CrystalEye and repositories: Jim explains the why and how of Atom

Since Atom may not be familiar to everyone Jim Downing has written two expositions on his blog. These explain his thinking of why a series of medium-sized chunks is a better way to support the download of CrystalEye than one or two giant files. Note that he is working on making available some Java code to help with the download – this should do the caching and remember where you left off. If you have technical questions I suggest you leave them on Jim’s blog. If you want to help the project in general use my blog. If you want to hurry the process along by mailing Jim, please refrain. He works very well on occasional beers (he is a brewing aficionado).

Using the Crystaleye Atom feed – November 5th, 2007
Incremental harvesting is done by [the same mechanism], but with a couple of extra bells and whistles to minimize bandwidth and redundant downloads. There are three ways you might do this: –

• The first way is to keep track of all the entry IDs you’ve seen, and to stop when you see an entry you’ve already seen.
• The easiest way is to keep track of the time you last harvested, and add an If-Modified-Since header to the HTTP requests when you harvest – when you receive a 304 (Not Modified) in return, you’ve finished the increment.
• The most thorough way is to keep track of the ETag header returned with each file, and use it in the If-None-Match header in your incremental harvest. Again, this will return 304 (Not Modified) whenever your copy is good.

Implementing a harvester

Atom archiving is easy to code to in any language with decent HTTP and XML support. As an example, I’ve written a Java harvester (binary, source). The source builds with Maven2. The binary can be run using
java -jar crystaleye-harvester.jar [directory to stick data in]
Letting this rip for a full harvest will take a while, and will take up ~10G of space (although less bandwidth since the content is compressed).

Being a friendly client

First and foremost, please do not multi-thread your requests. [PMR emphasis]
Please put a little delay in between requests. A few 100ms should be enough; the sample harvester uses 500ms – which should be as much as we need.
If you send an HTTP header “Accept-Encoding: gzip,deflate”, CrystalEye will send the content compressed (and you’ll need to gunzip it at the client end). This can save a lot of bandwidth, which helps.

PMR: Many people don’t think of things like this when they write spiders. Jim’s software should do all the thinking for you.

OJD: Atom History vs Large Archive Files – November 5th, 2007
Incremental harvest is a requirement for data repositories, and the “web-way” is to do it through the uniform interface (HTTP), and connected resources.
We don’t have the resource to provide DVD’s of content for everyone who wants the data. Or turning that around – we hope more people will want the data than we have resource to provide for. This is isn’t about the cost of a DVD, or the cost of postage, it’s about manpower, which costs orders of magnitude more than bits of plastic and stamps.
I’ve particularly valued Andrew Dalke’s input on this subject (and I’d love to kick off a discussion on the idea of versioning in CrystalEye, but I don’t have time right now): –

AD: However, I would suggest that the experience with GenBank and other bioinformatics data sets, as well as PubChem, has been that some sort of bulk download is useful. As a consumer of such data I prefer fetching the bulk data for my own use. It makes more efficient bandwidth use (vs. larger numbers of GET requests, even with HTTP 1.1 pipelining), it compresses better, I’m more certain about internal integrity, and I can more quickly get up and working because I can just point an ftp or similar client at it. When I see a data provider which requires scraping or record-by-record retrieval I feel they don’t care as much about letting others play in their garden.

(Andrew Dalke)… and earlier …

… using a system like Amazon’s S3 makes it easy to distribute the data, and cost about US $20 for the bandwidth costs of a 100GB download. (You would need to use multiple files because Amazon has a 5GB cap on file size.) Using S3 would not affect your systems at all, except for the one-shot upload time and the time it would take to put such a system into place.

(Andrew Dalke)Completely fair points. I’ll certainly look at implementing a system to offer access through S3, although everyone might have to be even more patient than they have been for these Atom feeds. We do care about making this data available – compare the slight technical difficulties in implementing an Atom harvester with the time and effort it’s taken Nick to implement and maintain spiders to get this data from the publishers in order to make it better available!
PMR: The clear point is that this is more work than it looks from the outside. Part of the point is that we are trying to improve the process of spidering the scientific web. Nick spent a LOT of time writing spiders – one publisher changed their website design several times over the last two years. If publishers were as friendly to spiders as we are trying to be the process would be much easier. So if the work with Atom is successful, forward-looking publishers might light to implement it.

ChemSpiderMan Says:
November 5th, 2007 at 4:33 pm eThanks to Egon for asking his question. As I have been expressing all I want to do also is “- link to CrystalEye entries”. We will work to support the atom feeds…
“- link to CrystalEye entries (assuming the CMLs contains a CrystalEye identifier). [PMR: The Atom feed contains the link – see above]”
all that is left now is access to the backfile of entries.

PMR: Again to clarify this. The links to the entries are already published in the Atom feed. Each link points to an entry from which (a) the InChI and (b) the CompleteCML are available. The access is there. It’s purely a question of the software (which anyone can write, but Jim is addressing for those who want it customised).