| import os |
| import ujson as json |
| import pygit2 |
| import shutil |
| from pygit2.enums import MergeFavor |
|
|
| from phylogeny import compute_all_P, compute_sim_matrix |
| from plotting import get_color, UNKNOWN_COLOR, DEFAULT_COLOR |
| |
| |
| |
| |
| |
| def load_data(force_clone=False): |
| global UNKNOWN_COLOR, DEFAULT_COLOR, MODEL_SEARCHED_X |
| data, model_names,families = load_git(force_clone=force_clone) |
| if data is None: |
| return |
| |
| |
| with open('family_table.json','r') as f: |
| rename_table = json.load(f) |
|
|
| for i in range(len(model_names)): |
| try: |
| families[i] = rename_table[model_names[i]] |
| except KeyError: |
| pass |
|
|
| all_P = compute_all_P(data, model_names) |
| sim_matrix = compute_sim_matrix(model_names, all_P) |
|
|
| k = list(all_P.keys())[0] |
|
|
| unknown_color = UNKNOWN_COLOR |
|
|
| unique_families = list(set([f for f in families])) |
| colors = {} |
| idx = 0 |
| for i, family in enumerate(unique_families): |
| color = get_color(idx) |
| idx += 1 |
| while color == unknown_color: |
| color = get_color(idx) |
| idx += 1 |
| colors[family] = color |
|
|
| colors['?'] = unknown_color |
| |
| return data, model_names, families, sim_matrix, colors |
|
|
| def load_git(force_clone = False): |
| cred = pygit2.UserPass(os.environ['GITHUB_USERNAME'], os.environ['GITHUB_TOKEN']) |
| if not os.path.exists('Data') or force_clone: |
| |
| if os.path.exists('Data'): |
| shutil.rmtree('Data') |
| repo = pygit2.clone_repository('https://github.com/PhyloLM/Data', './Data', bare=False, callbacks=GitHubRemoteCallbacks(os.environ['GITHUB_USERNAME'], os.environ['GITHUB_TOKEN'])) |
| else: |
| repo = pygit2.Repository('Data') |
| remote = repo.remotes['origin'] |
| fetch_results = remote.fetch() |
| print(fetch_results) |
|
|
| |
| branch_name = repo.head.shorthand |
|
|
| |
| remote_ref_name = f'refs/remotes/origin/{branch_name}' |
|
|
| |
| remote_commit = repo.lookup_reference(remote_ref_name).target |
| |
| |
| try: |
| repo.merge(remote_commit) |
| except Exception as e: |
| print(f"Merge error: {e}") |
| |
| return load_git(force_clone=True) |
| data_array = [] |
| model_names = [] |
| families = [] |
| for foname in os.listdir('Data/math'): |
| |
| if not os.path.isdir(os.path.join('Data/math',foname)): |
| continue |
| for fname in os.listdir('Data/math/'+foname): |
| if not fname.endswith('.json'): |
| continue |
| with open(os.path.join('Data/math',foname,fname),'r') as f: |
| d = json.load(f) |
| families.append(d['family']) |
| model_names.append(foname+'/'+fname[:-5]) |
| data_array.append(d['alleles']) |
|
|
| if data_array == []: |
| return None,[],[] |
| return data_array,model_names,families |
|
|
| |
| |
| |
| |
| |
|
|
| class GitHubRemoteCallbacks(pygit2.RemoteCallbacks): |
| def __init__(self, username, token): |
| self.username = username |
| self.token = token |
| super().__init__() |
| |
| def credentials(self, url, username_from_url, allowed_types): |
| return pygit2.UserPass(self.username, self.token) |
| |
| |
| |
| |
| |
| |
|
|
| def save_git(alleles,genes,model,family): |
| repo = pygit2.Repository('Data') |
| remo = repo.remotes['origin'] |
|
|
| d = {'family':family,'alleles':alleles} |
| model_name = model |
| data_path = f'math/{model_name}.json' |
| path = os.path.join('Data',data_path) |
| |
| if not os.path.exists(os.path.dirname(path)): |
| os.makedirs(os.path.dirname(path), exist_ok=True) |
| |
| with open(path,'w') as f: |
| json.dump(d,f) |
|
|
| repo.index.add(data_path) |
| repo.index.write() |
| reference='HEAD' |
| tree = repo.index.write_tree() |
| author = pygit2.Signature(os.environ['GITHUB_USERNAME'], os.environ['GITHUB_MAIL']) |
| commiter = pygit2.Signature(os.environ['GITHUB_USERNAME'], os.environ['GITHUB_MAIL']) |
| oid = repo.create_commit(reference, author, commiter, f'Add data for model {model}', tree, [repo.head.target]) |
| remo.push(['refs/heads/main'],callbacks=GitHubRemoteCallbacks(os.environ['GITHUB_USERNAME'],os.environ['GITHUB_TOKEN'])) |
