Where to look for a report page NullPointerException?

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Where to look for a report page NullPointerException?

Sam Hokin-3
I've been beating my head over this subtle NullPointerException that occurs on my Publication report page for the entities table. As
far as I can tell, all the entities associated with this Publication are fine, and a Query Builder query on the Publication that
shows the entities works fine. All they need to be is Annotatable, which they extend.

Any thoughts? I'm throwing diagnostic output into report.jsp to no avail. Nothing shows up on tomcat status or the localhost log.
The browser inspector reveals nothing.


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Screenshot_2020-07-02 SoyMine Publication Genome-wide association study, genomic prediction and marker-assisted selection f[...](1).png (230K) Download Attachment
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Re: Where to look for a report page NullPointerException?

Daniela Butano-2
Hi Sam,
I am not able to reproduce it.
I have tried several publication report pages and they works
I have tried the "QTL : Canopy wilt 2-1 G. max" report page and then
clicked on the publication associated to it and it works.
Have I misunderstood the problem?
Daniela

> I've been beating my head over this subtle NullPointerException that
> occurs on my Publication report page for the entities table. As far as
> I can tell, all the entities associated with this Publication are
> fine, and a Query Builder query on the Publication that shows the
> entities works fine. All they need to be is Annotatable, which they
> extend.
>
> Any thoughts? I'm throwing diagnostic output into report.jsp to no
> avail. Nothing shows up on tomcat status or the localhost log. The
> browser inspector reveals nothing.
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: Where to look for a report page NullPointerException?

Daniela Butano-2
In any case if you clinck on "Send an email" you should see the
exception

> Hi Sam,
> I am not able to reproduce it.
> I have tried several publication report pages and they works
> I have tried the "QTL : Canopy wilt 2-1 G. max" report page and then
> clicked on the publication associated to it and it works.
> Have I misunderstood the problem?
> Daniela
>> I've been beating my head over this subtle NullPointerException that
>> occurs on my Publication report page for the entities table. As far as
>> I can tell, all the entities associated with this Publication are
>> fine, and a Query Builder query on the Publication that shows the
>> entities works fine. All they need to be is Annotatable, which they
>> extend.
>>
>> Any thoughts? I'm throwing diagnostic output into report.jsp to no
>> avail. Nothing shows up on tomcat status or the localhost log. The
>> browser inspector reveals nothing.
>>
>>
>> _______________________________________________
>> 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: Where to look for a report page NullPointerException?

Sam Hokin-3
Yeah it just reports the NullPointerException with no context. This is on the dev server, not the production SoyMine. Here's the page:

https://dev.mines.lis.ncgr.org/soymine/report.do?id=7000041

I've got a new data model and it's breaking Publication reports somehow.

On 7/2/20 9:54 AM, [hidden email] wrote:
> In any case if you clinck on "Send an email" you should see the exception
>> Hi Sam, I am not able to reproduce it. I have tried several publication report pages and they works I have tried the "QTL :
>> Canopy wilt 2-1 G. max" report page and then clicked on the publication associated to it and it works. Have I misunderstood the
>> problem? Daniela
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Re: Where to look for a report page NullPointerException?

Daniela Butano-2
I will have a look tomorrow Sam
 From Inspect Element -> COnsole I see some javascript errors...not sure
if this might be the cause...
Yo, Kevin, what do you think?
Daniela

> Yeah it just reports the NullPointerException with no context. This is
> on the dev server, not the production SoyMine. Here's the page:
>
> https://dev.mines.lis.ncgr.org/soymine/report.do?id=7000041
>
> I've got a new data model and it's breaking Publication reports
> somehow.
>
> On 7/2/20 9:54 AM, [hidden email] wrote:
>> In any case if you clinck on "Send an email" you should see the
>> exception
>>> Hi Sam, I am not able to reproduce it. I have tried several
>>> publication report pages and they works I have tried the "QTL :
>>> Canopy wilt 2-1 G. max" report page and then clicked on the
>>> publication associated to it and it works. Have I misunderstood the
>>> problem? Daniela

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Re: Where to look for a report page NullPointerException?

