CEVOpen
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petermr
Building ami
Can you build ami? from the repository?
https://github.com/ContentMine/cephis.git and https://github.com/petermr/normami.git If so great!
You have to build cephis before normami
On Fri, Aug 30, 2019 at 9:52 AM Ambarish Kumar [email protected] wrote:
Yes sir, I can run maven.
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Sir,
I do not think the cephis web-link has any content (any thing to build). Relevant one is here at https://github.com/petermr/cephis.git.
It is the dev branch on the ContentMine/cephis repo.
Don't know why it didn't show on git remote -v
On Fri, Aug 30, 2019 at 10:28 AM Ambarish Kumar [email protected] wrote:
Sir,
I do not think the cephis web-link https://github.com/ContentMine/cephis.git has any content (any thing to build). Relevant one is here at https://github.com/petermr/cephis.git.
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Sir, build for https://github.com/petermr/cephis.git is almost complete.
Getting the cephis from the dev branch of ContenMine.
Cloning of normami is taking slightly longer time.
On Fri, Aug 30, 2019 at 12:37 PM Ambarish Kumar [email protected] wrote:
Sir, currently build for https://github.com/petermr/cephis.git is almost complete.
Is it running tests?
BTW you are building cephis, not cephis.git (which is the command / hook to clone/download it)
Getting the cephis from the dev branch of ContenMine.
Cloning of normami is taking slightly longer time.
Yes, this worries me. It's bloated and needs cleaning... not quite sure what to do
P.
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Sir, It has skipped tests.
cloning of normami has failed. Please go through the error. Even, I tried to download it's .zip file, but while extracting the file, it reports it as a corrupt one.
I'm not an expert on git. This looks like a timeout because of slow bandwidth. I don't know whether I can make a new leaner build. Suggest you have another attempt. Useful to record datetime so we know how long it takes
On Fri, Aug 30, 2019 at 2:52 PM Ambarish Kumar [email protected] wrote:
Sir, clone of normami has failed. Please go through the error. Even, I tried to download it's .zip file, but while extracting the file, it report it as corrupt one.
[image: normami] https://user-images.githubusercontent.com/36997739/64025943-6c3e5e80-cb5b-11e9-94c1-7df1bd601893.png
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Sir, due to bandwidth issue cloning of normami failed multiple times. I tried to get it's pom.xml and normami-0.1-SNAPSHOT-jar-with-dependencies.jar and build normami separately but it is not successful.
Hmmm, I think I need to purge/gc the system. I'll have a go at some stage.
On Mon, Sep 2, 2019 at 1:20 PM Ambarish Kumar [email protected] wrote:
Sir, due to bandwidth issue cloning of normami failed multiple times. I tried to get it's pom.xml and normami-0.1-SNAPSHOT-jar-with-dependencies.jar and build normami separately but it is not successful.
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Sir, cloning of normami got happened without any interruption today. Re-build cephis (after downloading from dev branch of ContentMine) but building normami is not successful.
- snapshot of building
cephis
- snapshot of building
normami
I am going to open an Issue or page on opennotebook repo. I will also return to posting daily jars.
Does /home/cbl /CEVOpen exist? Do you have enough diskspace? Do you have write permission?
I probably can't solve your issue, but post it on the opennotebook repo
under Cannot build normami
On Tue, Sep 3, 2019 at 9:11 AM Ambarish Kumar [email protected] wrote:
Sir, cloning of normami is without any interruption today. Re-build cephis (after downloading from dev branch of ContentMine) but building normami is not successful.
snapshot of building cephis [image: cephis-dev] https://user-images.githubusercontent.com/36997739/64155403-51683480-ce50-11e9-86ef-9ae662d16cf5.png
snapshot of building normami [image: normami-buildfailure] https://user-images.githubusercontent.com/36997739/64155518-8d9b9500-ce50-11e9-8a08-beae4cf105a4.png
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OK sir.
- Yes, /home/cbl/CEVOpen exists.
- Yes, I have enough disk space.
- Yes, I have write permission.
Does /home/cbl/CEVOpen/target exist? No - try to create it; is there a problem? Does /home/cbl/CEVOpen/target/classes exist? If they do, delete and try again.
On Tue, Sep 3, 2019 at 10:50 AM Ambarish Kumar [email protected] wrote:
OK sir.
