InterMine 4.1.3 release

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InterMine 4.1.3 release

Daniela Butano-2
Dear all,
We have released InterMine 4.1.3 which contains a small batch of bug
fixes:

* deleting a template doesn't leave the template in the Templates page
anymore,
* public template creation works properly,
* the service/web-properties returns a valid response,
* in the report page, the links to HumanMine/FlyMine are displayed.

This is a non-disruptive release.
Read here
(https://github.com/intermine/intermine/releases/tag/intermine-4.1.3)
for detailed information.

InterMine Team
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Re: InterMine 4.1.3 release

Pengcheng Yang

Hi,

The links to HumanMine work quite well now, but the links to FlyMine still not work. Please take a look at the following two examples:

In page [1], the links to HumanMine work well, but the link to FlyMine do not work, although there is homologue using FBgn0029888 as primaryIdentifier.

In page 3  is linked from FlyMine page [2], but the reverse doesn't work. But there is indeed three fly homologues, which can be found in the Homologues section in the page [3]

[1] http://insectmine.org:8080/fawmine/gene:SFR01273

[2] https://www.flymine.org/flymine/gene:FBgn0005558

[3] https://www.humanmine.org/humanmine/portal.do?externalids=5078&class=Gene&origin=FlyMine

Thank you and best,

Pengcheng Yang

On 2020-3-10 20:03, [hidden email] wrote:
Dear all,
We have released InterMine 4.1.3 which contains a small batch of bug fixes:

* deleting a template doesn't leave the template in the Templates page anymore,
* public template creation works properly,
* the service/web-properties returns a valid response,
* in the report page, the links to HumanMine/FlyMine are displayed.

This is a non-disruptive release.
Read here (https://github.com/intermine/intermine/releases/tag/intermine-4.1.3) for detailed information.

InterMine Team
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[hidden email]
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External links

Daniela Butano-2
Hi Pengcheng,

you are right.
On HumanMine, the report page for the gene PAX4  doesn't display the 3
links to FlyMine for the genes FBgn0005558, FBgn0005561,
FBgn0019650...but it should, at least from my understanding.
Rachel, Sergio what do you think? Could you please have a look on it?

Pengcheng, just to clarified, the issue releated to external links
(toward FlyMine nd HumanMIne) which has been fixed in the latest
InterMine release, was releated to the wrong configuration (http intead
of https)

Best wishes,
Danielae

> Hi,
>
> The links to HumanMine work quite well now, but the links to FlyMine
> still not work. Please take a look at the following two examples:
>
> In page [1], the links to HumanMine work well, but the link to FlyMine
> do not work, although there is homologue using _FBgn0029888_ as
> primaryIdentifier.
>
> In page 3  is linked from FlyMine page [2], but the reverse doesn't
> work. But there is indeed three fly homologues, which can be found in
> the Homologues section in the page [3]
>
> [1] http://insectmine.org:8080/fawmine/gene:SFR01273
>
> [2] https://www.flymine.org/flymine/gene:FBgn0005558
>
> [3]
> https://www.humanmine.org/humanmine/portal.do?externalids=5078&class=Gene&origin=FlyMine
>
>
> Thank you and best,
>
> Pengcheng Yang
> On 2020-3-10 20:03, [hidden email] wrote:
>
>> Dear all,
>> We have released InterMine 4.1.3 which contains a small batch of bug
>> fixes:
>>
>> * deleting a template doesn't leave the template in the Templates
>> page anymore,
>> * public template creation works properly,
>> * the service/web-properties returns a valid response,
>> * in the report page, the links to HumanMine/FlyMine are displayed.
>>
>> This is a non-disruptive release.
>> Read here
>>
> (https://github.com/intermine/intermine/releases/tag/intermine-4.1.3)
>> for detailed information.
>>
>> InterMine Team
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: External links

sergio contrino-2
i think it is because we have released the patch for flymine, but not
for humanmine.
if urgent i could do a test in beta, i was waiting for the new set up
but we can use the current one.
if not too pressing i would happily wait for after 20/3 (isa meeting).
thanks
sergio

On 12/03/2020 16:15, [hidden email] wrote:

