openchemistry/mongochemserver issues and pull requests

#198 - Bump nbconvert from 5.4.1 to 6.5.1 in /girder/notebooks

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#197 - Bump nbconvert from 5.4.1 to 6.3.0 in /girder/notebooks

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#196 - Add the concept of a reusable ML model

Pull Request - State: open - Opened by alesgenova about 3 years ago

#195 - Update various packages to avoid ContextualVersionConflict

Pull Request - State: closed - Opened by cjh1 almost 4 years ago

#194 - Push python to 3.8

Pull Request - State: closed - Opened by cjh1 almost 4 years ago

#193 - Add notebook to run quantum calculation container

Pull Request - State: open - Opened by bnmajor almost 4 years ago - 2 comments

#192 - Remove path collision

Pull Request - State: closed - Opened by cjh1 almost 4 years ago

#191 - Fix download of a calculation cjson data

Pull Request - State: open - Opened by alesgenova over 4 years ago - 1 comment

#190 - Remove string start anchor from name search

Pull Request - State: closed - Opened by psavery over 4 years ago - 1 comment

#189 - Use "latest" instead of "latest-py3" for girder

Pull Request - State: closed - Opened by psavery over 4 years ago - 3 comments

#188 - Add a single endpoint to launch taskflows

Pull Request - State: closed - Opened by psavery over 4 years ago

#187 - Simplify requests needed to submit a calculation

Issue - State: closed - Opened by psavery over 4 years ago - 2 comments

#186 - Fix generation of lowest orbital

Pull Request - State: closed - Opened by alesgenova over 4 years ago

#185 - Name search should use contains, not starts with

Issue - State: closed - Opened by cryos over 4 years ago - 4 comments
Labels: enhancement

#184 - Update notebooks

Pull Request - State: closed - Opened by cryos over 4 years ago

#183 - Add rest API endpoints for images

Pull Request - State: closed - Opened by psavery over 4 years ago

#182 - Improve robustness of the queue plugin

Pull Request - State: closed - Opened by alesgenova almost 5 years ago

#181 - Enforce access controls on all endpoints

Issue - State: open - Opened by psavery almost 5 years ago

#180 - Have models default to being public

Pull Request - State: closed - Opened by psavery almost 5 years ago - 1 comment

#179 - Errors when submitting more than the "maxRunning" number of jobs

Issue - State: closed - Opened by psavery almost 5 years ago - 4 comments
Labels: bug

#178 - Update notebook example to use torchani:1.2

Pull Request - State: closed - Opened by psavery almost 5 years ago

#177 - Fix spelling: JuptyerLab -> JupyterLab

Pull Request - State: closed - Opened by psavery almost 5 years ago

#176 - Add example of chain optimizations with RMSD

Pull Request - State: closed - Opened by psavery almost 5 years ago

#175 - Fix GET /calculations with a geometry ID

Pull Request - State: closed - Opened by psavery almost 5 years ago

#174 - Make findmol -> find_molecule - fix inconsistency

Pull Request - State: closed - Opened by cryos almost 5 years ago

#173 - Return None when 3D output requested for 0D mol

Pull Request - State: closed - Opened by psavery almost 5 years ago

#172 - Add example of setting gen3d options

Pull Request - State: closed - Opened by psavery almost 5 years ago - 1 comment

#171 - Convert steps to int for generating 3D coordinates

Pull Request - State: closed - Opened by psavery almost 5 years ago

#170 - Allow user to pass in name or wikipedia link

Pull Request - State: closed - Opened by bnmajor almost 5 years ago - 1 comment

#169 - Add forcefield and steps options for gen3d

Pull Request - State: closed - Opened by psavery almost 5 years ago

#168 - Upgrade openbabel to 3.0.0

Pull Request - State: closed - Opened by psavery almost 5 years ago - 3 comments

#167 - Save optimized geometry IDs in calculations

Pull Request - State: closed - Opened by psavery almost 5 years ago

#166 - Add token scope to needed endpoint

Pull Request - State: closed - Opened by psavery about 5 years ago

#165 - Expose the code information for calculations

Pull Request - State: closed - Opened by bnmajor about 5 years ago

#164 - Check for exception on asynchronous orbital calculation

Pull Request - State: closed - Opened by bnmajor about 5 years ago

#163 - Improve the readability of create_molecule()