- Yes, /home/cbl/CEVOpen exists.
- Yes, I have enough disk space.
- Yes, I have write permission.
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Sir,
There does not exist /home/cbl/CEVOpen/target/classes.
Now, I have /home/cbl/CEVOpen/target.
Tested one ami-jars - ami20190903. After running ami-search, there is one log.xml file into it.
<?xml version="1.0" encoding="UTF-8"?>
<log date="2019-09-04T12:15:04.137+05:30"/>
does it work now?
On Wed, Sep 4, 2019 at 7:29 AM Ambarish Kumar [email protected] wrote:
Sir,
There does not exist /home/cbl/CEVOpen/target/classes.
Now, I have created /home/cbl/CEVOpen/target.
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-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
Hi @petermr and @ambarishK, would you please complete this information request so everyone can be clear about the purpose, importance of this Issue, and perhaps find ways we can assist in it? Thanks!
The Big WHY
We are building AMI so that: Type of User: ______________________ can: _____________ without: _________
Goals: Describe the Challenge, the solution we will bring, and the Desired End State by which all will know we have achieved excellence.
A. B. C.
Desired Results: A clear and concise description / outline of the final "state or vision" of the project — the evidence we will see when our goals are achieved.
A. B. C.
Guiding principles: What principles will guide our decisions as we do our part to fulfill the mission?
A. B. C.
Massive Action Steps: What massive actions will generate the Desired Results?
A. B. C.
Roles and responsibilities: Who will do what for when?
Interim Deliverable #1: Milestone: Milestone Date: Single Individual Responsible for ensuring this Milestone is reached on time:
Interim Deliverable #2 Milestone: Milestone Date: Single Individual Responsible for ensuring this Milestone is reached on time:
Tips, Tools, Shortcuts and Resources: Anything done or used to make the desired outcome more likely to occur.
A. B. C.
Rules and Responsibilities for Achieving Excellence
Always: A. B. C.
Never: A. B. C.
OK - this is our project management, thanks.
On Fri, Sep 13, 2019 at 3:57 AM Emanuel Faria [email protected] wrote:
We are building AMI so that:
Type of User: Anyone interested in science and medicine can: read the scientific literature in bulk and use machines to help___ without: ____knowing technical software _____
Goals: Describe the Challenge, the solution we will bring, and the Desired End State by which all will know we have achieved excellence.
A. Challenge: make published scientific literature accessible to everyone (from teens onwards)B.
B. Solution: ami3 and getpapers are a trivially installed Free package that
runs on any machine, along with copious examples and tutorials C.End state: global movement and acceptance, e.g. with blogs, tutorials conventions, workshops Similar to R, Jupyter,
Desired Results: A clear and concise description / outline of the final "state or vision" of the project — the evidence we will see when our goals are achieved.
A. A large percentage of the scientific community will have heard of AMI B. An early adopter community outside academia will have formed C. public meetings and conventions
Guiding principles: What principles will guide our decisions as we do our part to fulfill the mission?
A. Everything is Open B. The goal is to make valuable useful knowledge available to everyone C. We challenge injustice , especially the enclosure of knowledge
Massive Action Steps: What massive actions will generate the Desired Results?
I am not sure I'd phrase it like this, but
A. blogs, examples, tutorials B. Fellowships for early adopters C. systematic mining and publication of results in particular subjects
Roles and responsibilities: Who will do what for when?
I suggest we use "best endeavour" and "forgiveness". IOW I will do my best at medium priority , and hope that others will deliver in the same way.
More later
Interim Deliverable #1 https://github.com/petermr/CEVOpen/issues/1: Milestone: Milestone Date: Single Individual Responsible for ensuring this Milestone is reached on time:
Interim Deliverable #2 https://github.com/petermr/CEVOpen/issues/2 Milestone: Milestone Date: Single Individual Responsible for ensuring this Milestone is reached on time:
Tips, Tools, Shortcuts and Resources: Anything done or used to make the desired outcome more likely to occur.
A. B. C.
Rules and Responsibilities for Achieving Excellence
Always: A. B. C.
Never: A. B. C.
[image: image] https://user-images.githubusercontent.com/9612595/64834621-fe615080-d5b8-11e9-887c-059e02fd3703.png
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