> Hi Pengcheng,
>
> you are right.
> On HumanMine, the report page for the gene PAX4  doesn't display the 3
> links to FlyMine for the genes FBgn0005558, FBgn0005561,
> FBgn0019650...but it should, at least from my understanding.
> Rachel, Sergio what do you think? Could you please have a look on it?
>
> Pengcheng, just to clarified, the issue releated to external links
> (toward FlyMine nd HumanMIne) which has been fixed in the latest
> InterMine release, was releated to the wrong configuration (http intead
> of https)
>
> Best wishes,
> Danielae
>
>> Hi,
>>
>> The links to HumanMine work quite well now, but the links to FlyMine
>> still not work. Please take a look at the following two examples:
>>
>> In page [1], the links to HumanMine work well, but the link to FlyMine
>> do not work, although there is homologue using _FBgn0029888_ as
>> primaryIdentifier.
>>
>> In page 3  is linked from FlyMine page [2], but the reverse doesn't
>> work. But there is indeed three fly homologues, which can be found in
>> the Homologues section in the page [3]
>>
>> [1] http://insectmine.org:8080/fawmine/gene:SFR01273
>>
>> [2] https://www.flymine.org/flymine/gene:FBgn0005558
>>
>> [3]
>> https://www.humanmine.org/humanmine/portal.do?externalids=5078&class=Gene&origin=FlyMine 
>>
>>
>>
>> Thank you and best,
>>
>> Pengcheng Yang
>> On 2020-3-10 20:03, [hidden email] wrote:
>>
>>> Dear all,
>>> We have released InterMine 4.1.3 which contains a small batch of bug
>>> fixes:
>>>
>>> * deleting a template doesn't leave the template in the Templates
>>> page anymore,
>>> * public template creation works properly,
>>> * the service/web-properties returns a valid response,
>>> * in the report page, the links to HumanMine/FlyMine are displayed.
>>>
>>> This is a non-disruptive release.
>>> Read here
>>>
>> (https://github.com/intermine/intermine/releases/tag/intermine-4.1.3)
>>> for detailed information.
>>>
>>> InterMine Team
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: External links

Daniela Butano-2
You are right Sergio. This explain why HumanMine report page doesn't
show the links.
But still doesn't explain why
http://insectmine.org:8080/fawmine/gene:SFR01273 (which has the
homologue FBgn0029888) do not display the link to flymine.
fawmine has just been updated to InterMine 4.1.3

Any ideas?
Thanks

> i think it is because we have released the patch for flymine, but not
> for humanmine.
> if urgent i could do a test in beta, i was waiting for the new set up
> but we can use the current one.
> if not too pressing i would happily wait for after 20/3 (isa meeting).
> thanks
> sergio
>
> On 12/03/2020 16:15, [hidden email] wrote:
>> Hi Pengcheng,
>>
>> you are right.
>> On HumanMine, the report page for the gene PAX4  doesn't display the 3
>> links to FlyMine for the genes FBgn0005558, FBgn0005561,
>> FBgn0019650...but it should, at least from my understanding.
>> Rachel, Sergio what do you think? Could you please have a look on it?
>>
>> Pengcheng, just to clarified, the issue releated to external links
>> (toward FlyMine nd HumanMIne) which has been fixed in the latest
>> InterMine release, was releated to the wrong configuration (http
>> intead of https)
>>
>> Best wishes,
>> Danielae
>>
>>> Hi,
>>>
>>> The links to HumanMine work quite well now, but the links to FlyMine
>>> still not work. Please take a look at the following two examples:
>>>
>>> In page [1], the links to HumanMine work well, but the link to
>>> FlyMine
>>> do not work, although there is homologue using _FBgn0029888_ as
>>> primaryIdentifier.
>>>
>>> In page 3  is linked from FlyMine page [2], but the reverse doesn't
>>> work. But there is indeed three fly homologues, which can be found in
>>> the Homologues section in the page [3]
>>>
>>> [1] http://insectmine.org:8080/fawmine/gene:SFR01273
>>>
>>> [2] https://www.flymine.org/flymine/gene:FBgn0005558
>>>
>>> [3]
>>> https://www.humanmine.org/humanmine/portal.do?externalids=5078&class=Gene&origin=FlyMine 
>>> Thank you and best,
>>>
>>> Pengcheng Yang
>>> On 2020-3-10 20:03, [hidden email] wrote:
>>>
>>>> Dear all,
>>>> We have released InterMine 4.1.3 which contains a small batch of bug
>>>> fixes:
>>>>
>>>> * deleting a template doesn't leave the template in the Templates
>>>> page anymore,
>>>> * public template creation works properly,
>>>> * the service/web-properties returns a valid response,
>>>> * in the report page, the links to HumanMine/FlyMine are displayed.
>>>>
>>>> This is a non-disruptive release.
>>>> Read here
>>>>
>>> (https://github.com/intermine/intermine/releases/tag/intermine-4.1.3)
>>>> for detailed information.
>>>>
>>>> InterMine Team
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>

