "work based on the Library" means either the
Library or any derivative work under copyright law: that is to say, a work
containing the Library or a portion of it, either verbatim or with modifications
and/or translated straightforwardly into another language. (Hereinafter,
translation is included without limitation in the term "modification".)
"Source code" for a work means the preferred form of the work for making
modifications to it. For a library, complete source code means all the source
code for all modules it contains, plus any associated interface definition
files, plus the scripts used to control compilation and installation of the
library.
Activities other than copying, distribution and modification are not covered by
this License; they are outside its scope. The act of running a program using the
Library is not restricted, and output from such a program is covered only if its
contents constitute a work based on the Library (independent of the use of the
Library in a tool for writing it). Whether that is true depends on what the
Library does and what the program that uses the Library does.
1. You may copy and distribute verbatim copies of the Library's complete source
code as you receive it, in any medium, provided that you conspicuously and
appropriately publish on each copy an appropriate copyright notice and
disclaimer of warranty; keep intact all the notices that refer to this License
and to the absence of any warranty; and distribute a copy of this License along
with the Library.
You may charge a fee for the physical act of transferring a copy, and you may at
your option offer warranty protection in exchange for a fee.
2. You may modify your copy or copies of the Library or any portion of it, thus
forming a work based on the Library, and copy and distribute such modifications
or work under the terms of Section 1 above, provided that you also meet all of
these conditions:
a) The modified work must itself be a software library.
b) You must cause the files modified to carry prominent notices stating that you
changed the files and the date of any change.
c) You must cause the whole of the work to be licensed at no charge to all third
parties under the terms of this License.
d) If a facility in the modified Library refers to a function or a table of data
to be supplied by an application program that uses the facility, other than as
an argument passed when the facility is invoked, then you must make a good faith
effort to ensure that, in the event an application does not supply such function
or table, the facility still operates, and performs whatever part of its
purpose remains meaningful.
(For example, a function in a library to compute square roots has a purpose that
is entirely well-defined independent of the application. Therefore, Subsection
2d requires that any application-supplied function or table used by this
function must be optional: if the application does not supply it, the square
root function must still compute square roots.)
These requirements apply to the modified work as a whole. If identifiable
sections of that work are not derived from the Library, and can be reasonably
considered independent and separate works in themselves, then this License, and
its terms, do not apply to those sections when you distribute them as separate
works. But when you distribute the same sections as part of a whole which is a
work based on the Library, the distribution of the whole must be on the terms of
this License, whose permissions for other licensees extend to the entire whole,
and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest your
rights to work written entirely by you; rather, the intent is to exercise the
right to control the distribution of derivative or collective works based on the
Library.
In addition, mere aggregation of another work not based on the Library with the
Library (or with a work based on the Library) on a volume of a storage or
distribution medium does not bring the other work under the scope of this
License.
3. You may opt to apply the terms of the ordinary GNU General Public License
instead of this License to a given copy of the Library. To do this, you must
alter all the notices that refer to this License, so that they refer to the
ordinary GNU General Public License, version 2, instead of to this License. (If
a newer version than version 2 of the ordinary GNU General Public License has
appeared, then you can specify that version instead if you wish.) Do not make
any other change in these notices.
Once this change is made in a given copy, it is irreversible for that copy, so
the ordinary GNU General Public License applies to all subsequent copies and
derivative works made from that copy.
This option is useful when you wish to copy part of the code of the Library into
a program that is not a library.
4. You may copy and distribute the Library (or a portion or derivative of it,
under Section 2) in object code or executable form under the terms of Sections 1
and 2 above provided that you accompany it with the complete corresponding
machine-readable source code, which must be distributed under the terms of
Sections 1 and 2 above on a medium customarily used for software interchange.
If distribution of object code is made by offering access to copy from a
designated place, then offering equivalent access to copy the source code from
the same place satisfies the requirement to distribute the source code, even
though third parties are not compelled to copy the source along with the object
code.
5. A program that contains no derivative of any portion of the Library, but is
designed to work with the Library by being compiled or linked with it, is called
a "work that uses the Library". Such a work, in isolation, is not a derivative
work of the Library, and therefore falls outside the scope of this License.
However, linking a "work that uses the Library" with the Library creates an
executable that is a derivative of the Library (because it contains portions of
the Library), rather than a "work that uses the library". The executable is
therefore covered by this License. Section 6 states terms for distribution of
such executables.
When a "work that uses the Library" uses material from a header file that is
part of the Library, the object code for the work may be a derivative work of
the Library even though the source code is not. Whether this is true is
especially significant if the work can be linked without the Library, or if the
work is itself a library. The threshold for this to be true is not precisely
defined by law.
If such an object file uses only numerical parameters, data structure layouts
and accessors, and small macros and small inline functions (ten lines or less in
length), then the use of the object file is unrestricted, regardless of whether
it is legally a derivative work. (Executables containing this object code plus
portions of the Library will still fall under Section 6.)
Otherwise, if the work is a derivative of the Library, you may distribute the
object code for the work under the terms of Section 6. Any executables
containing that work also fall under Section 6, whether or not they are linked
directly with the Library itself.
6. As an exception to the Sections above, you may also combine or link a "work
that uses the Library" with the Library to produce a work containing portions of
the Library, and distribute that work under terms of your choice, provided that
the terms permit modification of the work for the customer's own use and reverse
engineering for debugging such modifications.
