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Bugfix orderedset #10

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4063c45
Create LICENSE.txt
xdoan May 26, 2020
12a8eed
Merge pull request #1 from xdoan/patch-1
milen-sage May 26, 2020
13ac7f5
removing unneeded htan csv file from schema folder
milen-sage Sep 17, 2020
ffbb4c2
Merge pull request #275 from milen-sage/main
milen-sage Sep 17, 2020
72304fe
Update README.md
milen-sage Sep 17, 2020
b28f901
Update README.md
milen-sage Sep 17, 2020
2afdc54
Update README.md
milen-sage Sep 17, 2020
5102931
Merge pull request #281 from Sage-Bionetworks/develop
milen-sage Sep 26, 2020
275b8e4
Merge pull request #286 from milen-sage/develop-schema-update
milen-sage Sep 30, 2020
5bf50f6
Merge pull request #4 from milen-sage/develop-schema-update
milen-sage Oct 1, 2020
7c6b18c
Merge pull request #290 from milen-sage/develop-schema-update
milen-sage Oct 1, 2020
8179448
Merge pull request #294 from milen-sage/develop-schema-update
xdoan Oct 6, 2020
f969b10
Merge pull request #299 from milen-sage/develop-hotfix-tables
xdoan Oct 6, 2020
d2dae4f
Merge pull request #304 from milen-sage/develop-schema-update
xdoan Oct 8, 2020
83c8368
Merge pull request #301 from milen-sage/develop-file-hierarchy
xdoan Oct 13, 2020
46be35a
Merge branch 'develop-file-hierarchy' into main
milen-sage Oct 13, 2020
8c984ad
Merge pull request #5 from Sage-Bionetworks/main
milen-sage Oct 15, 2020
5585198
Updating README references to ncihtan repo
milen-sage Oct 15, 2020
ac072ec
Merge branch 'develop-schema-update' into main
milen-sage Oct 16, 2020
d18240c
Merge pull request #313 from milen-sage/develop-schema-update
xdoan Oct 20, 2020
117178e
Merge pull request #319 from milen-sage/develop-schema-update
xdoan Oct 21, 2020
cd02fda
Merge pull request #322 from milen-sage/develop-schema-update
xdoan Oct 23, 2020
05aea2e
Merge pull request #321 from milen-sage/develop-excel-export
xdoan Oct 23, 2020
0ccc462
Merge pull request #323 from milen-sage/develop-excel-export
xdoan Oct 23, 2020
8a521af
Update issue templates
ychae Oct 29, 2020
830e53f
Update bug_report.md
ychae Oct 29, 2020
1ab87ad
Merge pull request #332 from Sage-Bionetworks/ychae-issue-templates
ychae Oct 29, 2020
d3d185f
added updates to clinical data schema: molecular test; tier 2; tier 3
milen-sage Nov 3, 2020
5e2c81f
Merge pull request #339 from milen-sage/develop-schema-update
xdoan Nov 3, 2020
05d4d9c
fixing extra apostrophe added by google sheet API on string values in…
milen-sage Nov 5, 2020
912773b
Merge pull request #342 from milen-sage/develop-excel-export
xdoan Nov 6, 2020
47da266
update to address issue with Family History; added Alcohol exposure v…
milen-sage Nov 6, 2020
a42c3e1
Merge pull request #343 from milen-sage/develop-schema-update
xdoan Nov 7, 2020
659ceaf
Added workflow version to scRNA-seq level 3
milen-sage Nov 10, 2020
41c181f
Merge pull request #346 from milen-sage/develop-schema-update
xdoan Nov 10, 2020
e7140e6
adding csv schema input
milen-sage Nov 11, 2020
eae6748
Merge branch 'main' of https://github.com/Sage-Bionetworks/HTAN-data-…
milen-sage Nov 19, 2020
eae52f2
changes to schema reflecting clinical data updates and date-related f…
milen-sage Dec 15, 2020
c7479cd
adding country of residence ot demographics
milen-sage Dec 15, 2020
e451c5e
updated conoutry of residence desc
milen-sage Dec 15, 2020
a1a9e06
Merge pull request #365 from milen-sage/develop-schema-update
xdoan Dec 15, 2020
f75cf48
changes to sequencing assays adding read indicator for paired sequenc…
milen-sage Dec 16, 2020
968eee7
minor changes to attribute description for start/stop date for events…
milen-sage Dec 16, 2020
b290415
Merge pull request #367 from milen-sage/develop-schema-update
xdoan Dec 17, 2020
19673fb
Minor updates: adding MERFISH to imaging level 2
milen-sage Dec 18, 2020
ecf6fbd
Merge pull request #371 from milen-sage/develop-schema-update
xdoan Dec 18, 2020
748aa58
Merge branch 'main' of https://github.com/Sage-Bionetworks/HTAN-data-…
milen-sage Dec 22, 2020
1e12d0c
Added Nuclei Isolation as an option for scRNA-seq level 1 Single Cell…
milen-sage Jan 15, 2021
6debfe5
Merge pull request #379 from milen-sage/develop-schema-update
xdoan Jan 18, 2021
573a30f
added trim_commas_df() to fix trailing commas in manifest file
sujaypatil96 Jan 19, 2021
78892c5
Merge branch 'main' of https://github.com/Sage-Bionetworks/HTAN-data-…
milen-sage Jan 20, 2021
c6cae0b
all dropdown values are now stored in hidden sheet explicitly; previo…
milen-sage Jan 20, 2021
36d9f22
added trim_commas_df() to fix trailing commas in manifest file
sujaypatil96 Jan 20, 2021
9bd594e
Merge pull request #384 from milen-sage/main
xdoan Jan 21, 2021
49dc69b
trim_commas_df to remove only trailing empty columns
sujaypatil96 Jan 28, 2021
8b97ac6
Merge pull request #391 from Sage-Bionetworks/main-trim_commas_df-bugfix
xdoan Jan 29, 2021
f9eb3f4
removing unneeded calls to Synapse, which result in large delays for …
milen-sage Feb 5, 2021
d37a231
removing unneeded error handling
milen-sage Feb 5, 2021
92dbac4
Merge pull request #395 from milen-sage/main
xdoan Feb 5, 2021
8cc36b1
update store.py
allaway Feb 6, 2021
2bcde3b
Merge pull request #399 from Sage-Bionetworks/allaway/useSchemaLabel
milen-sage Feb 6, 2021
8f71a18
fix typo
allaway Feb 6, 2021
0d48594
Merge pull request #400 from Sage-Bionetworks/allaway-patch-1
milen-sage Feb 6, 2021
dd1e55c
handler for mismatched component and template type in validator
sujaypatil96 Feb 9, 2021
be17448
handler for mismatched component and template type in validator
sujaypatil96 Feb 9, 2021
cfe7424
added duct carcinoma to HTAN clinical data
milen-sage Feb 17, 2021
294dd72
added duct carcinoma to HTAN clinical data; added a third read to scA…
milen-sage Feb 17, 2021
894c6a6
Merge pull request #408 from milen-sage/main
xdoan Feb 19, 2021
3c717b0
Merge pull request #6 from Sage-Bionetworks/main
milen-sage Feb 22, 2021
94210f4
minor updates to schema reflecting requests for 1st HTAN data release
milen-sage Mar 1, 2021
426ada8
change 'cell' to 'cell am' format to avoid conflict with entity Cell …
milen-sage Mar 2, 2021
5c3ac5d
Merge pull request #7 from milen-sage/main
milen-sage Mar 9, 2021
5981eb1
Changed dependency: orderedset -> ordered-set
joeflack4 Jul 15, 2021
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32 changes: 32 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.md
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---
name: Bug report
about: Create a report to help us improve
title: ''
labels: bug
assignees: ''