Pull Request - State: closed - Opened by psavery about 5 years ago

#162 - Save the code info of calculations if provided

Pull Request - State: closed - Opened by psavery about 5 years ago

#161 - Add token scopes to @access.user decorators

Pull Request - State: closed - Opened by psavery about 5 years ago

#160 - Conversions

Pull Request - State: closed - Opened by bnmajor about 5 years ago

#159 - Ensure molecule exists before generating the SVG

Pull Request - State: closed - Opened by cjh1 about 5 years ago

#158 - POST /molecules/conversions/{output_format} not working

Issue - State: closed - Opened by psavery about 5 years ago - 3 comments

#157 - New API Key Interface: "You must be logged in"

Issue - State: closed - Opened by psavery about 5 years ago - 3 comments

#156 - Hash input params on server for calc search

Pull Request - State: closed - Opened by psavery about 5 years ago

#155 - Molecule Access Levels

Issue - State: closed - Opened by psavery about 5 years ago - 2 comments

#154 - Add autojoin plugin

Pull Request - State: closed - Opened by cjh1 about 5 years ago

#153 - Use xyz when autodetecting bonds with Open Babel

Pull Request - State: closed - Opened by psavery about 5 years ago

#152 - Avogadro flask

Pull Request - State: closed - Opened by bnmajor about 5 years ago - 4 comments

#151 - Check bonds for 3D inputs and auto generate

Pull Request - State: closed - Opened by psavery about 5 years ago - 2 comments

#150 - Ensure we have an index on the inchikey property

Pull Request - State: closed - Opened by cjh1 about 5 years ago - 1 comment

#149 - Remove molecules GET min/max values from interface

Pull Request - State: closed - Opened by psavery about 5 years ago

#148 - Use inchi instead of smiles to generate properties

Pull Request - State: closed - Opened by psavery about 5 years ago

#147 - Molecule ingestion routines - two use cases

Issue - State: closed - Opened by cryos about 5 years ago

#146 - When generating inchi, do not convert to xyz first

Pull Request - State: closed - Opened by psavery about 5 years ago - 1 comment

#145 - Open Babel bond perception doesn't work for water

Issue - State: closed - Opened by psavery over 5 years ago - 4 comments

#144 - Added basic Open Babel flask container

Pull Request - State: closed - Opened by psavery over 5 years ago - 4 comments

#143 - Generate SVG image asynchronously

Pull Request - State: closed - Opened by psavery over 5 years ago - 3 comments

#142 - Added ability to specify provenance for molecules

Pull Request - State: closed - Opened by psavery over 5 years ago

#141 - Ensure str is passed to create_molecule(...)