Yo Yehudi-2
the JS errors look like symptoms of the the nullpointer to me - for example "Uncaught ReferenceError: $SERVICE is not defined" - $SERVICE should be a variable for the url to the mine, for the JS to use - so presumably the mine is erroring before it can output relevant variables

(a healthy $SERVICE variable from flymine shown below, don't steal my token).

image.png


On Thu, 2 Jul 2020 at 18:12, <[hidden email]> wrote:
I will have a look tomorrow Sam
 From Inspect Element -> COnsole I see some javascript errors...not sure
if this might be the cause...
Yo, Kevin, what do you think?
Daniela

> Yeah it just reports the NullPointerException with no context. This is
> on the dev server, not the production SoyMine. Here's the page:
>
> https://dev.mines.lis.ncgr.org/soymine/report.do?id=7000041
>
> I've got a new data model and it's breaking Publication reports
> somehow.
>
> On 7/2/20 9:54 AM, [hidden email] wrote:
>> In any case if you clinck on "Send an email" you should see the
>> exception
>>> Hi Sam, I am not able to reproduce it. I have tried several
>>> publication report pages and they works I have tried the "QTL :
>>> Canopy wilt 2-1 G. max" report page and then clicked on the
>>> publication associated to it and it works. Have I misunderstood the
>>> problem? Daniela

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Re: Where to look for a report page NullPointerException?

sergio contrino-2
In reply to this post by Sam Hokin-3
hi sam,
i suppose you did a clean before redeploying (needed in case of a change
of model).
i like your partial report of the stacktrace in your screenshot, but i
cannot see it on the live instance you pointed at.
thanks
sergio

On 2020-07-02 17:34, Sam Hokin wrote:

> Yeah it just reports the NullPointerException with no context. This is
> on the dev server, not the production SoyMine. Here's the page:
>
> https://dev.mines.lis.ncgr.org/soymine/report.do?id=7000041
>
> I've got a new data model and it's breaking Publication reports
> somehow.
>
> On 7/2/20 9:54 AM, [hidden email] wrote:
>> In any case if you clinck on "Send an email" you should see the
>> exception
>>> Hi Sam, I am not able to reproduce it. I have tried several
>>> publication report pages and they works I have tried the "QTL :
>>> Canopy wilt 2-1 G. max" report page and then clicked on the
>>> publication associated to it and it works. Have I misunderstood the
>>> problem? Daniela
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: Where to look for a report page NullPointerException?

Sam Hokin-3
There is no stacktrace. All there is is the NullPointerException. I'd love to have a stacktrace!

On 7/3/20 1:15 AM, [hidden email] wrote:
> hi sam,
> i suppose you did a clean before redeploying (needed in case of a change of model).
> i like your partial report of the stacktrace in your screenshot, but i cannot see it on the live instance you pointed at.
> thanks
> sergio
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Re: Where to look for a report page NullPointerException?

Daniela Butano-2
Sam,
did you solve the issue?
Have you tried what Sergio suggested? (run the task clean before
cargoRedeployRemote)
Daniela

> There is no stacktrace. All there is is the NullPointerException. I'd
> love to have a stacktrace!
>
> On 7/3/20 1:15 AM, [hidden email] wrote:
>> hi sam,
>> i suppose you did a clean before redeploying (needed in case of a
>> change of model).
>> i like your partial report of the stacktrace in your screenshot, but i
>> cannot see it on the live instance you pointed at.
>> thanks
>> sergio

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Re: Where to look for a report page NullPointerException?

Sam Hokin-3
In reply to this post by Sam Hokin-3
Oh, yeah, I did those things many times, along with other black magic and debug output. Still haven't solved it. It could be I've
revealed a really subtle bug, dunno, I'll find it eventually. I'll have to hack report.jsp and *gasp* maybe some javascript to find
it, methinks. It's an uninformative NullPointerException that is getting caught without any indication of where it occurred, so I
have to _not_ catch it so I can get a stacktrace in the Tomcat log. :)

On 7/6/20 7:41 AM, [hidden email] wrote:

> Sam,
> did you solve the issue?
> Have you tried what Sergio suggested? (run the task clean before cargoRedeployRemote)
> Daniela
>
>> There is no stacktrace. All there is is the NullPointerException. I'd
>> love to have a stacktrace!
>>
>> On 7/3/20 1:15 AM, [hidden email] wrote:
>>> hi sam,
>>> i suppose you did a clean before redeploying (needed in case of a change of model).
>>> i like your partial report of the stacktrace in your screenshot, but i cannot see it on the live instance you pointed at.
>>> thanks
>>> sergio
>
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Re: Where to look for a report page NullPointerException?

Yo Yehudi-2
I'm reasonably confident the error is in the java and not the JS, so I'm pretty skeptical that adding JS debug would give you any useful information based on the errors in the js console :) I'm curious though - what happens when you run a web service query against this object? does it return anything?