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Re: External links

sergio contrino-2
maybe i am not right then.. what does the fix do?

i can see it displays homologue in human (?!)
https://www.humanmine.org/humanmine/portal.do?externalids=4714&class=Gene&origin=FAWMine
and that also this has no flymine link (as expected?).
thanks
sergio


On 12/03/2020 18:24, [hidden email] wrote:

> You are right Sergio. This explain why HumanMine report page doesn't
> show the links.
> But still doesn't explain why
> http://insectmine.org:8080/fawmine/gene:SFR01273 (which has the
> homologue FBgn0029888) do not display the link to flymine.
> fawmine has just been updated to InterMine 4.1.3
>
> Any ideas?
> Thanks
>
>> i think it is because we have released the patch for flymine, but not
>> for humanmine.
>> if urgent i could do a test in beta, i was waiting for the new set up
>> but we can use the current one.
>> if not too pressing i would happily wait for after 20/3 (isa meeting).
>> thanks
>> sergio
>>
>> On 12/03/2020 16:15, [hidden email] wrote:
>>> Hi Pengcheng,
>>>
>>> you are right.
>>> On HumanMine, the report page for the gene PAX4  doesn't display the
>>> 3 links to FlyMine for the genes FBgn0005558, FBgn0005561,
>>> FBgn0019650...but it should, at least from my understanding.
>>> Rachel, Sergio what do you think? Could you please have a look on it?
>>>
>>> Pengcheng, just to clarified, the issue releated to external links
>>> (toward FlyMine nd HumanMIne) which has been fixed in the latest
>>> InterMine release, was releated to the wrong configuration (http
>>> intead of https)
>>>
>>> Best wishes,
>>> Danielae
>>>
>>>> Hi,
>>>>
>>>> The links to HumanMine work quite well now, but the links to FlyMine
>>>> still not work. Please take a look at the following two examples:
>>>>
>>>> In page [1], the links to HumanMine work well, but the link to FlyMine
>>>> do not work, although there is homologue using _FBgn0029888_ as
>>>> primaryIdentifier.
>>>>
>>>> In page 3  is linked from FlyMine page [2], but the reverse doesn't
>>>> work. But there is indeed three fly homologues, which can be found in
>>>> the Homologues section in the page [3]
>>>>
>>>> [1] http://insectmine.org:8080/fawmine/gene:SFR01273
>>>>
>>>> [2] https://www.flymine.org/flymine/gene:FBgn0005558
>>>>
>>>> [3]
>>>> https://www.humanmine.org/humanmine/portal.do?externalids=5078&class=Gene&origin=FlyMine 
>>>> Thank you and best,
>>>>
>>>> Pengcheng Yang
>>>> On 2020-3-10 20:03, [hidden email] wrote:
>>>>
>>>>> Dear all,
>>>>> We have released InterMine 4.1.3 which contains a small batch of bug
>>>>> fixes:
>>>>>
>>>>> * deleting a template doesn't leave the template in the Templates
>>>>> page anymore,
>>>>> * public template creation works properly,
>>>>> * the service/web-properties returns a valid response,
>>>>> * in the report page, the links to HumanMine/FlyMine are displayed.
>>>>>
>>>>> This is a non-disruptive release.
>>>>> Read here
>>>>>
>>>> (https://github.com/intermine/intermine/releases/tag/intermine-4.1.3)
>>>>> for detailed information.
>>>>>
>>>>> InterMine Team
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: External links

