private async Task <List <DeserializedInfo> > GetToolsAsync()
{
Logger.LogDebug("Getting tools list from ToolShed.");
using var client = new HttpClient();
HttpResponseMessage response = await client.GetAsync(new Uri(Repo.URI + _repositoriesEndpoint)).ConfigureAwait(false);
string content;
if (response.IsSuccessStatusCode)
{
content = await response.Content.ReadAsStringAsync().ConfigureAwait(false);
}
else
{
/// TODO: replace with an exception.
return(null);
}
Logger.LogDebug("Received tools from ToolShed, deserializing them.");
DeserializedInfo.TryDeserialize(
content,
ToolJsonSerializerSettings,
ToolRepoAssoJsonSerializerSettings,
out List <DeserializedInfo> deserializedInfos);
foreach (var info in deserializedInfos)
{
info.SetStagingArea(SessionTempPath);
}
return(deserializedInfos);
}
private void TraverseArchive(string archiveFileName)
{
try
{
using ZipArchive archive = ZipFile.OpenRead(archiveFileName);
foreach (ZipArchiveEntry entry in archive.Entries)
{
if (entry.FullName.EndsWith("meta.yaml", StringComparison.OrdinalIgnoreCase))
{
string extractedFileName = SessionTempPath + Utilities.GetRandomString() + ".yaml";
try
{
entry.ExtractToFile(extractedFileName);
using var reader = new StreamReader(extractedFileName);
var yaml = new YamlStream();
yaml.Load(reader);
if (!DeserializedInfo.TryDeserialize(yaml, out DeserializedInfo deserializedInfo))
{
Logger.LogInformation($"Cannot deserialize tool info from {entry.FullName}.");
continue;
}
if (deserializedInfo.ToolRepoAssociation != null &&
deserializedInfo.ToolRepoAssociation.Tool != null &&
deserializedInfo.ToolRepoAssociation.Tool.Name != null &&
_addedDates.ContainsKey(deserializedInfo.ToolRepoAssociation.Tool.Name))
{
deserializedInfo.ToolRepoAssociation.DateAddedToRepository =
_addedDates[deserializedInfo.ToolRepoAssociation.Tool.Name];
}
if (!TryAddEntities(deserializedInfo))
{
// TODO: log why this tool will not be added to db.
}
}
catch (Exception e) when(e is YamlDotNet.Core.YamlException ||
e is YamlDotNet.Core.SyntaxErrorException ||
e is YamlDotNet.Core.SemanticErrorException)
{
Logger.LogDebug($"Cannot parse the YAML file {entry.FullName}: {e.Message}");
}
finally
{
File.Delete(extractedFileName);
}
}
}
}
catch (Exception e)
{
Logger.LogError($"Error occurred traversing Bioconda repository: {e.Message}");
}
finally
{
File.Delete(archiveFileName);
}
}
private void TraverseArchive(string archiveFileName)
{
try
{
using ZipArchive archive = ZipFile.OpenRead(archiveFileName);
foreach (ZipArchiveEntry entry in archive.Entries)
{
if (entry.FullName.EndsWith(".json", StringComparison.OrdinalIgnoreCase) &&
!entry.FullName.EndsWith("oeb.json", StringComparison.OrdinalIgnoreCase))
{
string extractedFileName = SessionTempPath + Utilities.GetRandomString() + ".json";
try
{
entry.ExtractToFile(extractedFileName);
using var reader = new StreamReader(extractedFileName);
if (!DeserializedInfo.TryDeserialize(
reader.ReadToEnd(),
ToolJsonSerializerSettings,
ToolRepoAssoJsonSerializerSettings,
PublicationSerializerSettings,
CategorySerializerSettings,
out DeserializedInfo deserializedInfo))
{
// TODO: log this.
continue;
}
if (!TryAddEntities(deserializedInfo))
{
// TODO: log why this tool will not be added to db.
}
}
catch (IOException e)
{
// TODO: log this.
}
finally
{
File.Delete(extractedFileName);
}
}
}
}
catch (Exception e)
{
// TODO: log the exception.
// TODO: if this exception has occurred, the caller job's status should be set to failed.
}
finally
{
File.Delete(archiveFileName);
}
}