Add a sample test repository

[dgarijo]

This repository: https://github.com/tpronk/somef-demo-repo should be added in the documentation

[tpronk]

I have to confess it's not really that good yet. However, my attention during the ELIXIR BioHackathon has already been requested for other tasks... hope to have an update soon!

[dgarijo]

no rush!

[tpronk]

Back in business! Below, I'll add things I noticed while creating the demo repo. As I won't be done today, more might follow...

• The field acknowledgment is missing from the SOMEF README and docs
• I can find the field image (singular) in the SOMEF output, but the docs say images (plural)

[dgarijo]

Thanks, let me open this in a new issue. Many people have been editing the d ocs, and keeping everything consistent can be challenging

[tpronk]

Having too many contributors sounds like a lovely problem to have :). Below, I got two more potential issues... I'll post them in separate comments

[tpronk]

I think there might be an issue with extracting a logo when there is no slash (/) in the path to the logo. For illustration, below is a snippet of the README.md of the somef-demo-repo, followed by a snippet of the JSON output of SOMEF. Note that logo1.png is not recognized as a logo, but logo_directory/logo2.png is. Same result if I use logo.png and if I don't have the logo_directory/logo2.png in the README.md

README.md

# Image
Images used to illustrate the software component.
![logo1.png](logo1.png)

# Logo
Main logo used to represent the target software component.
![logo2.png](logo_directory/logo2.png)

SOMEF Output

"logo": [
  {
    "result": {
      "type": "Url",
      "value": "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/logo_directory/logo2.png"
    },
    "confidence": 1,
    "technique": "regular_expression",
    "source": "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/README.md"
  }
],
"image": [
  {
    "result": {
      "type": "Url",
      "value": "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/logo1.png"
    },
    "confidence": 1,
    "technique": "regular_expression",
    "source": "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/README.md"
  }
]

[tpronk]

At the Hackathon, we've been extracting metadata from around 65 repos, but in none of the SOMEF output can I find the field has_executable_notebook. Also, in the SOMEF source code, I couldn't easily identify any snippets that extract it. Does this field still work? If so, might you have an example for me of a repo where it can be extracted from?

[tpronk]

I found a case where values extracted for the invocation field were attributed to README.md, but on visual inspection, I found them in README.Rmd instead. It concerns this repo. Below is a snippet of the SOMEF output. Credits to Esteban for providing this dataset :)

    "invocation": [
        {
            "result": {
                "type": "Text_excerpt",
                "value": "\n```{r, echo=FALSE, results='asis', message = FALSE}\nmy_apc %>% select(institution, euro) %>% \n  group_by(institution) %>% \n  ezsummary::ezsummary(n = TRUE, digits= 0, median = TRUE,\n                       extra = c(\n                         sum = \"sum(., na.rm = TRUE)\",\n                         min = \"min(., na.rm = TRUE)\",\n                         max = \"max(., na.rm = TRUE)\"\n                         )) %>%\n  mutate_all(format, big.mark=',') %>%\n  ezsummary::ezmarkup('...[. (.)]..[. - .]') %>%\n#> get rid of blanks\n  mutate(`mean (sd)` = gsub(\"\\\\(  \", \"(\", .$`mean (sd)`)) %>% \n  select(institution, n, sum, `mean (sd)`, median, `min - max`) %>%\n  arrange(desc(n)) %>%\n  knitr::kable(col.names = c(\"Institution\", \"Articles\", \"Spending total (in \u20ac)\", \"Mean (SD)\", \"Median\", \"Minimum - Maximum\"), align = c(\"l\",\"r\", \"r\", \"r\", \"r\", \"r\"))\n``` \n",
                "original_header": "Fully Open Access Journals"
            },
            "confidence": 0.906763643352601,
            "technique": "supervised_classification",
            "source": "https://raw.githubusercontent.com/MPDL/unibiAPC/master/README.md"
        },
        {
            "result": {
                "type": "Text_excerpt",
                "value": "```{r, echo = FALSE, warning = TRUE}\n\nknitr::opts_knit$set(base.url = \"/\")\nknitr::opts_chunk$set(\n  comment = \"#>\",\n  collapse = TRUE,\n  warning = FALSE,\n  message = FALSE,\n  echo = FALSE,\n  fig.width = 9,\n  fig.height = 6\n)\noptions(scipen = 999, digits = 0, tibble.width = Inf, tibble.print_max = Inf)\n\nknitr::knit_hooks$set(inline = function(x) {\n  prettyNum(x, big.mark = \",\")\n})\n```\n```{r}\nrequire(dplyr)\nrequire(ggplot2)\nrequire(ezsummary)\nrequire(pander)\n```\n```{r, echo=FALSE, cache = FALSE}\nmy_apc <- readr::read_csv(\"data/apc_de.csv\")\n```\n \n"
            },
            "confidence": 0.9211067534061969,
            "technique": "supervised_classification",
            "source": "https://raw.githubusercontent.com/MPDL/unibiAPC/master/README.md"
        }
    ]

[dgarijo]

Thanks for these issues. executable_notebook should return the my binder links. I see that now these are added in executable_example. This may need a review (the schema suffered a few changes). All other issues are legit. Thanks a lot! We'll need to address them

[dgarijo]

If you find any more, please open them! I usually open them as I test in diverse repos, but some time is tricky getting to these edge cases

[tpronk]

Bueno & gracias. I'll keep 'em coming then :)

[tpronk]

Wrapping things up, I compared fields mentioned in the README.md of SOMEF to the fields in constants.py. These are the discrepancies I found in terms of entries I couldn't find in one or the other, ignoring cases where they probably just have a different name

• changelog. Yes in README, not in constants
• code_repository. Not in README, yes in constants
• contributing_guidelines. Not in README, yes in constants
• date_created. Not in README, yes in constants
• date_updated. Not in README, yes in constants

[tpronk]

All right then. SOMEF 0.9.4 can extract a total of 48 fields from this version of somef-demo-repo, which can make it a nice integration test I guess

[dgarijo]

Definitely. Thanks!!