On Mon, 6 Jul 2020 at 15:29, Sam Hokin <[hidden email]> wrote:
Oh, yeah, I did those things many times, along with other black magic and debug output. Still haven't solved it. It could be I've
revealed a really subtle bug, dunno, I'll find it eventually. I'll have to hack report.jsp and *gasp* maybe some javascript to find
it, methinks. It's an uninformative NullPointerException that is getting caught without any indication of where it occurred, so I
have to _not_ catch it so I can get a stacktrace in the Tomcat log. :)

On 7/6/20 7:41 AM, [hidden email] wrote:
> Sam,
> did you solve the issue?
> Have you tried what Sergio suggested? (run the task clean before cargoRedeployRemote)
> Daniela
>
>> There is no stacktrace. All there is is the NullPointerException. I'd
>> love to have a stacktrace!
>>
>> On 7/3/20 1:15 AM, [hidden email] wrote:
>>> hi sam,
>>> i suppose you did a clean before redeploying (needed in case of a change of model).
>>> i like your partial report of the stacktrace in your screenshot, but i cannot see it on the live instance you pointed at.
>>> thanks
>>> sergio
>
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Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs

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Re: Where to look for a report page NullPointerException?

Sam Hokin-3
In reply to this post by Daniela Butano-2
So I finally was able to track this down, with getting the stacktrace. The problem was that
intermine/api/src/main/resources/uri_keys.properties lists Publication_URI = pubMedId. But many of my publications do not have a
pubMedId. The crash occurred in intermine/webapp/src/main/java/org/intermine/web/uri/InterMineLUI.java here:

     public String toString() {
         try {
             String encodedIdentifier = URLEncoder.encode(identifier, "UTF-8");
             // The URLEncoder class is based on RFC 2396, and there are few differences
             // between the unreserved characters in case of RFC 2396 and RFC 3986
             encodedIdentifier = encodedIdentifier.replaceAll("%3A", ":")
                     .replaceAll("\\+", "%20");
             return className.toLowerCase() + LOCAL_ID_SEPARATOR + encodedIdentifier;
         } catch (UnsupportedEncodingException ex) {
             return className.toLowerCase() + LOCAL_ID_SEPARATOR + identifier;
         }
     }

The try block catches an UnsupportedEncodingException but it does NOT catch a NullPointerException when identifier==null, which it
does if the object's attribute listed in uri_keys.properties is missing.

There are a number of ways do handle this, but I'll leave it to Daniela or let her task me with it. Ideally we would get an error
message on the report saying something like "Yo, you need to update your mine's class_keys.properties FooBar_URI entry because the
current one is null!"

On 7/2/20 9:51 AM, [hidden email] wrote:

> Hi Sam,
> I am not able to reproduce it.
> I have tried several publication report pages and they works
> I have tried the "QTL : Canopy wilt 2-1 G. max" report page and then clicked on the publication associated to it and it works.
> Have I misunderstood the problem?
> Daniela
>> I've been beating my head over this subtle NullPointerException that
>> occurs on my Publication report page for the entities table. As far as
>> I can tell, all the entities associated with this Publication are
>> fine, and a Query Builder query on the Publication that shows the
>> entities works fine. All they need to be is Annotatable, which they
>> extend.
>>
>> Any thoughts? I'm throwing diagnostic output into report.jsp to no
>> avail. Nothing shows up on tomcat status or the localhost log. The
>> browser inspector reveals nothing.
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
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Re: Where to look for a report page NullPointerException?

Daniela Butano-2
Ohhh, my fault!!!
Tomorrow I will have a look,
I am not at home right now.
Which version of intermine are you using?
I am asking, because I have slightly changed the share link
mechanism/configuration.
Daniela

On 2020-07-08 17:14, Sam Hokin wrote:

