pubmeder for firefox, will retain as an add-on in the sandbox for a while

I submit this add-on for public a while ago, and today, finally get the reviewer's decision...

Hi,
I got the addon to work after your latest instructions but I feel the addon needs some more work. The description mentions nothing about how the addon works - no mention of blue or red lines or that the data is sent in batches of 10 - which is why it took 3 requests for information to get this far.

The blue line appears on pages that don't contain any articles also (e.g. http://www.ncbi.nlm.nih.gov/guide/) making it an ineffectual indicator. It should be a bit more obvious. Some text saying 'Added to pubmder' or similar wouldn't hurt as would sending every article, or at least giving the option of manually sending the 'cache' so far and/or setting the limit to something or than 10.

As a firefox add-on directly converted from a greasemonkey userscript, I didn't except too much - just gave a try. My chrome extension and the safari extension for pubmeder.appspot.com are much more functional. Both have the ability to decide the size of basket for uploading the date. However, if you are using the userscript on firefox, change the only value 9 into 4, for example, your data will be uploaded every 5. The code related is:

// alert(currentList);
if (new_d.length > 9) {
  var urlurl = 'http://pubmeder.appspot.com/input?pmid=' + currentList + tail;

Since the add-on is working, I decide not to implant the suggestions and let the add-on stay in sandbox for now. The specific page the reviewer mentioned does have an article information, which is "Church D.M., Lappalainen I., Sneddon T.P., Hinton J., Maguire M., Lopez J., Garner J., Paschall J., DiCuccio M., Yaschenko E., Scherer S.W., Feuk L., Flicek P. (2010 Oct). Public data archives for genomic structural variation. Nat Genet. 42, 813-4".

I attach my response to his previous emails here, for you to better understand what this add-on do. Thanks and Enjoy Pubmed-er!

This plugin is directly converted from a greasemonkey user script http://userscripts.org/scripts/show/85346 .

The plugin capture any DOI or PMID information on the page (display a thin blue line on the top of the page) and send it to the server at http://pubmeder.appspot.com (display a thin red line on the top of the page, send every ten entries).

You can visit http://pubmed.org and search any keyword, and browse the result to test ...

When firefox opens, it checks whether user specific information has stored, if not, it will open http://pubmeder.appspot.com/registration to fetch the information - the error you encounter is caused by app engine, not the plugin / there is nothing I can improve.

But the login is not required, anonymous can input info to the server.

http://www.ncbi.nlm.nih.gov/pubmed/20960490

http://www.ncbi.nlm.nih.gov/pubmed/20960390

http://www.ncbi.nlm.nih.gov/pubmed/20959891

http://www.sciencemag.org/cgi/content/full/330/6003/468

http://www.sciencemag.org/cgi/content/full/330/6003/472

http://www.sciencemag.org/cgi/content/full/330/6003/477

... links out on those pages also contain DOI/PMID info

The plugin is silently running as a recorder of the articles (with DOI/PMID information) you read.

Every time it captures an article, a very thin blue line will be added to the top of the page, which you should see when you are visiting the links I gave you before. Once the plugin collects ten articles, it will send the information to the server, indicated by a thin red line added to the top of the page. I only gave you 6 links, but most of the links on those pages will link to other pages with different DOI/PMID information.

The information will be added to the server, and the front page of http://pubmeder.appspot.com will display the most recent entries, which should be the ones you just read.

If you login with your google account at http://pubmeder.appspot.com/registration, these paper will be added only to your account, which means you have to login to see them at the front page.

Hope these information help. Thanks.

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