Example URL https://bioconductor.org/packages/release/bioc/VIEWS

Currently I'm splitting each individual clump of metadata by every blank line, then converting to a dictionary splitting on the first colon using the string before as the key and the string after as the value. THE ISSUE I'm running is that I am going line by line through each package metadata, some lines do not have colons and I want to append that to the previous value as one complete string.

    response = requests.get(
    'https://bioconductor.org/packages/release/bioc/VIEWS')

    package_list = response.text.split('\n\n')

    package_dict = {
        package_list.split(':')[0]: package_list.split(':')[1] for package in package_list
    }

CodePudding user response：

Try using regex to parse the data:

import re
import requests

url = "https://bioconductor.org/packages/release/bioc/VIEWS"
data = requests.get(url).text

pat = re.compile(
    r"^([^\s][^:]*): (. ?)\s*(?=^[^\s][^:]*:|\Z)", flags=re.S | re.M
)

out = []
for chunk in data.split("\n\n"):
    if chunk:
        out.append(dict(pat.findall(chunk)))

print(out)

Prints:

[
    {
        "Package": "a4",
        "Version": "1.44.0",
        "Depends": "a4Base, a4Preproc, a4Classif, a4Core, a4Reporting",
        "Suggests": "MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats",
        "License": "GPL-3",
        "MD5sum": "cc696d3373a9f258d293f2d966da11d5",
        "NeedsCompilation": "no",
        "Title": "Automated Affymetrix Array Analysis Umbrella Package",
        "Description": "Umbrella package is available for the entire Automated\n        Affymetrix Array Analysis suite of package.",
        "biocViews": "Microarray",
        "Author": "Willem Talloen [aut], Tobias Verbeke [aut], Laure Cougnaud\n        [cre]",
        "Maintainer": "Laure Cougnaud <[email protected]>",
        "git_url": "https://git.bioconductor.org/packages/a4",
        "git_branch": "RELEASE_3_15",
        "git_last_commit": "5b0fc5a",
        "git_last_commit_date": "2022-04-26",
        "Date/Publication": "2022-04-26",
        "source.ver": "src/contrib/a4_1.44.0.tar.gz",
        "win.binary.ver": "bin/windows/contrib/4.2/a4_1.44.0.zip",
        "mac.binary.ver": "bin/macosx/contrib/4.2/a4_1.44.0.tgz",
        "vignettes": "vignettes/a4/inst/doc/a4vignette.pdf",
        "vignetteTitles": "a4vignette",
        "hasREADME": "FALSE",
        "hasNEWS": "TRUE",
        "hasINSTALL": "FALSE",
        "hasLICENSE": "FALSE",
        "Rfiles": "vignettes/a4/inst/doc/a4vignette.R",
        "dependencyCount": "82"
    },
    {
        "Package": "a4Base",
        "Version": "1.44.0",
        "Depends": "a4Preproc, a4Core",
        "Imports": "methods, graphics, grid, Biobase, annaffy, mpm, genefilter,\n        limma, multtest, glmnet, gplots",
        "Suggests": "Cairo, ALL, hgu95av2.db, nlcv",
        "Enhances": "gridSVG, JavaGD",
        "License": "GPL-3",
        "MD5sum": "094c0a1c87b18ff8f16a3dbe4d06da64",
        "NeedsCompilation": "no",
        "Title": "Automated Affymetrix Array Analysis Base Package",
        "Description": "Base utility functions are available for the Automated\n        Affymetrix Array Analysis set of packages.",
        "biocViews": "Microarray",
        "Author": "Willem Talloen [aut], Tine Casneuf [aut], An De Bondt [aut],\n        Steven Osselaer [aut], Hinrich Goehlmann [aut], Willem\n        Ligtenberg [aut], Tobias Verbeke [aut], Laure Cougnaud [cre]",
        "Maintainer": "Laure Cougnaud <[email protected]>",
        "git_url": "https://git.bioconductor.org/packages/a4Base",
        "git_branch": "RELEASE_3_15",
        "git_last_commit": "9ae69e0",
        "git_last_commit_date": "2022-04-26",
        "Date/Publication": "2022-04-26",
        "source.ver": "src/contrib/a4Base_1.44.0.tar.gz",
        "win.binary.ver": "bin/windows/contrib/4.2/a4Base_1.44.0.zip",
        "mac.binary.ver": "bin/macosx/contrib/4.2/a4Base_1.44.0.tgz",
        "hasREADME": "FALSE",
        "hasNEWS": "TRUE",
        "hasINSTALL": "FALSE",
        "hasLICENSE": "FALSE",
        "dependsOnMe": "a4",
        "suggestsMe": "epimutacions",
        "dependencyCount": "73"
    },
 
...and so on.