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('nn')
package_dict = {
package_list.split(':')[0]: package_list.split(':')[1] for package in package_list
}
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Answer
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("nn"):
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 Automatedn Affymetrix Array Analysis suite of package.",
"biocViews": "Microarray",
"Author": "Willem Talloen [aut], Tobias Verbeke [aut], Laure Cougnaudn [cre]",
"Maintainer": "Laure Cougnaud <laure.cougnaud@openanalytics.eu>",
"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 Automatedn 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], Willemn Ligtenberg [aut], Tobias Verbeke [aut], Laure Cougnaud [cre]",
"Maintainer": "Laure Cougnaud <laure.cougnaud@openanalytics.eu>",
"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.