Daniela Butano-2
In the global.web.properties file we store the link to the friendly
mines (which include HumanMine and FlyMine).
Those where broken(they pointed to http instead of https) and have been
fixed with 4.1.3
fawmine has been redeplyed using 4.1.3, so the report page should show
the links to HumanMine and FlyMine (if there are of course some
homologues)
For the gene SFR01273 in fawmine, there is an homologue for Homo sapiens
(the link to HumanMine is displayed) and there  is an homologue for
Drosophila (the link to FlyMIne is not dispalyed)



> maybe i am not right then.. what does the fix do?
>
> i can see it displays homologue in human (?!)
> https://www.humanmine.org/humanmine/portal.do?externalids=4714&class=Gene&origin=FAWMine
> and that also this has no flymine link (as expected?).
> thanks
> sergio
>
>
> On 12/03/2020 18:24, [hidden email] wrote:
>> You are right Sergio. This explain why HumanMine report page doesn't
>> show the links.
>> But still doesn't explain why
>> http://insectmine.org:8080/fawmine/gene:SFR01273 (which has the
>> homologue FBgn0029888) do not display the link to flymine.
>> fawmine has just been updated to InterMine 4.1.3
>>
>> Any ideas?
>> Thanks
>>
>>> i think it is because we have released the patch for flymine, but not
>>> for humanmine.
>>> if urgent i could do a test in beta, i was waiting for the new set up
>>> but we can use the current one.
>>> if not too pressing i would happily wait for after 20/3 (isa
>>> meeting).
>>> thanks
>>> sergio
>>>
>>> On 12/03/2020 16:15, [hidden email] wrote:
>>>> Hi Pengcheng,
>>>>
>>>> you are right.
>>>> On HumanMine, the report page for the gene PAX4  doesn't display the
>>>> 3 links to FlyMine for the genes FBgn0005558, FBgn0005561,
>>>> FBgn0019650...but it should, at least from my understanding.
>>>> Rachel, Sergio what do you think? Could you please have a look on
>>>> it?
>>>>
>>>> Pengcheng, just to clarified, the issue releated to external links
>>>> (toward FlyMine nd HumanMIne) which has been fixed in the latest
>>>> InterMine release, was releated to the wrong configuration (http
>>>> intead of https)
>>>>
>>>> Best wishes,
>>>> Danielae
>>>>
>>>>> Hi,
>>>>>
>>>>> The links to HumanMine work quite well now, but the links to
>>>>> FlyMine
>>>>> still not work. Please take a look at the following two examples:
>>>>>
>>>>> In page [1], the links to HumanMine work well, but the link to
>>>>> FlyMine
>>>>> do not work, although there is homologue using _FBgn0029888_ as
>>>>> primaryIdentifier.
>>>>>
>>>>> In page 3  is linked from FlyMine page [2], but the reverse doesn't
>>>>> work. But there is indeed three fly homologues, which can be found
>>>>> in
>>>>> the Homologues section in the page [3]
>>>>>
>>>>> [1] http://insectmine.org:8080/fawmine/gene:SFR01273
>>>>>
>>>>> [2] https://www.flymine.org/flymine/gene:FBgn0005558
>>>>>
>>>>> [3]
>>>>> https://www.humanmine.org/humanmine/portal.do?externalids=5078&class=Gene&origin=FlyMine 
>>>>> Thank you and best,
>>>>>
>>>>> Pengcheng Yang
>>>>> On 2020-3-10 20:03, [hidden email] wrote:
>>>>>
>>>>>> Dear all,
>>>>>> We have released InterMine 4.1.3 which contains a small batch of
>>>>>> bug
>>>>>> fixes:
>>>>>>
>>>>>> * deleting a template doesn't leave the template in the Templates
>>>>>> page anymore,
>>>>>> * public template creation works properly,
>>>>>> * the service/web-properties returns a valid response,
>>>>>> * in the report page, the links to HumanMine/FlyMine are
>>>>>> displayed.
>>>>>>
>>>>>> This is a non-disruptive release.
>>>>>> Read here
>>>>>>
>>>>> (https://github.com/intermine/intermine/releases/tag/intermine-4.1.3)
>>>>>> for detailed information.
>>>>>>
>>>>>> InterMine Team
>>>>>> _______________________________________________
>>>>>> dev mailing list
>>>>>> [hidden email]
>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>
>>

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