---

**Describe the bug**
A clear and concise description of what the bug is.

**To Reproduce**
Steps to reproduce the behavior:
1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

**Expected behavior**
A clear and concise description of what you expected to happen.

**Screenshots**
If applicable, add screenshots to help explain your problem.

**Desktop (if applicable, please complete the following information):**
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]

**Additional context**
Add any other context about the problem here.
27 changes: 27 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.md
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---
name: Feature request
about: Suggest an idea for this project
title: ''
labels: feature
assignees: ''

---

**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

**Describe the solution you'd like**
A clear and concise description of what you want to happen.

**How important is this feature?** Select from the options below:
• Low - it's an enhancement but not crucial for work
• Medium - can do work without it; but it's important (e.g. to save time or for convenience)
• Important - it's a blocker and can't do work without it

**When will use cases depending on this become relevant?** Select from the options below:
• Short-term - 2-4 weeks
• Mid-term - 2-4 months
• Long-term - 6 months - 1 year

**Additional context**
Add any other context or screenshots about the feature request here.
201 changes: 201 additions & 0 deletions LICENSE.txt
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Apache License
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16 changes: 11 additions & 5 deletions README.md
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@@ -1,14 +1,20 @@
# HTAN Data Ingress Pipeline
# Schematic

## Usage

### Virtual Environment Setup

Python 3 has built-in support for virtual environments (using `venv` module). Perform the following steps:

_Note: It is assumed that you are running all the below commands from the main/root (`HTAN-data-pipeline`) directory._
_Note: It is assumed that you are running all the below commands from the main/root (`schematic`) directory._

After cloning the git repository, navigate into the `HTAN-data-pipeline` directory and run the command as below:
Clone this branch of the git repository

```
git clone --single-branch --branch main https://github.com/ncihtan/schematic.git
```

Navigate into the `schematic` directory and run the command as below:

```bash
python[3] -m venv .venv
Expand Down Expand Up @@ -88,9 +94,9 @@ _Note: You can get your Synapse API key by: **logging into Synapse > Settings >
Clone a copy of the repository here:

```bash
git clone --single-branch --branch develop https://github.com/Sage-Bionetworks/HTAN-data-pipeline.git
git clone --single-branch --branch develop https://github.com/Sage-Bionetworks/schematic.git
```

Modify your files, add them to the staging area, use a descriptive commit message and push to the same branch as a pull request for review.

* Please consult [CONTRIBUTION.md](https://github.com/Sage-Bionetworks/HTAN-data-pipeline/blob/develop/CONTRIBUTION.md) for further reference.
* Please consult [CONTRIBUTION.md](https://github.com/Sage-Bionetworks/schematic/blob/develop/CONTRIBUTION.md) for further reference.
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