Pull Request - State: closed - Opened by cjh1 over 5 years ago

#140 - Allow use of molecules query in GET /molecules

Pull Request - State: closed - Opened by psavery over 5 years ago

#139 - Add ability to search calculations by molecule name/inchi/etc

Pull Request - State: closed - Opened by alesgenova over 5 years ago - 1 comment

#138 - Add molecule id to GET /molecules/{id}

Pull Request - State: closed - Opened by psavery over 5 years ago

#137 - Add notebook example for doing multiple calcs

Pull Request - State: closed - Opened by psavery over 5 years ago - 5 comments

#136 - Add production docker image, with Girder running in production mode

Issue - State: closed - Opened by cjh1 over 5 years ago - 1 comment

#135 - Install OAuth plugin

Pull Request - State: closed - Opened by cjh1 over 5 years ago

#134 - Fix up settings for upstream Girder change

Pull Request - State: closed - Opened by cjh1 over 5 years ago

#133 - Remove default argument for Setting.get

Pull Request - State: closed - Opened by psavery over 5 years ago

#132 - Add basic get/set for orcid and twitter account

Pull Request - State: closed - Opened by psavery over 5 years ago - 7 comments

#131 - Allow molecules to be searched with min/max values

Pull Request - State: closed - Opened by psavery over 5 years ago - 8 comments

#130 - Use fields to get specific keys from molecules

Pull Request - State: closed - Opened by psavery over 5 years ago

#129 - Count total number of matches (no limit) for GET

Pull Request - State: closed - Opened by psavery over 5 years ago

#128 - Move formula search to `GET /molecules`

Pull Request - State: closed - Opened by psavery over 5 years ago

#127 - Improve calculation search capabilities

Pull Request - State: closed - Opened by psavery over 5 years ago - 1 comment

#126 - Updates for the girder 3 changes in past month

Pull Request - State: closed - Opened by psavery over 5 years ago - 5 comments

#125 - Strange InChI for Cactus Imported Ethane

Issue - State: closed - Opened by psavery over 5 years ago - 1 comment

#124 - Improve Molecule Search Capabilities

Pull Request - State: closed - Opened by psavery over 5 years ago - 15 comments

#123 - Add 'site' deployment configuration

Pull Request - State: closed - Opened by cjh1 over 5 years ago - 1 comment

#122 - Add footer elements to the configurable settings

Pull Request - State: closed - Opened by alesgenova over 5 years ago

#121 - Only auto-detect bonds if we have 3D coordinates

Pull Request - State: closed - Opened by psavery over 5 years ago - 2 comments

#120 - Add function to check if a mol has 3d coords

Pull Request - State: closed - Opened by psavery over 5 years ago - 3 comments

#119 - Allow 2d outputs to be obtained via GET

Pull Request - State: closed - Opened by psavery over 5 years ago - 3 comments

#118 - Do not add default names for molecules

Pull Request - State: closed - Opened by psavery over 5 years ago - 5 comments

#117 - Allow users to patch molecule names

Pull Request - State: closed - Opened by psavery over 5 years ago - 1 comment

#116 - Generate 3d coords async

Pull Request - State: closed - Opened by psavery over 5 years ago - 16 comments

#115 - Fixes to the SVG endpoint

Pull Request - State: closed - Opened by alesgenova over 5 years ago - 1 comment

#114 - Bump version of openbabel

Pull Request - State: closed - Opened by cjh1 over 5 years ago

#113 - Save an SVG for molecules upon creation

Pull Request - State: closed - Opened by psavery over 5 years ago - 4 comments

#112 - Added basic geometry collection

Pull Request - State: closed - Opened by psavery over 5 years ago - 13 comments

#111 - Autodetect bonds on calculation ingestion

Pull Request - State: closed - Opened by alesgenova over 5 years ago - 4 comments

#110 - Updated to adapt to changed CACTUS API

Pull Request - State: closed - Opened by cryos over 5 years ago - 3 comments

#109 - Allow 'chemical json' for cjson version key

Pull Request - State: closed - Opened by psavery over 5 years ago - 1 comment

#107 - Add start of InChI validator to prevent OB crashes

Pull Request - State: closed - Opened by psavery over 5 years ago

#106 - 3D coordinate generation too slow for import line format

Issue - State: closed - Opened by cryos over 5 years ago - 4 comments
Labels: bug

#103 - Migrate all plugins to girder 3.x

Pull Request - State: closed - Opened by psavery over 5 years ago - 8 comments

#100 - Added ability to create a molecule with smiles

Pull Request - State: closed - Opened by psavery over 5 years ago - 2 comments

#99 - Add endpoint to remove a calculation

Pull Request - State: closed - Opened by alesgenova over 5 years ago

#98 - Install app plugin

Pull Request - State: closed - Opened by cjh1 over 5 years ago

#97 - MongoChemServer changes to query spectra

Pull Request - State: closed - Opened by muammar over 5 years ago

#96 - MongoChemServer changes to query spectra

Pull Request - State: closed - Opened by muammar over 5 years ago - 2 comments

#95 - Bump version of nbconvert to fix tornado attribute issue

Pull Request - State: closed - Opened by cjh1 over 5 years ago

#94 - Add a geometry collection for molecular geometries

Issue - State: closed - Opened by cryos almost 6 years ago

GitHub / openchemistry/mongochemserver issues and pull requests