You must give prominent notice with each copy of the work that the Library is
used in it and that the Library and its use are covered by this License. You
must supply a copy of this License. If the work during execution displays
copyright notices, you must include the copyright notice for the Library among
them, as well as a reference directing the user to the copy of this License.
Also, you must do one of these things:
a) Accompany the work with the complete corresponding machine-readable source
code for the Library including whatever changes were used in the work (which
must be distributed under Sections 1 and 2 above); and, if the work is an
executable linked with the Library, with the complete machine-readable "work
that uses the Library", as object code and/or source code, so that the user can
modify the Library and then relink to produce a modified executable containing
the modified Library. (It is understood that the user who changes the contents
of definitions files in the Library will not necessarily be able to recompile
the application to use the modified definitions.)
b) Use a suitable shared library mechanism for linking with the Library. A
suitable mechanism is one that (1) uses at run time a copy of the library
already present on the user's computer system, rather than copying library
functions into the executable, and (2) will operate properly with a modified
version of the library, if the user installs one, as long as the modified
version is interface-compatible with the version that the work was made with.
c) Accompany the work with a written offer, valid for at least three years, to
give the same user the materials specified in Subsection 6a, above, for a charge
no more than the cost of performing this distribution.
d) If distribution of the work is made by offering access to copy from a
designated place, offer equivalent access to copy the above specified materials
from the same place.
e) Verify that the user has already received a copy of these materials or that
you have already sent this user a copy.
For an executable, the required form of the "work that uses the Library" must
include any data and utility programs needed for reproducing the executable from
it. However, as a special exception, the materials to be distributed need not
include anything that is normally distributed (in either source or binary form)
with the major components (compiler, kernel, and so on) of the operating system
on which the executable runs, unless that component itself accompanies the
executable.
It may happen that this requirement contradicts the license restrictions of
other proprietary libraries that do not normally accompany the operating system.
Such a contradiction means you cannot use both them and the Library together in
an executable that you distribute.
7. You may place library facilities that are a work based on the Library
side-by-side in a single library together with other library facilities not
covered by this License, and distribute such a combined library, provided that
the separate distribution of the work based on the Library and of the other
library facilities is otherwise permitted, and provided that you do these two
things:
a) Accompany the combined library with a copy of the same work based on the
Library, uncombined with any other library facilities. This must be distributed
under the terms of the Sections above.
b) Give prominent notice with the combined library of the fact that part of it
is a work based on the Library, and explaining where to find the accompanying
uncombined form of the same work.
8. You may not copy, modify, sublicense, link with, or distribute the Library
except as expressly provided under this License. Any attempt otherwise to copy,
modify, sublicense, link with, or distribute the Library is void, and will
automatically terminate your rights under this License. However, parties who
have received copies, or rights, from you under this License will not have their
licenses terminated so long as such parties remain in full compliance.
9. You are not required to accept this License, since you have not signed it.
However, nothing else grants you permission to modify or distribute the Library
or its derivative works. These actions are prohibited by law if you do not
accept this License. Therefore, by modifying or distributing the Library (or any
work based on the Library), you indicate your acceptance of this License to do
so, and all its terms and conditions for copying, distributing or modifying the
Library or works based on it.
10. Each time you redistribute the Library (or any work based on the Library),
the recipient automatically receives a license from the original licensor to
copy, distribute, link with or modify the Library subject to these terms and
conditions. You may not impose any further restrictions on the recipients'
exercise of the rights granted herein. You are not responsible for enforcing
compliance by third parties with this License.
11. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues), 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 distribute so as to satisfy
simultaneously your obligations under this License and any other pertinent
obligations, then as a consequence you may not distribute the Library at all.
For example, if a patent license would not permit royalty-free redistribution
of the Library by all those who receive copies directly or indirectly through
you, then the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Library.
If any portion of this section is held invalid or unenforceable under any
particular circumstance, the balance of the section is intended to apply, and
the section as a whole is intended to apply in other circumstances.
It is not the purpose of this section to induce you to infringe any patents or
other property right claims or to contest validity of any such claims; this
section has the sole purpose of protecting the integrity of the free software
distribution system which is implemented by public license practices. Many
people have made generous contributions to the wide range of software
distributed through that system in reliance on consistent application of that
system; it is up to the author/donor to decide if he or she is willing to
distribute software through any other system and a licensee cannot impose that
choice.
This section is intended to make thoroughly clear what is believed to be a
consequence of the rest of this License.
12. If the distribution and/or use of the Library is restricted in certain
countries either by patents or by copyrighted interfaces, the original copyright
holder who places the Library under this License may add an explicit
geographical distribution limitation excluding those countries, so that
distribution is permitted only in or among countries not thus excluded. In such
case, this License incorporates the limitation as if written in the body of this
License.
13. The Free Software Foundation may publish revised and/or new versions of the
Lesser 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 Library specifies
a version number of this License which applies to it and "any later version",
you have the option of following the terms and conditions either of that version
or of any later version published by the Free Software Foundation. If the
Library does not specify a license version number, you may choose any version
ever published by the Free Software Foundation.
14. If you wish to incorporate parts of the Library into other free programs
whose distribution conditions are incompatible with these, write to the author
to ask for permission. For software which is copyrighted by the Free Software
Foundation, write to the Free Software Foundation; we sometimes make exceptions
for this. Our decision will be guided by the two goals of preserving the free
status of all derivatives of our free software and of promoting the sharing and
reuse of software generally.
NO WARRANTY
15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE
LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED
IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE LIBRARY "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
LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
LIBRARY 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 LIBRARY (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 LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER
OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS