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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| """ | ||
| Script to get Biomodels project info | ||
| """ | ||
|
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| import json | ||
| import pprint | ||
| from loadbiomodels import get_model_identifiers, get_model_info | ||
|
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| verbose = True # | ||
| verbose = False | ||
|
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| info_all = {} | ||
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|
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| if __name__ == "__main__": | ||
| min_index = 0 | ||
| max_index = 20 | ||
| index = 0 | ||
|
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| from loadbiomodels import get_model_identifiers | ||
|
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| model_ids = get_model_identifiers()["models"] | ||
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| selection = model_ids[min_index:max_index] | ||
|
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| for model_id in selection: | ||
| print( | ||
| "\n-------- Model (%i/%i, order %i): %s:\n" | ||
| % (index, len(selection), index + min_index, model_id) | ||
| ) | ||
|
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| model_link = f"[{model_id}](https://www.ebi.ac.uk/biomodels/{model_id})" | ||
| info = get_model_info(model_id) | ||
| model_name = info["name"] | ||
| print(f" {model_id}: \n {pprint.pformat(info['name'])}--") | ||
|
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| info_all[model_id] = info | ||
| """ | ||
| son.loads(get_page('https://modeldb.science/api/v1/models/%s'%model)) | ||
| print(' %s'%info[model]['name']) | ||
| if 'gitrepo' in info[model] and info[model]['gitrepo']: | ||
| with_gitrepo+=1 | ||
| print(' gitrepo: %s'%info[model]['gitrepo']) | ||
| else: | ||
| print(' gitrepo: %s'%False) | ||
| expected_forks = 0 | ||
| possible_mdb_repo = 'ModelDBRepository/%s'%(info[model]['id']) | ||
| try: | ||
| mdb_repo = gh.get_repo(possible_mdb_repo) | ||
| repo_to_use = mdb_repo | ||
| print(' Exists at: %s (def branch: %s; forks: %i)'%(mdb_repo.html_url, mdb_repo.default_branch, mdb_repo.forks)) | ||
| possible_osbgh_repo = 'OpenSourceBrain/%s'%(info[model]['id']) | ||
| try: | ||
| osb_repo = gh.get_repo(possible_osbgh_repo) | ||
| msg = ' Exists at: %s (def branch: %s; forks: %i), order %i'%(osb_repo.html_url, osb_repo.default_branch, osb_repo.forks, index+min_index) | ||
| on_osbv2.append(msg) | ||
| print(msg) | ||
| repo_to_use = osb_repo | ||
| expected_forks+=1 | ||
| info[model]['osbv2_gh_repo'] = repo_to_use.html_url | ||
| info[model]['osbv2_gh_branch'] = repo_to_use.default_branch | ||
| except: | ||
| print(' Missing fork: %s, forking now: %s'%(possible_osbgh_repo, fork_if_missing)) | ||
| if fork_if_missing: | ||
| print(' Forking to: %s...'%possible_osbgh_repo) | ||
| org = gh.get_organization('OpenSourceBrain') | ||
| org.create_fork(mdb_repo,default_branch_only=False) | ||
| msg = ' Forked to: %s...'%possible_osbgh_repo | ||
| print(msg) | ||
| forked_now.append(msg) | ||
| else: | ||
| msg = ' Yet to be forked: %i, order %i; %s'%(info[model]['id'], index+min_index,info[model]['name']) | ||
| print(msg) | ||
| to_be_forked.append(msg) | ||
| if (not mdb_repo.forks==expected_forks) and (not (info[model]['id'] in known_to_have_other_forks)): | ||
| msg = ' Unexpected forks for %i (%s != %s)...'%(info[model]['id'], mdb_repo.forks,expected_forks) | ||
| print(msg) | ||
| many_forks.append(msg) | ||
| except: | ||
| msg = ' Problem locating repo for: %i (%i/%i) %s'%(info[model]['id'],index, len(selection), info[model]['name']) | ||
| print(msg) | ||
| errors.append(msg)""" | ||
|
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| index += 1 | ||
|
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| if verbose: | ||
| infop = pprint.pprint(info_all, compact=True) | ||
|
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| print("\nThere were %i models checked\n" % (len(info))) | ||
|
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| filename = "cached_info/biomodels.json" | ||
|
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| strj = json.dumps(info_all, indent=" ", sort_keys=True) | ||
| with open(filename, "w") as fp: | ||
| fp.write(strj) | ||
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| print("Data on Biomodels (%i models) written to %s" % (len(info), filename)) |
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