Yao Yao

`ESIndex.doc_feeder` has a `search` call to ES client (see [es.py#L489](https://github.com/biothings/biothings.api/blob/master/biothings/utils/es.py#L489)): ```python res = self._es.search(index=self._index, doc_type=self._doc_type, body=q, size=_size, search_type='scan', scroll=scroll, **kwargs) ``` However, `'scan'` is no longer a valid `search_type`.

```python Nov 13 17:01:50 su12 python[3420]: ERROR:asyncio:Exception in callback Cron.set_result(

E.g. when creating a new incremental release of build `superhot_hg19_20221111_pjnuj6kh`, the following warning appears: ```python Nov 13 16:29:21 su12 python[3420]: INFO:diff_superhot_hg19_20220729_i4cddsyl_superhot_hg19_20221111_pjnuj6kh:Diff file containing mapping differences generated: None Nov 13 16:29:21...

```python Nov 11 15:52:47 su12 python[3420]: requests.exceptions.SSLError: HTTPSConnectionPool(host='hooks.slack.com', port=443): Max retries exceeded with url: /services/T02FW1EMK/BCL41LAG0/jD5MolpaCopPA2QWaNc2981T (Caused by SSLError(SSLZeroReturnError(6, 'TLS/SSL connection has been closed (EOF) (_ssl.c:997)'))) Nov 11 15:52:48 su12 python[3420]:...

fix outdated command "rebuild_cache"

1

`MyVariantHubServer::rebuild_cache` method, defined in [src/bin/hub.py#L67](https://github.com/biothings/myvariant.info/blob/master/src/bin/hub.py#L67), uses a `get_latest_build(build_name)` function. However this function was removed in [ecb98dd](https://github.com/biothings/biothings.api/commit/ecb98ddb089e02efdfd4f3639ad0a0b0c666c346#diff-70865aa925d2121f214e2b07b681dd85c805f3aa75b435540e349d223f3df2fe). What's more, the `build_name` parameter seems to be a `build_config` name actually (e.g. `"warm_hg19"`)....

## Modules Involved In use; don't touch: - `hub.py` Are they obsolete? Delete or revise: - `build.py`: wrong paths of imports - `dispatcher.py`: imports `DocDispatcher` which is not available now...

duplicated drug mechanism records in CHEMBL

2

E.g. on [`CHEMBL1201631` Compound Report Card](https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1201631/), there is only one drug mechanism record. However, [http://mychem.info/v1/chem/CHEMBL1201631](http://mychem.info/v1/chem/CHEMBL1201631) shows two. The duplication comes from the original source file, [https://www.ebi.ac.uk/chembl/api/data/mechanism.json](https://www.ebi.ac.uk/chembl/api/data/mechanism.json). Same problem may occur...

`obonet` is incapable to parse the `definition` terms correctly in obo files

2

## Version ```python obonet==0.3.0 ``` ## Related To - [Issue#83](https://github.com/biothings/mychem.info/issues/83) - [PR#106](https://github.com/biothings/mychem.info/pull/106) ## Priority **Low**. Currently it's not an issue. Maybe an issue in the future. ## Problem The `def`...

fda_orphan_drug plugin migration

1

Currently `fda_orphan_drug` is the only plugin under the [plugins](https://github.com/biothings/mychem.info/tree/master/src/plugins) folder. It also relies on upstream data processing described in Sander's [fda_orphan_drug](https://github.com/r76941156/fda_orphan_drug) repo. Shall we upgrade it into an advance plugin,...

Update DrugBank with its vocabulary data

2

Thanks to @rjawesome, we now know the existence of [DrugBank Vocabulary](https://go.drugbank.com/releases/latest#open-data) data. They can be used to update our Drugbank API. P.S. there is an SDF file of drug structures...