> So I finally was able to track this down, with getting the stacktrace.
> The problem was that
> intermine/api/src/main/resources/uri_keys.properties lists
> Publication_URI = pubMedId. But many of my publications do not have a
> pubMedId. The crash occurred in
> intermine/webapp/src/main/java/org/intermine/web/uri/InterMineLUI.java
> here:
>
>     public String toString() {
>         try {
>             String encodedIdentifier = URLEncoder.encode(identifier,
> "UTF-8");
>             // The URLEncoder class is based on RFC 2396, and there
> are few differences
>             // between the unreserved characters in case of RFC 2396
> and RFC 3986
>             encodedIdentifier = encodedIdentifier.replaceAll("%3A",
> ":")
>                     .replaceAll("\\+", "%20");
>             return className.toLowerCase() + LOCAL_ID_SEPARATOR +
> encodedIdentifier;
>         } catch (UnsupportedEncodingException ex) {
>             return className.toLowerCase() + LOCAL_ID_SEPARATOR +
> identifier;
>         }
>     }
>
> The try block catches an UnsupportedEncodingException but it does NOT
> catch a NullPointerException when identifier==null, which it does if
> the object's attribute listed in uri_keys.properties is missing.
>
> There are a number of ways do handle this, but I'll leave it to
> Daniela or let her task me with it. Ideally we would get an error
> message on the report saying something like "Yo, you need to update
> your mine's class_keys.properties FooBar_URI entry because the current
> one is null!"
>
> On 7/2/20 9:51 AM, [hidden email] wrote:
>> Hi Sam,
>> I am not able to reproduce it.
>> I have tried several publication report pages and they works
>> I have tried the "QTL : Canopy wilt 2-1 G. max" report page and then
>> clicked on the publication associated to it and it works.
>> Have I misunderstood the problem?
>> Daniela
>>> I've been beating my head over this subtle NullPointerException that
>>> occurs on my Publication report page for the entities table. As far
>>> as
>>> I can tell, all the entities associated with this Publication are
>>> fine, and a Query Builder query on the Publication that shows the
>>> entities works fine. All they need to be is Annotatable, which they
>>> extend.
>>>
>>> Any thoughts? I'm throwing diagnostic output into report.jsp to no
>>> avail. Nothing shows up on tomcat status or the localhost log. The
>>> browser inspector reveals nothing.
>>>
>>>
>>> _______________________________________________
>>> 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: Where to look for a report page NullPointerException?

Daniela Butano-2
In reply to this post by Sam Hokin-3
Sam,
I'm going to create a ticket for that.
I was sure that I had tested that use case too, but clarly I didn't!

I have just checked soymine and it seems that you don't have
publications right now.
If the publications in soymine have doi not null, set in the
class_keys.properties of your mine (under dbmodel/resources)  this line
Publication_URI = doi

This overrides the default provided by intermine

Daniela


> So I finally was able to track this down, with getting the stacktrace.
> The problem was that
> intermine/api/src/main/resources/uri_keys.properties lists
> Publication_URI = pubMedId. But many of my publications do not have a
> pubMedId. The crash occurred in
> intermine/webapp/src/main/java/org/intermine/web/uri/InterMineLUI.java
> here:
>
>     public String toString() {
>         try {
>             String encodedIdentifier = URLEncoder.encode(identifier,
> "UTF-8");
>             // The URLEncoder class is based on RFC 2396, and there
> are few differences
>             // between the unreserved characters in case of RFC 2396
> and RFC 3986
>             encodedIdentifier = encodedIdentifier.replaceAll("%3A",
> ":")
>                     .replaceAll("\\+", "%20");
>             return className.toLowerCase() + LOCAL_ID_SEPARATOR +
> encodedIdentifier;
>         } catch (UnsupportedEncodingException ex) {
>             return className.toLowerCase() + LOCAL_ID_SEPARATOR +
> identifier;
>         }
>     }
>
> The try block catches an UnsupportedEncodingException but it does NOT
> catch a NullPointerException when identifier==null, which it does if
> the object's attribute listed in uri_keys.properties is missing.
>
> There are a number of ways do handle this, but I'll leave it to
> Daniela or let her task me with it. Ideally we would get an error
> message on the report saying something like "Yo, you need to update
> your mine's class_keys.properties FooBar_URI entry because the current
> one is null!"
>
> On 7/2/20 9:51 AM, [hidden email] wrote:
>> Hi Sam,
>> I am not able to reproduce it.
>> I have tried several publication report pages and they works
>> I have tried the "QTL : Canopy wilt 2-1 G. max" report page and then
>> clicked on the publication associated to it and it works.
>> Have I misunderstood the problem?
>> Daniela
>>> I've been beating my head over this subtle NullPointerException that
>>> occurs on my Publication report page for the entities table. As far
>>> as
>>> I can tell, all the entities associated with this Publication are
>>> fine, and a Query Builder query on the Publication that shows the
>>> entities works fine. All they need to be is Annotatable, which they
>>> extend.
>>>
>>> Any thoughts? I'm throwing diagnostic output into report.jsp to no
>>> avail. Nothing shows up on tomcat status or the localhost log. The
>>> browser inspector reveals nothing.
>>>
>>>
>>> _______________________________________________
>>> 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: Where to look for a report page NullPointerException?

