legacy OTN dataset registration 7

[jhpoelen]

legacy OTN dataset registration 7 from #45 as suggested by @bmaitner

-
    Timestamp: 9/17/2019 5:21:45
    datasetDOI_URL: https://doi.org/10.1111/jvs.12646
    contactName: Markus Bernhardt‐Römermann
    contactEmail: 
    license: CC-By
    traitList: "growth form | stem | shoot length | life form |  life strategy | protonema | Hyalin\nhairpoint | dominants | distribution of gametangia | seta | capsules | size of spores | spore ornamentation | fruiting | vegetative dispersal traits"
    higherGeography: Germany
    decimalLatitude: 
    decimalLongitude: 
    taxon: Embryophyta | Bryophyta
    eventDate: 
    paperDOIcitation: https://doi.org/10.1111/jvs.12646
    description: A compilation of autecological information and morphological and regenerative trait data on different stages of the life cycle of bryophytes occurring in forest ecosystems. The database contains information for 35 traits and 721 Central European bryophyte species; in total more than 23,000 trait values
    taxaList: 721 Central European bryophyte species
    usefulClasses: NA
    dataStandard: 
    standardizationScripts: 
    datasetName: 
    datasetID: 
-
    Timestamp: 9/17/2019 5:44:30
    datasetDOI_URL: http://doi.org/10.5061/dryad.1cv08,
    contactName: Joanne Bennett
    contactEmail: joanne.bennett@idiv.de
    license: CC-BY
    traitList: "Tmax | max_metric | error | error measure | Multiple measures | max_interval_after_LT0 | Tmax_2 | max_metric_2\terror | error measure | max_interval_before_LT100 | max_pretreatment | max_ramp | lat_max | long_max\televation_max | REF_max | location_max | N | tmin | min_metric | Multiple measures_min | min_interval_after_LT0 | tmin_2 | min_metric_2 | min_interval_before_LT100 | min_pretreatment | ramp_min\t"
    higherGeography: Global
    decimalLatitude: 
    decimalLongitude: 
    taxon: Chlorophyta | Plantae | Fungi | Animalia
    eventDate: 
    paperDOIcitation: doi: 10.1038/sdata.2018.22
    description: Thermal tolerance metrics for 2,133 species of multicellular algae, plants, fungi, and animals in 43 classes, 203 orders and 525 families from marine, intertidal, freshwater, and terrestrial realms, extracted from published studies. Updates to the data and metadata will be curated through the iDiv data portal https://idata.idiv.de/
    taxaList: Chlorophyta | Plantae | Fungi | Animalia
    usefulClasses: NA
    dataStandard: 
    standardizationScripts: 
    datasetName: 
    datasetID: 
-
    Timestamp: 9/17/2019 5:49:20
    datasetDOI_URL: https://doi.org/10.5061/dryad.f6t39kj
    contactName: Shai Meiri
    contactEmail: uncshai@post.tau.ac.il
    license: CC-BY
    traitList: body size | ecological | thermal biology | geographic | phylogenetic | life history data
    higherGeography: Global
    decimalLatitude: 
    decimalLongitude: 
    taxon: Reptilia
    eventDate: 
    paperDOIcitation: https://doi.org/10.1111/geb.12773
    description: Geographical, morphological, ecological, physiological and life history data for the 6,657 known species of lizards
    taxaList: Reptilia
    usefulClasses: NA
    dataStandard: 
    standardizationScripts: 
    datasetName: 
    datasetID: 

[BErfanian]

Hi @jhpoelen Two first datasets were added, however, the preview is not working. Please check them and let me know how I could fix the error. Then, I'll add the other datasets.

[jhpoelen]

Hey @BErfanian - thanks for proposing the two legacy datasets via https://github.com/open-traits-network/open-traits-network.github.io/pull/129 and https://github.com/open-traits-network/open-traits-network.github.io/pull/128 .

@willpearse @lembrechtsjonas @JonathonMifsud - do you have any ideas on why the pull requests above seem to contain malformed Jekyll yaml front matter ? Perhaps using tools like http://www.yamllint.com/ help to highlight funny syntax errors.

[BErfanian]

Hi @jhpoelen I've checked both files in yamllint, the answer was: Valid YAML!

[JonathonMifsud]

Hi @jhpoelen @BErfanian

Like @BErfanian both files were valid in yamllint. I noticed that the end of bennett-2019 line 10 contains a tab, are these invalid in YAML? https://github.com/open-traits-network/open-traits-network.github.io/blob/914f351e70aa40828f67ed6e85ee5d5764df9248/_datasets/bennett-2018#L10

I haven't spotted anything in #128 yet.

I haven't had any experience with YAML so this was just a guess!

[jhpoelen]

Thanks @JonathonMifsud for taking a peek at this.

@BErfanian I realize it might be frustrating to figure this thing out. . . I admire your persistence and care you take to make sure to understand what is happening.

One thing I sometimes do to troubleshoot formatting issues is to run the site locally on my laptop using "jekyll" command-line tool:

steps are something like:

1. clone the repository to a local directory
2. checkout the branch you are working on
3. run "jekyll s" (shorthand for "jekyll serve" and "jekyll server")
4. in browser, visit http://localhost:4000

Here's the output I see when I run it on my laptop:

$ jekyll s
Configuration file: /xxxx/open-traits-network.github.io/_config.yml
            Source: /xxxx/open-traits-network.github.io
       Destination: /xxxx/open-traits-network.github.io/_site
 Incremental build: disabled. Enable with --incremental
      Generating... 
       Jekyll Feed: Generating feed for posts
                    done in 9.734 seconds.
 Auto-regeneration: enabled for '/xxxx/opentraits/open-traits-network.github.io'
    Server address: http://127.0.0.1:4000/
  Server running... press ctrl-c to stop.

If the dataset page related to your additions look fine on your local machine, it might just be a github website issue. Otherwise, you'll probably see jekyll logging error messages.

Hope this helps!

[BErfanian]

Hi @JonathonMifsud Thanks for the suggestion @jhpoelen I'll check it in Jekyll

[BErfanian]

Hi @jhpoelen

Configuration file: c:/check/_config.yml
Source: c:/check
Destination: c:/check/_site
Incremental build: disabled. Enable with --incremental
Generating...
Jekyll Feed: Generating feed for posts done in 5.157 seconds.
Auto-regeneration: enabled for 'c:/check'
Server address: http://127.0.0.1:4000/
Server running... press ctrl-c to stop.

Everything looks ok on the local site.

[jhpoelen]

@BErfanian Thanks for making the effort to check the additions! This result suggests that the Github preview might not work all the time.

[jhpoelen]

@BErfanian the root cause of the issue was the the added files did not have ```.md```` file extensions.

I fixed the issue via https://github.com/open-traits-network/open-traits-network.github.io/commit/8ffb003bfe2c0b80bb7bf712ef1a8582935466fb .

[BErfanian]

All datasets were added to the site.