Sam Hokin-3
Yeah, I'm all set on that. I just didn't know that was the issue until I figured out that that was the issue. SoyMine is a bit odd
in that it has all these weird old papers in weird old breeding journals that aren't carried on PubMed, but of course everything has
a DOI these days.

BTW I have a post-processor that digs out the PMID and DOI from a journal title using a bit of really crude "fuzzy logic". It uses
the PubMed and CrossRef APIs:

https://github.com/legumeinfo/lis-bio-postprocess/tree/master/lis-populate-publications

I'm using 4.2.0 -- I always run the latest greatest on my dev mines. It's certainly a worthwhile fix to handle a null identifier,
but also good to spit out a message since the stable URLs are a thing desired by our faithful users. (All 7 of them!)

On 7/9/20 7:48 AM, [hidden email] wrote:

> Sam,
> I'm going to create a ticket for that.
> I was sure that I had tested that use case too, but clarly I didn't!
>
> I have just checked soymine and it seems that you don't have publications right now.
> If the publications in soymine have doi not null, set in the class_keys.properties of your mine (under dbmodel/resources)  this line
> Publication_URI = doi
>
> This overrides the default provided by intermine
>
> Daniela
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Re: Where to look for a report page NullPointerException?

Daniela Butano-2
In reply to this post by Daniela Butano-2
Hi Sam,
I fixed the issue and created a PR
(https://github.com/intermine/intermine/pull/2281) which I will probably
merge before the next release in September.
I don't do an intermine patch release right now, we think it's not
urgent (you can avoid the npe, udapting the class_keys.properties file).
Thank you for your contribute debuging the code!!!

Daniela

> Sam,
> I'm going to create a ticket for that.
> I was sure that I had tested that use case too, but clarly I didn't!
>
> I have just checked soymine and it seems that you don't have
> publications right now.
> If the publications in soymine have doi not null, set in the
> class_keys.properties of your mine (under dbmodel/resources)  this
> line
> Publication_URI = doi
>
> This overrides the default provided by intermine
>
> Daniela
>
>
>> So I finally was able to track this down, with getting the stacktrace.
>> The problem was that
>> intermine/api/src/main/resources/uri_keys.properties lists
>> Publication_URI = pubMedId. But many of my publications do not have a
>> pubMedId. The crash occurred in
>> intermine/webapp/src/main/java/org/intermine/web/uri/InterMineLUI.java
>> here:
>>
>>     public String toString() {
>>         try {
>>             String encodedIdentifier = URLEncoder.encode(identifier,
>> "UTF-8");
>>             // The URLEncoder class is based on RFC 2396, and there
>> are few differences
>>             // between the unreserved characters in case of RFC 2396
>> and RFC 3986
>>             encodedIdentifier = encodedIdentifier.replaceAll("%3A",
>> ":")
>>                     .replaceAll("\\+", "%20");
>>             return className.toLowerCase() + LOCAL_ID_SEPARATOR +
>> encodedIdentifier;
>>         } catch (UnsupportedEncodingException ex) {
>>             return className.toLowerCase() + LOCAL_ID_SEPARATOR +
>> identifier;
>>         }
>>     }
>>
>> The try block catches an UnsupportedEncodingException but it does NOT
>> catch a NullPointerException when identifier==null, which it does if
>> the object's attribute listed in uri_keys.properties is missing.
>>
>> There are a number of ways do handle this, but I'll leave it to
>> Daniela or let her task me with it. Ideally we would get an error
>> message on the report saying something like "Yo, you need to update
>> your mine's class_keys.properties FooBar_URI entry because the current
>> one is null!"
>>
>> On 7/2/20 9:51 AM, [hidden email] wrote:
>>> Hi Sam,
>>> I am not able to reproduce it.
>>> I have tried several publication report pages and they works
>>> I have tried the "QTL : Canopy wilt 2-1 G. max" report page and then
>>> clicked on the publication associated to it and it works.
>>> Have I misunderstood the problem?
>>> Daniela
>>>> I've been beating my head over this subtle NullPointerException that
>>>> occurs on my Publication report page for the entities table. As far
>>>> as
>>>> I can tell, all the entities associated with this Publication are
>>>> fine, and a Query Builder query on the Publication that shows the
>>>> entities works fine. All they need to be is Annotatable, which they
>>>> extend.
>>>>
>>>> Any thoughts? I'm throwing diagnostic output into report.jsp to no
>>>> avail. Nothing shows up on tomcat status or the localhost log. The
>>>> browser inspector reveals nothing.
>>>>
>>>>
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